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Seidelin JB, Bronze M, Poulsen A, Attauabi M, Woetmann A, Mead BE, Karp JM, Riis LB, Bjerrum JT. Non-TGFβ profibrotic signaling in ulcerative colitis after in vivo experimental intestinal injury in humans. Am J Physiol Gastrointest Liver Physiol 2024; 327:G70-G79. [PMID: 38713614 DOI: 10.1152/ajpgi.00074.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 05/09/2024]
Abstract
Although impaired regeneration is important in many gastrointestinal diseases including ulcerative colitis (UC), the dynamics of mucosal regeneration in humans are poorly investigated. We have developed a model to study these processes in vivo in humans. Epithelial restitution (ER) and extracellular matrix (ECM) regulation after an experimental injury of the sigmoid colonic mucosa was assessed by repeated high-resolution endoscopic imaging, histological assessment, RNA sequencing, deconvolution analysis, and 16S rDNA sequencing of the injury niche microbiome of 19 patients with UC in remission and 20 control subjects. Human ER had a 48-h lag before induction of regenerative epithelial cells [wound-associated epithelial (WAE) and transit amplifying (TA) cells] along with the increase of fibroblast-derived stem cell growth factor gremlin 1 mRNA (GREM1). However, UC deconvolution data showed rapid induction of inflammatory fibroblasts and upregulation of major structural ECM collagen mRNAs along with tissue inhibitor of metalloproteinase 1 (TIMP1), suggesting increased profibrotic ECM deposition. No change was seen in transforming growth factor β (TGFβ) mRNA, whereas the profibrotic cytokines interleukin 13 (IL13) and IL11 were upregulated in UC, suggesting that human postinjury responses could be TGFβ-independent. In conclusion, we found distinct regulatory layers of regeneration in the normal human colon and a potential targetable profibrotic dysregulation in UC that could lead to long-term end-organ failure, i.e., intestinal damage.NEW & NOTEWORTHY The study reveals the regulatory dynamics of epithelial regeneration and extracellular matrix remodeling after experimental injury of the human colon in vivo and shows that human intestinal regeneration is different from data obtained from animals. A lag phase in epithelial restitution is associated with induction of stromal cell-derived epithelial growth factors. Postinjury regeneration is transforming growth factor β-independent, and we find a profibrotic response in patients with ulcerative colitis despite being in remission.
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Affiliation(s)
- Jakob B Seidelin
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mariana Bronze
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- LEO Foundation Skin Immunology Research Center, University of Copenhagen, Copenhagen, Denmark
| | - Anja Poulsen
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mohamed Attauabi
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders Woetmann
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- LEO Foundation Skin Immunology Research Center, University of Copenhagen, Copenhagen, Denmark
| | - Benjamin E Mead
- Division of Health Sciences and Technology, Harvard-Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
- Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
- Harvard Stem Cell Institute, Cambridge, Massachusetts, United States
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
- Department of Chemistry; Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts, United States
| | - Jeffrey M Karp
- Division of Health Sciences and Technology, Harvard-Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
- Harvard Stem Cell Institute, Cambridge, Massachusetts, United States
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States
- Harvard Medical School, Boston, Massachusetts, United States
- Department of Anesthesiology, Perioperative and Pain Medicine,Brigham and Women's Hospital, Cambridge, Massachusetts, United States
| | - Lene B Riis
- Department of Pathology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Jacob T Bjerrum
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
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2
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Gao C, Ge H, Kuan SF, Cai C, Lu X, Esni F, Schoen RE, Wang JH, Chu E, Hu J. FAK loss reduces BRAF V600E-induced ERK phosphorylation to promote intestinal stemness and cecal tumor formation. eLife 2024; 13:RP94605. [PMID: 38921956 PMCID: PMC11208045 DOI: 10.7554/elife.94605] [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] [Indexed: 06/27/2024] Open
Abstract
BRAFV600E mutation is a driver mutation in the serrated pathway to colorectal cancers. BRAFV600E drives tumorigenesis through constitutive downstream extracellular signal-regulated kinase (ERK) activation, but high-intensity ERK activation can also trigger tumor suppression. Whether and how oncogenic ERK signaling can be intrinsically adjusted to a 'just-right' level optimal for tumorigenesis remains undetermined. In this study, we found that FAK (Focal adhesion kinase) expression was reduced in BRAFV600E-mutant adenomas/polyps in mice and patients. In Vil1-Cre;BRAFLSL-V600E/+;Ptk2fl/fl mice, Fak deletion maximized BRAFV600E's oncogenic activity and increased cecal tumor incidence to 100%. Mechanistically, our results showed that Fak loss, without jeopardizing BRAFV600E-induced ERK pathway transcriptional output, reduced EGFR (epidermal growth factor receptor)-dependent ERK phosphorylation. Reduction in ERK phosphorylation increased the level of Lgr4, promoting intestinal stemness and cecal tumor formation. Our findings show that a 'just-right' ERK signaling optimal for BRAFV600E-induced cecal tumor formation can be achieved via Fak loss-mediated downregulation of ERK phosphorylation.
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Affiliation(s)
- Chenxi Gao
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of MedicinePittsburghUnited States
| | - Huaibin Ge
- UPMC Hillman Cancer Center, Division of Hematology and Oncology, Department of Medicine, University of PittsburghPittsburghUnited States
| | - Shih-Fan Kuan
- Department of Pathology, University of Pittsburgh School of MedicinePittsburghUnited States
| | - Chunhui Cai
- Department of Biomedical Informatics, University of PittsburghPittsburghUnited States
| | - Xinghua Lu
- Department of Biomedical Informatics, University of PittsburghPittsburghUnited States
| | - Farzad Esni
- Department of Surgery, University of Pittsburgh School of MedicinePittsburghUnited States
| | - Robert E Schoen
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of MedicinePittsburghUnited States
| | - Jing H Wang
- UPMC Hillman Cancer Center, Division of Hematology and Oncology, Department of Medicine, University of PittsburghPittsburghUnited States
| | - Edward Chu
- UPMC Hillman Cancer Center, Division of Hematology and Oncology, Department of Medicine, University of PittsburghPittsburghUnited States
| | - Jing Hu
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of MedicinePittsburghUnited States
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3
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Fey SK, Vaquero-Siguero N, Jackstadt R. Dark force rising: Reawakening and targeting of fetal-like stem cells in colorectal cancer. Cell Rep 2024; 43:114270. [PMID: 38787726 DOI: 10.1016/j.celrep.2024.114270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/14/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Stem cells play pivotal roles in maintaining intestinal homeostasis, orchestrating regeneration, and in key steps of colorectal cancer (CRC) initiation and progression. Intriguingly, adult stem cells are reduced during many of these processes. On the contrary, primitive fetal programs, commonly detected in development, emerge during tissue repair, CRC metastasis, and therapy resistance. Recent findings indicate a dynamic continuum between adult and fetal stem cell programs. We discuss critical mechanisms facilitating the plasticity between stem cell states and highlight the heterogeneity observed upon the appearance of fetal-like states. We focus on therapeutic opportunities that arise by targeting fetal-like CRC cells and how those concepts can be translated into the clinic.
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Affiliation(s)
- Sigrid K Fey
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Cancer Progression and Metastasis Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Nuria Vaquero-Siguero
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Cancer Progression and Metastasis Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Rene Jackstadt
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Cancer Progression and Metastasis Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), DKFZ, Core Center Heidelberg, 69120 Heidelberg, Germany.
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4
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Cañellas-Socias A, Sancho E, Batlle E. Mechanisms of metastatic colorectal cancer. Nat Rev Gastroenterol Hepatol 2024:10.1038/s41575-024-00934-z. [PMID: 38806657 DOI: 10.1038/s41575-024-00934-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/17/2024] [Indexed: 05/30/2024]
Abstract
Despite extensive research and improvements in understanding colorectal cancer (CRC), its metastatic form continues to pose a substantial challenge, primarily owing to limited therapeutic options and a poor prognosis. This Review addresses the emerging focus on metastatic CRC (mCRC), which has historically been under-studied compared with primary CRC despite its lethality. We delve into two crucial aspects: the molecular and cellular determinants facilitating CRC metastasis and the principles guiding the evolution of metastatic disease. Initially, we examine the genetic alterations integral to CRC metastasis, connecting them to clinically marked characteristics of advanced CRC. Subsequently, we scrutinize the role of cellular heterogeneity and plasticity in metastatic spread and therapy resistance. Finally, we explore how the tumour microenvironment influences metastatic disease, emphasizing the effect of stromal gene programmes and the immune context. The ongoing research in these fields holds immense importance, as its future implications are projected to revolutionize the treatment of patients with mCRC, hopefully offering a promising outlook for their survival.
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Affiliation(s)
- Adrià Cañellas-Socias
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
| | - Elena Sancho
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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5
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Kinoshita H, Martinez-Ordoñez A, Cid-Diaz T, Han Q, Duran A, Muta Y, Zhang X, Linares JF, Nakanishi Y, Kasashima H, Yashiro M, Maeda K, Albaladejo-Gonzalez A, Torres-Moreno D, García-Solano J, Conesa-Zamora P, Inghirami G, Diaz-Meco MT, Moscat J. Epithelial aPKC deficiency leads to stem cell loss preceding metaplasia in colorectal cancer initiation. Dev Cell 2024:S1534-5807(24)00299-5. [PMID: 38815584 DOI: 10.1016/j.devcel.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 12/19/2023] [Accepted: 05/03/2024] [Indexed: 06/01/2024]
Abstract
The early mechanisms of spontaneous tumor initiation that precede malignancy are largely unknown. We show that reduced aPKC levels correlate with stem cell loss and the induction of revival and metaplastic programs in serrated- and conventional-initiated premalignant lesions, which is perpetuated in colorectal cancers (CRCs). Acute inactivation of PKCλ/ι in vivo and in mouse organoids is sufficient to stimulate JNK in non-transformed intestinal epithelial cells (IECs), which promotes cell death and the rapid loss of the intestinal stem cells (ISCs), including those that are LGR5+. This is followed by the accumulation of revival stem cells (RSCs) at the bottom of the crypt and fetal-metaplastic cells (FMCs) at the top, creating two spatiotemporally distinct cell populations that depend on JNK-induced AP-1 and YAP. These cell lineage changes are maintained during cancer initiation and progression and determine the aggressive phenotype of human CRC, irrespective of their serrated or conventional origin.
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Affiliation(s)
- Hiroto Kinoshita
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Anxo Martinez-Ordoñez
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Tania Cid-Diaz
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Qixiu Han
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Angeles Duran
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Yu Muta
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Xiao Zhang
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Juan F Linares
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Yuki Nakanishi
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hiroaki Kasashima
- Department of Gastroenterological Surgery, Osaka Metropolitan University Graduate School of Medicine, 1-4-3 Asahimachi, Abeno-ku, Osaka city 545-8585, Japan
| | - Masakazu Yashiro
- Department of Gastroenterological Surgery, Osaka Metropolitan University Graduate School of Medicine, 1-4-3 Asahimachi, Abeno-ku, Osaka city 545-8585, Japan
| | - Kiyoshi Maeda
- Department of Gastroenterological Surgery, Osaka Metropolitan University Graduate School of Medicine, 1-4-3 Asahimachi, Abeno-ku, Osaka city 545-8585, Japan
| | - Ana Albaladejo-Gonzalez
- Department of Histology and Pathology, Faculty of Life Sciences, Universidad Católica de Murcia (UCAM), 30107 Murcia, Spain; Department of Pathology, Santa Lucía General University Hospital (HGUSL), Calle Mezquita sn, 30202 Cartagena, Spain
| | - Daniel Torres-Moreno
- Department of Histology and Pathology, Faculty of Life Sciences, Universidad Católica de Murcia (UCAM), 30107 Murcia, Spain; Department of Clinical Analysis, Santa Lucía General University Hospital (HGUSL), Calle Mezquita sn, 30202 Cartagena, Spain
| | - José García-Solano
- Department of Histology and Pathology, Faculty of Life Sciences, Universidad Católica de Murcia (UCAM), 30107 Murcia, Spain; Department of Pathology, Santa Lucía General University Hospital (HGUSL), Calle Mezquita sn, 30202 Cartagena, Spain
| | - Pablo Conesa-Zamora
- Department of Histology and Pathology, Faculty of Life Sciences, Universidad Católica de Murcia (UCAM), 30107 Murcia, Spain; Department of Clinical Analysis, Santa Lucía General University Hospital (HGUSL), Calle Mezquita sn, 30202 Cartagena, Spain
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Maria T Diaz-Meco
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Jorge Moscat
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA.
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6
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Díez-Sánchez A, Lindholm HT, Vornewald PM, Ostrop J, Yao R, Single AB, Marstad A, Parmar N, Shaw TN, Martín-Alonso M, Oudhoff MJ. LSD1 drives intestinal epithelial maturation and controls small intestinal immune cell composition independent of microbiota in a murine model. Nat Commun 2024; 15:3412. [PMID: 38649356 PMCID: PMC11035651 DOI: 10.1038/s41467-024-47815-2] [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: 09/10/2023] [Accepted: 04/12/2024] [Indexed: 04/25/2024] Open
Abstract
Postnatal development of the gastrointestinal tract involves the establishment of the commensal microbiota, the acquisition of immune tolerance via a balanced immune cell composition, and maturation of the intestinal epithelium. While studies have uncovered an interplay between the first two, less is known about the role of the maturing epithelium. Here we show that intestinal-epithelial intrinsic expression of lysine-specific demethylase 1A (LSD1) is necessary for the postnatal maturation of intestinal epithelium and maintenance of this developed state during adulthood. Using microbiota-depleted mice, we find plasma cells, innate lymphoid cells (ILCs), and a specific myeloid population to depend on LSD1-controlled epithelial maturation. We propose that LSD1 controls the expression of epithelial-derived chemokines, such as Cxcl16, and that this is a mode of action for this epithelial-immune cell interplay in local ILC2s but not ILC3s. Together, our findings suggest that the maturing epithelium plays a dominant role in regulating the local immune cell composition, thereby contributing to gut homeostasis.
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Affiliation(s)
- Alberto Díez-Sánchez
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.
| | - Håvard T Lindholm
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Pia M Vornewald
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jenny Ostrop
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Rouan Yao
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Andrew B Single
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Anne Marstad
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Naveen Parmar
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Tovah N Shaw
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Mara Martín-Alonso
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Menno J Oudhoff
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.
- Department of Health Sciences, Carleton University, Ottawa, Ontario, ON, Canada.
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7
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Morral C, Ayyaz A, Kuo HC, Fink M, Verginadis II, Daniel AR, Burner DN, Driver LM, Satow S, Hasapis S, Ghinnagow R, Luo L, Ma Y, Attardi LD, Koumenis C, Minn AJ, Wrana JL, Lee CL, Kirsch DG. p53 promotes revival stem cells in the regenerating intestine after severe radiation injury. Nat Commun 2024; 15:3018. [PMID: 38589357 PMCID: PMC11001929 DOI: 10.1038/s41467-024-47124-8] [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: 03/03/2023] [Accepted: 03/20/2024] [Indexed: 04/10/2024] Open
Abstract
Ionizing radiation induces cell death in the gastrointestinal (GI) epithelium by activating p53. However, p53 also prevents animal lethality caused by radiation-induced acute GI syndrome. Through single-cell RNA-sequencing of the irradiated mouse small intestine, we find that p53 target genes are specifically enriched in regenerating epithelial cells that undergo fetal-like reversion, including revival stem cells (revSCs) that promote animal survival after severe damage of the GI tract. Accordingly, in mice with p53 deleted specifically in the GI epithelium, ionizing radiation fails to induce fetal-like revSCs. Using intestinal organoids, we show that transient p53 expression is required for the induction of revival stem cells and is controlled by an Mdm2-mediated negative feedback loop. Together, our findings reveal that p53 suppresses severe radiation-induced GI injury by promoting fetal-like reprogramming of irradiated intestinal epithelial cells.
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Affiliation(s)
- Clara Morral
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Arshad Ayyaz
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Hsuan-Cheng Kuo
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Mardi Fink
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Ioannis I Verginadis
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrea R Daniel
- Department of Radiation Oncology, Duke University, Durham, NC, USA
| | - Danielle N Burner
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Lucy M Driver
- Department of Radiation Oncology, Duke University, Durham, NC, USA
- Department of Pathology, Duke University, Durham, NC, USA
| | - Sloane Satow
- Department of Radiation Oncology, Duke University, Durham, NC, USA
| | | | - Reem Ghinnagow
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lixia Luo
- Department of Radiation Oncology, Duke University, Durham, NC, USA
| | - Yan Ma
- Department of Radiation Oncology, Duke University, Durham, NC, USA
| | - Laura D Attardi
- Departments of Radiation Oncology and Genetics, Stanford University, Palo Alto, CA, USA
| | - Constantinos Koumenis
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andy J Minn
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Mark Foundation Center for Immunotherapy, Immune Signaling, and Radiation, University of Pennsylvania, Philadelphia, PA, USA
| | - Jeffrey L Wrana
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
| | - Chang-Lung Lee
- Department of Radiation Oncology, Duke University, Durham, NC, USA.
- Department of Pathology, Duke University, Durham, NC, USA.
| | - David G Kirsch
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA.
- Department of Radiation Oncology, Duke University, Durham, NC, USA.
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Departments of Radiation Oncology and Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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8
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Ogasawara N, Kano Y, Yoneyama Y, Kobayashi S, Watanabe S, Kirino S, Velez-Bravo FD, Hong Y, Ostapiuk A, Lutsik P, Onishi I, Yamauchi S, Hiraguri Y, Ito G, Kinugasa Y, Ohashi K, Watanabe M, Okamoto R, Tejpar S, Yui S. Discovery of non-genomic drivers of YAP signaling modulating the cell plasticity in CRC tumor lines. iScience 2024; 27:109247. [PMID: 38439969 PMCID: PMC10910304 DOI: 10.1016/j.isci.2024.109247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 03/06/2024] Open
Abstract
In normal intestines, a fetal/regenerative/revival cell state can be induced upon inflammation. This plasticity in cell fate is also one of the current topics in human colorectal cancer (CRC). To dissect the underlying mechanisms, we generated human CRC organoids with naturally selected genetic mutation profiles and exposed them to two different conditions by modulating the extracellular matrix (ECM). Among tested mutation profiles, a fetal/regenerative/revival state was induced following YAP activation via a collagen type I-enriched microenvironment. Mechanistically, YAP transcription was promoted by activating AP-1 and TEAD-dependent transcription and suppressing intestinal lineage-determining transcription via mechanotransduction. The phenotypic conversion was also involved in chemoresistance, which could be potentially resolved by targeting the underlying YAP regulatory elements, a potential target of CRC treatment.
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Affiliation(s)
- Nobuhiko Ogasawara
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yoshihito Kano
- Department of Clinical Oncology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yosuke Yoneyama
- Institute of Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Sakurako Kobayashi
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Satoshi Watanabe
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Sakura Kirino
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | | | - Yourae Hong
- Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | | | - Pavlo Lutsik
- Computational Cancer Biology and Epigenomics, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Iichiroh Onishi
- Department of Diagnostic Pathology, Tokyo Medical and Dental University Hospital, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Shinichi Yamauchi
- Department of Gastrointestinal Surgery, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yui Hiraguri
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Go Ito
- Advanced Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yusuke Kinugasa
- Department of Gastrointestinal Surgery, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Kenichi Ohashi
- Department of Human Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Mamoru Watanabe
- Advanced Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Ryuichi Okamoto
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Sabine Tejpar
- Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Shiro Yui
- Center for Stem Cell and Regenerative Medicine, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
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9
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Tape CJ. Plastic persisters: revival stem cells in colorectal cancer. Trends Cancer 2024; 10:185-195. [PMID: 38071119 DOI: 10.1016/j.trecan.2023.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 03/16/2024]
Abstract
Colorectal cancer (CRC) is traditionally considered to be a genetically driven disease. However, nongenetic plasticity has recently emerged as a major driver of tumour initiation, metastasis, and therapy response in CRC. Central to these processes is a recently discovered cell type, the revival colonic stem cell (revCSC). In contrast to traditional proliferative CSCs (proCSCs), revCSCs prioritise survival over propagation. revCSCs play an essential role in primary tumour formation, metastatic dissemination, and nongenetic chemoresistance. Current evidence suggests that CRC tumours leverage intestinal stem cell plasticity to both proliferate (via proCSCs) when unchallenged and survive (via revCSCs) in response to cell-extrinsic pressures. Although revCSCs likely represent a major source of therapeutic failure in CRC, our increasing knowledge of this important stem cell fate provides novel opportunities for therapeutic intervention.
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Affiliation(s)
- Christopher J Tape
- Cell Communication Lab, Department of Oncology, University College London Cancer Institute, 72 Huntley Street, London, WC1E 6DD, UK.
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10
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Goto N, Westcott PMK, Goto S, Imada S, Taylor MS, Eng G, Braverman J, Deshpande V, Jacks T, Agudo J, Yilmaz ÖH. SOX17 enables immune evasion of early colorectal adenomas and cancers. Nature 2024; 627:636-645. [PMID: 38418875 DOI: 10.1038/s41586-024-07135-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024]
Abstract
A hallmark of cancer is the avoidance of immune destruction. This process has been primarily investigated in locally advanced or metastatic cancer1-3; however, much less is known about how pre-malignant or early invasive tumours evade immune detection. Here, to understand this process in early colorectal cancers (CRCs), we investigated how naive colon cancer organoids that were engineered in vitro to harbour Apc-null, KrasG12D and Trp53-null (AKP) mutations adapted to the in vivo native colonic environment. Comprehensive transcriptomic and chromatin analyses revealed that the endoderm-specifying transcription factor SOX17 became strongly upregulated in vivo. Notably, whereas SOX17 loss did not affect AKP organoid propagation in vitro, its loss markedly reduced the ability of AKP tumours to persist in vivo. The small fraction of SOX17-null tumours that grew displayed notable interferon-γ (IFNγ)-producing effector-like CD8+ T cell infiltrates in contrast to the immune-suppressive microenvironment in wild-type counterparts. Mechanistically, in both endogenous Apc-null pre-malignant adenomas and transplanted organoid-derived AKP CRCs, SOX17 suppresses the ability of tumour cells to sense and respond to IFNγ, preventing anti-tumour T cell responses. Finally, SOX17 engages a fetal intestinal programme that drives differentiation away from LGR5+ tumour cells to produce immune-evasive LGR5- tumour cells with lower expression of major histocompatibility complex class I (MHC-I). We propose that SOX17 is a transcription factor that is engaged during the early steps of colon cancer to orchestrate an immune-evasive programme that permits CRC initiation and progression.
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Affiliation(s)
- Norihiro Goto
- Department of Biology, The David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peter M K Westcott
- Department of Biology, The David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Saori Goto
- Department of Biology, The David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Shinya Imada
- Department of Biology, The David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Martin S Taylor
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - George Eng
- Department of Biology, The David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jonathan Braverman
- Department of Biology, The David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Vikram Deshpande
- Department of Pathology, Beth Israel Deaconess Hospital and Harvard Medical School, Boston, MA, USA
| | - Tyler Jacks
- Department of Biology, The David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Judith Agudo
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Immunology, Harvard Medical School, Boston, MA, USA.
- Ludwig Center at Harvard, Boston, MA, USA.
- Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA, USA.
- New York Stem Cell Foundation-Robertson Investigator, New York, NY, USA.
| | - Ömer H Yilmaz
- Department of Biology, The David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Beth Israel Deaconess Hospital and Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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11
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Gao C, Ge H, Kuan SF, Cai C, Lu X, Esni F, Schoen R, Wang J, Chu E, Hu J. FAK loss reduces BRAF V600E-induced ERK phosphorylation to promote intestinal stemness and cecal tumor formation. RESEARCH SQUARE 2024:rs.3.rs-2531119. [PMID: 36778401 PMCID: PMC9915899 DOI: 10.21203/rs.3.rs-2531119/v2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
BRAF V600E mutation is a driver mutation in the serrated pathway to colorectal cancers. BRAFV600E drives tumorigenesis through constitutive downstream extracellular signal-regulated kinase (ERK) activation, but high-intensity ERK activation can also trigger tumor suppression. Whether and how oncogenic ERK signaling can be intrinsically adjusted to a "just-right" level optimal for tumorigenesis remains undetermined. In this study, we found that FAK (Focal adhesion kinase) expression was reduced in BRAFV600E-mutant adenomas/polyps in mice and patients. In Vill-Cre;BRAFV600E/+;Fakfl/fl mice, Fak deletion maximized BRAFV600E's oncogenic activity and increased cecal tumor incidence to 100%. Mechanistically, our results showed that Fak loss, without jeopardizing BRAFV600E-induced ERK pathway transcriptional output, reduced EGFR (epidermal growth factor receptor)-dependent ERK phosphorylation. Reduction in ERK phosphorylation increased the level of Lgr4, promoting intestinal stemness and cecal tumor formation. Our findings show that a "just-right" ERK signaling optimal for BRAFV600E-induced cecal tumor formation can be achieved via Fak loss-mediated downregulation of ERK phosphorylation.
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Affiliation(s)
| | | | | | | | | | | | | | - Jing Wang
- UPMC Hillman Cancer Center/University of Pittsburgh
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12
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Fey C, Truschel T, Nehlsen K, Damigos S, Horstmann J, Stradal T, May T, Metzger M, Zdzieblo D. Enhancing pre-clinical research with simplified intestinal cell line models. J Tissue Eng 2024; 15:20417314241228949. [PMID: 38449469 PMCID: PMC10916479 DOI: 10.1177/20417314241228949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/12/2024] [Indexed: 03/08/2024] Open
Abstract
Two-dimensional culture remains widely employed to determine the bioavailability of orally delivered drugs. To gain more knowledge about drug uptake mechanisms and risk assessment for the patient after oral drug admission, intestinal in vitro models demonstrating a closer similarity to the in vivo situation are needed. In particular, Caco-2 cell-based Transwell® models show advantages as they are reproducible, cost-efficient, and standardized. However, cellular complexity is impaired and cell function is strongly modified as important transporters in the apical membrane are missing. To overcome these limitations, primary organoid-based human small intestinal tissue models were developed recently but the application of these cultures in pre-clinical research still represents an enormous challenge, as culture setup is complex as well as time- and cost-intensive. To overcome these hurdles, we demonstrate the establishment of primary organoid-derived intestinal cell lines by immortalization. Besides exhibiting cellular diversity of the organoid, these immortalized cell lines enable a standardized and more cost-efficient culture. Further, our cell line-based Transwell®-like models display an organ-specific epithelial barrier integrity, ultrastructural features and representative transport functions. Altogether, our novel model systems are cost-efficient with close similarity to the in vivo situation, therefore favoring their use in bioavailability studies in the context of pre-clinical screenings.
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Affiliation(s)
- Christina Fey
- Translational Center for Regenerative Therapies (TLZ-RT) Würzburg, Branch of the Fraunhofer Institute for Silicate Research (ISC), Würzburg, Germany
| | | | | | - Spyridon Damigos
- Department of Tissue Engineering and Regenerative Medicine (TERM), University Hospital Würzburg, Würzburg, Germany
| | - Julia Horstmann
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | | | - Marco Metzger
- Translational Center for Regenerative Therapies (TLZ-RT) Würzburg, Branch of the Fraunhofer Institute for Silicate Research (ISC), Würzburg, Germany
- Department of Tissue Engineering and Regenerative Medicine (TERM), University Hospital Würzburg, Würzburg, Germany
| | - Daniela Zdzieblo
- Translational Center for Regenerative Therapies (TLZ-RT) Würzburg, Branch of the Fraunhofer Institute for Silicate Research (ISC), Würzburg, Germany
- Department of Tissue Engineering and Regenerative Medicine (TERM), University Hospital Würzburg, Würzburg, Germany
- Project Center for Stem Cell Process Engineering (PZ-SPT), Branch of the Fraunhofer Institute for Silicate Research (ISC), Würzburg, Germany
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13
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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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14
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Parham LR, Williams PA, Katada K, Nettleford SK, Chatterji P, Acheampong KK, Danan CH, Ma X, Simon LA, Naughton KE, Mizuno R, Karakasheva T, McMillan EA, Whelan KA, Brady DC, Shaffer SM, Hamilton KE. IGF2BP1/IMP1 Deletion Enhances a Facultative Stem Cell State via Regulation of MAP1LC3B. Cell Mol Gastroenterol Hepatol 2023; 17:439-451. [PMID: 38081361 PMCID: PMC10835461 DOI: 10.1016/j.jcmgh.2023.12.001] [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: 10/14/2022] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 01/02/2024]
Abstract
BACKGROUND & AIMS The intestinal epithelium interfaces with a diverse milieu of luminal contents while maintaining robust digestive and barrier functions. Facultative intestinal stem cells are cells that survive tissue injury and divide to re-establish the epithelium. Prior studies have shown autophagic state as functional marker of facultative intestinal stem cells, but regulatory mechanisms are not known. The current study evaluated a post-transcriptional regulation of autophagy as an important factor for facultative stem cell state and tissue regeneration. METHODS We evaluated stem cell composition, autophagic vesicle content, organoid formation, and in vivo regeneration in mice with intestinal epithelial deletion of the RNA binding protein IGF2 messenger RNA binding protein 1 (IMP1). The contribution of autophagy to resulting in vitro and in vivo phenotypes was evaluated via genetic inactivation of Atg7. Molecular analyses of IMP1 modulation of autophagy at the protein and transcript localization levels were performed using IMP1 mutant studies and single-molecule fluorescent in situ hybridization. RESULTS Epithelial Imp1 deletion reduced leucine rich repeat containing G protein coupled receptor 5 cell frequency but enhanced both organoid formation efficiency and in vivo regeneration after irradiation. We confirmed prior studies showing increased autophagy with IMP1 deletion. Deletion of Atg7 reversed the enhanced regeneration observed with Imp1 deletion. IMP1 deletion or mutation of IMP1 phosphorylation sites enhanced expression of essential autophagy protein microtubule-associated protein 1 light chain 3β. Furthermore, immunofluorescence imaging coupled with single-molecule fluorescent in situ hybridization showed IMP1 colocalization with MAP1LC3B transcripts at homeostasis. Stress induction led to decreased colocalization. CONCLUSIONS Depletion of IMP1 enhances autophagy, which promotes intestinal regeneration via expansion of facultative intestinal stem cells.
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Affiliation(s)
- Louis R Parham
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Patrick A Williams
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Kay Katada
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Shaneice K Nettleford
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Priya Chatterji
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Kofi K Acheampong
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Charles H Danan
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Xianghui Ma
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Lauren A Simon
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Kaitlyn E Naughton
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Rei Mizuno
- Department of Surgery, Uji-Tokushukai Medical Center, Uji, Kyoto, Japan
| | - Tatiana Karakasheva
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Emily A McMillan
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Kelly A Whelan
- Department of Pathology and Laboratory Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania; Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| | - Donita C Brady
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sydney M Shaffer
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania; Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kathryn E Hamilton
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
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15
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Qin X, Cardoso Rodriguez F, Sufi J, Vlckova P, Claus J, Tape CJ. An oncogenic phenoscape of colonic stem cell polarization. Cell 2023; 186:5554-5568.e18. [PMID: 38065080 DOI: 10.1016/j.cell.2023.11.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 09/14/2023] [Accepted: 11/02/2023] [Indexed: 12/18/2023]
Abstract
Cancer cells are regulated by oncogenic mutations and microenvironmental signals, yet these processes are often studied separately. To functionally map how cell-intrinsic and cell-extrinsic cues co-regulate cell fate, we performed a systematic single-cell analysis of 1,107 colonic organoid cultures regulated by (1) colorectal cancer (CRC) oncogenic mutations, (2) microenvironmental fibroblasts and macrophages, (3) stromal ligands, and (4) signaling inhibitors. Multiplexed single-cell analysis revealed a stepwise epithelial differentiation phenoscape dictated by combinations of oncogenes and stromal ligands, spanning from fibroblast-induced Clusterin (CLU)+ revival colonic stem cells (revCSCs) to oncogene-driven LRIG1+ hyper-proliferative CSCs (proCSCs). The transition from revCSCs to proCSCs is regulated by decreasing WNT3A and TGF-β-driven YAP signaling and increasing KRASG12D or stromal EGF/Epiregulin-activated MAPK/PI3K flux. We find that APC loss and KRASG12D collaboratively limit access to revCSCs and disrupt stromal-epithelial communication-trapping epithelia in the proCSC fate. These results reveal that oncogenic mutations dominate homeostatic differentiation by obstructing cell-extrinsic regulation of cell-fate plasticity.
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Affiliation(s)
- Xiao Qin
- Cell Communication Lab, Department of Oncology, University College London Cancer Institute, 72 Huntley Street, London WC1E 6DD, UK
| | - Ferran Cardoso Rodriguez
- Cell Communication Lab, Department of Oncology, University College London Cancer Institute, 72 Huntley Street, London WC1E 6DD, UK
| | - Jahangir Sufi
- Cell Communication Lab, Department of Oncology, University College London Cancer Institute, 72 Huntley Street, London WC1E 6DD, UK
| | - Petra Vlckova
- Cell Communication Lab, Department of Oncology, University College London Cancer Institute, 72 Huntley Street, London WC1E 6DD, UK
| | - Jeroen Claus
- Phospho Biomedical Animation, The Greenhouse Studio 6, London N17 9QU, UK
| | - Christopher J Tape
- Cell Communication Lab, Department of Oncology, University College London Cancer Institute, 72 Huntley Street, London WC1E 6DD, UK.
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16
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Kim J, Kim S, Lee SY, Jo BK, Oh JY, Kwon EJ, Kim KT, Adpaikar AA, Kim EJ, Jung HS, Kim HR, Roe JS, Hong CP, Kim JK, Koo BK, Cha HJ. Partial in vivo reprogramming enables injury-free intestinal regeneration via autonomous Ptgs1 induction. SCIENCE ADVANCES 2023; 9:eadi8454. [PMID: 38000027 PMCID: PMC10672161 DOI: 10.1126/sciadv.adi8454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023]
Abstract
Tissue regeneration after injury involves the dedifferentiation of somatic cells, a natural adaptive reprogramming that leads to the emergence of injury-responsive cells with fetal-like characteristics. However, there is no direct evidence that adaptive reprogramming involves a shared molecular mechanism with direct cellular reprogramming. Here, we induced dedifferentiation of intestinal epithelial cells using OSKM (Oct4, Sox2, Klf4, and c-Myc) in vivo. The OSKM-induced forced dedifferentiation showed similar molecular features of intestinal regeneration, including a transition from homeostatic cell types to injury-responsive-like cell types. These injury-responsive-like cells, sharing gene signatures of revival stem cells and atrophy-induced villus epithelial cells, actively assisted tissue regeneration following damage. In contrast to normal intestinal regeneration involving Ptgs2 induction, the OSKM promotes autonomous production of prostaglandin E2 via epithelial Ptgs1 expression. These results indicate prostaglandin synthesis is a common mechanism for intestinal regeneration but involves a different enzyme when partial reprogramming is applied to the intestinal epithelium.
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Affiliation(s)
- Jumee Kim
- College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Somi Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Seung-Yeon Lee
- College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Beom-Ki Jo
- College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Ji-Young Oh
- College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Eun-Ji Kwon
- College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Keun-Tae Kim
- College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Anish Ashok Adpaikar
- Division in Anatomy and Developmental Biology, Department of Oral Biology, Taste Research Center, Oral Science Research Center, BK21 FOUR Project, Yonsei University College of Dentistry, Seoul, South Korea
| | - Eun-Jung Kim
- Division in Anatomy and Developmental Biology, Department of Oral Biology, Taste Research Center, Oral Science Research Center, BK21 FOUR Project, Yonsei University College of Dentistry, Seoul, South Korea
| | - Han-Sung Jung
- Division in Anatomy and Developmental Biology, Department of Oral Biology, Taste Research Center, Oral Science Research Center, BK21 FOUR Project, Yonsei University College of Dentistry, Seoul, South Korea
| | - Hwa-Ryeon Kim
- Department of Biochemistry, Yonsei University, Seoul, Korea
| | - Jae-Seok Roe
- Department of Biochemistry, Yonsei University, Seoul, Korea
| | - Chang Pyo Hong
- Theragen Bio Co., Ltd, Seongnam 13488, Republic of Korea
| | - Jong Kyoung Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Bon-Kyoung Koo
- Center for Genome Engineering, Institute for Basic Science, 55, Expo-ro, Yuseong-gu, Daejeon 34126, Republic of Korea
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, Vienna 1030, Austria
| | - Hyuk-Jin Cha
- College of Pharmacy, Seoul National University, Seoul, Republic of Korea
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17
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Liu CY, Girish N, Gomez ML, Kalski M, Bernard JK, Simons BD, Polk DB. Wound-healing plasticity enables clonal expansion of founder progenitor cells in colitis. Dev Cell 2023; 58:2309-2325.e7. [PMID: 37652012 PMCID: PMC10872951 DOI: 10.1016/j.devcel.2023.08.011] [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: 04/12/2022] [Revised: 05/30/2023] [Accepted: 08/05/2023] [Indexed: 09/02/2023]
Abstract
Chronic colonic injury and inflammation pose high risks for field cancerization, wherein injury-associated mutations promote stem cell fitness and gradual clonal expansion. However, the long-term stability of some colitis-associated mutational fields could suggest alternate origins. Here, studies of acute murine colitis reveal a punctuated mechanism of massive, neutral clonal expansion during normal wound healing. Through three-dimensional (3D) imaging, quantitative fate mapping, and single-cell transcriptomics, we show that epithelial wound repair begins with the loss of structural constraints on regeneration, forming fused labyrinthine channels containing epithelial cells reprogrammed to a non-proliferative plastic state. A small but highly proliferative set of epithelial founder progenitor cells (FPCs) subsequently emerges and undergoes extensive cell division, enabling fluid-like lineage mixing and spreading across the colonic surface. Crypt budding restores the glandular organization, imprinting the pattern of clonal expansion. The emergence and functions of FPCs within a critical window of plasticity represent regenerative targets with implications for preneoplasia.
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Affiliation(s)
- Cambrian Y Liu
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA; Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA.
| | - Nandini Girish
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA; Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA 92093, USA
| | - Marie L Gomez
- Program in Biomedical and Biological Sciences, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Martin Kalski
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Jessica K Bernard
- Program in Craniofacial Biology, Herman Ostrow School of Dentistry of the University of Southern California, Los Angeles, CA 90033, USA
| | - Benjamin D Simons
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge CB3 0WA, UK; Wellcome Trust, Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - D Brent Polk
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA; Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA 92093, USA; Department of Biochemistry and Molecular Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA; Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Rady Children's Hospital, San Diego, CA 92123, USA.
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18
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Chen L, Qiu X, Dupre A, Pellon-Cardenas O, Fan X, Xu X, Rout P, Walton KD, Burclaff J, Zhang R, Fang W, Ofer R, Logerfo A, Vemuri K, Bandyopadhyay S, Wang J, Barbet G, Wang Y, Gao N, Perekatt AO, Hu W, Magness ST, Spence JR, Verzi MP. TGFB1 induces fetal reprogramming and enhances intestinal regeneration. Cell Stem Cell 2023; 30:1520-1537.e8. [PMID: 37865088 PMCID: PMC10841757 DOI: 10.1016/j.stem.2023.09.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 07/03/2023] [Accepted: 09/28/2023] [Indexed: 10/23/2023]
Abstract
The gut epithelium has a remarkable ability to recover from damage. We employed a combination of high-throughput sequencing approaches, mouse genetics, and murine and human organoids and identified a role for TGFB signaling during intestinal regeneration following injury. At 2 days following irradiation (IR)-induced damage of intestinal crypts, a surge in TGFB1 expression is mediated by monocyte/macrophage cells at the location of damage. The depletion of macrophages or genetic disruption of TGFB signaling significantly impaired the regenerative response. Intestinal regeneration is characterized by the induction of a fetal-like transcriptional signature during repair. In organoid culture, TGFB1 treatment was necessary and sufficient to induce the fetal-like/regenerative state. Mesenchymal cells were also responsive to TGFB1 and enhanced the regenerative response. Mechanistically, pro-regenerative factors, YAP/TEAD and SOX9, are activated in the epithelium exposed to TGFB1. Finally, pre-treatment with TGFB1 enhanced the ability of primary epithelial cultures to engraft into damaged murine colon, suggesting promise for cellular therapy.
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Affiliation(s)
- Lei Chen
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China.
| | - Xia Qiu
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA
| | - Abigail Dupre
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA
| | - Oscar Pellon-Cardenas
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA
| | - Xiaojiao Fan
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Xiaoting Xu
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Prateeksha Rout
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA
| | - Katherine D Walton
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Joseph Burclaff
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, and North Carolina State University, Chapel Hill, NC 27695, USA; Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Ruolan Zhang
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Wenxin Fang
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Rachel Ofer
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA
| | - Alexandra Logerfo
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA
| | - Kiranmayi Vemuri
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA
| | - Sheila Bandyopadhyay
- Department of Biological Sciences, Rutgers University-Newark, Newark, NJ 07102, USA
| | - Jianming Wang
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers University-New Brunswick, New Brunswick, NJ 08903, USA
| | - Gaetan Barbet
- Child Health Institute of New Jersey, Rutgers University-New Brunswick, New Brunswick, NJ 08901, USA
| | - Yan Wang
- Center for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Nan Gao
- Department of Biological Sciences, Rutgers University-Newark, Newark, NJ 07102, USA
| | - Ansu O Perekatt
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, NJ 07030, USA
| | - Wenwei Hu
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers University-New Brunswick, New Brunswick, NJ 08903, USA
| | - Scott T Magness
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, and North Carolina State University, Chapel Hill, NC 27695, USA; Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Jason R Spence
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA
| | - Michael P Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA; Rutgers Cancer Institute of New Jersey, Rutgers University-New Brunswick, New Brunswick, NJ 08903, USA; Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University-New Brunswick, New Brunswick, NJ 08901, USA; NIEHS Center for Environmental Exposures and Disease (CEED), Rutgers EOHSI, Piscataway, NJ 08854, USA.
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19
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Fazilaty H, Basler K. Reactivation of embryonic genetic programs in tissue regeneration and disease. Nat Genet 2023; 55:1792-1806. [PMID: 37904052 DOI: 10.1038/s41588-023-01526-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 09/11/2023] [Indexed: 11/01/2023]
Abstract
Embryonic genetic programs are reactivated in response to various types of tissue damage, providing cell plasticity for tissue regeneration or disease progression. In acute conditions, these programs remedy the damage and then halt to allow a return to homeostasis. In chronic situations, including inflammatory diseases, fibrosis and cancer, prolonged activation of embryonic programs leads to disease progression and tissue deterioration. Induction of progenitor identity and cell plasticity, for example, epithelial-mesenchymal plasticity, are critical outcomes of reactivated embryonic programs. In this Review, we describe molecular players governing reactivated embryonic genetic programs, their role during disease progression, their similarities and differences and lineage reversion in pathology and discuss associated therapeutics and drug-resistance mechanisms across many organs. We also discuss the diversity of reactivated programs in different disease contexts. A comprehensive overview of commonalities between development and disease will provide better understanding of the biology and therapeutic strategies.
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Affiliation(s)
- Hassan Fazilaty
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland.
| | - Konrad Basler
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
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20
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Sharifkhodaei Z, Liu CY, Girish N, Huang Y, Punit S, Washington MK, Polk DB. Colitis-induced upregulation of tumor necrosis factor receptor-2 (TNFR2) terminates epithelial regenerative signaling to restore homeostasis. iScience 2023; 26:107829. [PMID: 37736049 PMCID: PMC10510063 DOI: 10.1016/j.isci.2023.107829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/04/2023] [Accepted: 09/01/2023] [Indexed: 09/23/2023] Open
Abstract
Colonic epithelial repair is a key determinant of health. Repair involves changes in epithelial differentiation, an extensive proliferative response, and upregulation of regeneration-associated "fetal-like" transcripts, including Ly6a (Sca-1), that represent Yap1 and interferon targets. However, little is known about how this regenerative program terminates and how homeostasis is restored during injury and inflammation. Here we show that, after the initial entry into the regenerative state, the subsequent upregulation of tumor necrosis factor (TNF) receptor 2 (R2, TNFR2, Tnfrsf1b) clears the regenerative signaling and restores homeostatic patterns of epithelial differentiation. Targeted deletion of epithelial TNFR2 in vivo and in colonoid cultures revealed persistent expression of Ly6a, hyperproliferation, and reduced secretory differentiation. Moreover, mice lacking epithelial TNFR2 also failed to complete colon ulcer healing, suggesting that partial resolution of regenerative signaling is essential for the completion of the repair process. These results demonstrate how epithelial cells dynamically leverage a colitis-associated cytokine to choreograph repair.
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Affiliation(s)
- Zohreh Sharifkhodaei
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Cambrian Y. Liu
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Nandini Girish
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Ying Huang
- The Saban Research Institute, Division of Pediatric Gastroenterology, Hepatology Nutrition, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Shivesh Punit
- The Saban Research Institute, Division of Pediatric Gastroenterology, Hepatology Nutrition, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - M. Kay Washington
- Department of Pathology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - D. Brent Polk
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
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21
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Giri AK, Aavikko M, Wartiovaara L, Lemmetyinen T, Karjalainen J, Mehtonen J, Palin K, Välimäki N, Tamlander M, Saikkonen R, Karhu A, Morgunova E, Sun B, Runz H, Palta P, Luo S, Joensuu H, Mäkelä TP, Kostiainen I, Schalin-Jäntti C, FinnGen, Palotie A, Aaltonen LA, Ollila S, Daly MJ. Genome-Wide Association Study Identifies 4 Novel Risk Loci for Small Intestinal Neuroendocrine Tumors Including a Missense Mutation in LGR5. Gastroenterology 2023; 165:861-873. [PMID: 37453564 DOI: 10.1053/j.gastro.2023.06.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/07/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND & AIMS Small intestinal neuroendocrine tumor (SI-NET) is a rare disease, but its incidence has increased over the past 4 decades. Understanding the genetic risk factors underlying SI-NETs can help in disease prevention and may provide clinically beneficial markers for diagnosis. Here the results of the largest genome-wide association study of SI-NETs performed to date with 405 cases and 614,666 controls are reported. METHODS Samples from 307 patients with SI-NETs and 287,137 controls in the FinnGen study were used for the identification of SI-NET risk-associated genetic variants. The results were also meta-analyzed with summary statistics from the UK Biobank (n = 98 patients with SI-NET and n = 327,529 controls). RESULTS We identified 6 genome-wide significant (P < 5 × 10-8) loci associated with SI-NET risk, of which 4 (near SEMA6A, LGR5, CDKAL1, and FERMT2) are novel and 2 (near LTA4H-ELK and in KIF16B) have been reported previously. Interestingly, the top hit (rs200138614; P = 1.80 × 10-19) was a missense variant (p.Cys712Phe) in the LGR5 gene, a bona-fide marker of adult intestinal stem cells and a potentiator of canonical WNT signaling. The association was validated in an independent Finnish collection of 70 patients with SI-NETs, as well as in the UK Biobank exome sequence data (n = 92 cases and n = 392,814 controls). Overexpression of LGR5 p.Cys712Phe in intestinal organoids abolished the ability of R-Spondin1 to support organoid growth, indicating that the mutation perturbed R-Spondin-LGR5 signaling. CONCLUSIONS Our study is the largest genome-wide association study to date on SI-NETs and reported 4 new associated genome-wide association study loci, including a novel missense mutation (rs200138614, p.Cys712Phe) in LGR5, a canonical marker of adult intestinal stem cells.
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Affiliation(s)
- Anil K Giri
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland; Foundation for the Finnish Cancer Institute, Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Mervi Aavikko
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland; Department of Medical and Clinical Genetics and Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Linnea Wartiovaara
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Toni Lemmetyinen
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Juha Karjalainen
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts; Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts; Stanley Center for Psychiatric Research, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Juha Mehtonen
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Kimmo Palin
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland; Department of Medical and Clinical Genetics and Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Niko Välimäki
- Department of Medical and Clinical Genetics and Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Max Tamlander
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Riikka Saikkonen
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Auli Karhu
- Department of Medical and Clinical Genetics and Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ekaterina Morgunova
- Karolinska Institute, Department of Medical Biochemistry and Biophysics, Stockholm, Sweden
| | - Benjamin Sun
- Translational Biology, Research and Development, Biogen Inc, Cambridge, Massachusetts
| | - Heiko Runz
- Translational Biology, Research and Development, Biogen Inc, Cambridge, Massachusetts
| | - Priit Palta
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland; Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Shuang Luo
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Heikki Joensuu
- Department of Oncology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Tomi P Mäkelä
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Iiro Kostiainen
- Endocrinology, Abdominal Center, University of Helsinki, Helsinki University Hospital, Helsinki, Finland
| | - Camilla Schalin-Jäntti
- Endocrinology, Abdominal Center, University of Helsinki, Helsinki University Hospital, Helsinki, Finland
| | - FinnGen
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Aarno Palotie
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts; Stanley Center for Psychiatric Research, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Lauri A Aaltonen
- Department of Medical and Clinical Genetics and Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Saara Ollila
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Mark J Daly
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts; Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts; Stanley Center for Psychiatric Research, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts.
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22
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Upadhyay SS, Devasahayam Arokia Balaya R, Parate SS, Dagamajalu S, Keshava Prasad TS, Shetty R, Raju R. An assembly of TROP2-mediated signaling events. J Cell Commun Signal 2023; 17:1105-1111. [PMID: 37014471 PMCID: PMC10409939 DOI: 10.1007/s12079-023-00742-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/15/2023] [Indexed: 04/05/2023] Open
Abstract
Trophoblast cell surface antigen 2 (TROP2) is a calcium-transducing transmembrane protein mainly involved in embryo development. The aberrant expression of TROP2 is observed in numerous cancers, including triple-negative breast cancer, gastric, colorectal, pancreatic, squamous cell carcinoma of the oral cavity, and prostate cancers. The main signaling pathways mediated by TROP2 are calcium signaling, PI3K/AKT, JAK/STAT, MAPKs, and β-catenin signaling. However, collective information about the TROP2-mediated signaling pathway is not available for visualization or analysis. In this study, we constructed a TROP2 signaling map with respect to its role in different cancers. The data curation was done manually by following the NetPath annotation criteria. The described map consists of different molecular events, including 8 activation/inhibition, 16 enzyme catalysis, 19 gene regulations, 12 molecular associations, 39 induced-protein expressions, and 2 protein translocation. The data of the TROP2 pathway map is made freely accessible through the WikiPathways Database ( https://www.wikipathways.org/index.php/Pathway:WP5300 ). Development of TROP2 signaling pathway map.
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Affiliation(s)
- Shubham Sukerndeo Upadhyay
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018 India
| | | | - Sakshi Sanjay Parate
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018 India
| | - Shobha Dagamajalu
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018 India
| | - T. S. Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018 India
| | - Rohan Shetty
- Department of Surgical Oncology, Yenepoya Medical College Hospital, Yenepoya (Deemed to Be University), Mangalore, 575018 India
| | - Rajesh Raju
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018 India
- Centre for Integrative Omics Data Science, Yenepoya (Deemed to Be University), Mangalore, 575018 India
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23
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Moorman AR, Cambuli F, Benitez EK, Jiang Q, Xie Y, Mahmoud A, Lumish M, Hartner S, Balkaran S, Bermeo J, Asawa S, Firat C, Saxena A, Luthra A, Sgambati V, Luckett K, Wu F, Li Y, Yi Z, Masilionis I, Soares K, Pappou E, Yaeger R, Kingham P, Jarnagin W, Paty P, Weiser MR, Mazutis L, D'Angelica M, Shia J, Garcia-Aguilar J, Nawy T, Hollmann TJ, Chaligné R, Sanchez-Vega F, Sharma R, Pe'er D, Ganesh K. Progressive plasticity during colorectal cancer metastasis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.18.553925. [PMID: 37662289 PMCID: PMC10473595 DOI: 10.1101/2023.08.18.553925] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Metastasis is the principal cause of cancer death, yet we lack an understanding of metastatic cell states, their relationship to primary tumor states, and the mechanisms by which they transition. In a cohort of biospecimen trios from same-patient normal colon, primary and metastatic colorectal cancer, we show that while primary tumors largely adopt LGR5 + intestinal stem-like states, metastases display progressive plasticity. Loss of intestinal cell states is accompanied by reprogramming into a highly conserved fetal progenitor state, followed by non-canonical differentiation into divergent squamous and neuroendocrine-like states, which is exacerbated by chemotherapy and associated with poor patient survival. Using matched patient-derived organoids, we demonstrate that metastatic cancer cells exhibit greater cell-autonomous multilineage differentiation potential in response to microenvironment cues than their intestinal lineage-restricted primary tumor counterparts. We identify PROX1 as a stabilizer of intestinal lineage in the fetal progenitor state, whose downregulation licenses non-canonical reprogramming.
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24
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Tanaka K, Kawai S, Fujii E, Yano M, Miyayama T, Nakano K, Terao K, Suzuki M. Development of rat duodenal monolayer model with effective barrier function from rat organoids for ADME assay. Sci Rep 2023; 13:12130. [PMID: 37495742 PMCID: PMC10372144 DOI: 10.1038/s41598-023-39425-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/25/2023] [Indexed: 07/28/2023] Open
Abstract
The in-depth analysis of the ADME profiles of drug candidates using in vitro models is essential for drug development since a drug's exposure in humans depends on its ADME properties. In contrast to efforts in developing human in vitro absorption models, only a limited number of studies have explored models using rats, the most frequently used species in in vivo DMPK studies. In this study, we developed a monolayer model with an effective barrier function for ADME assays using rat duodenal organoids as a cell source. At first, we developed rat duodenal organoids according to a previous report, but they were not able to generate a confluent monolayer. Therefore, we modified organoid culture protocols and developed cyst-enriched organoids; these strongly promoted the formation of a confluent monolayer. Furthermore, adding valproic acid to the culture accelerated the differentiation of the monolayer, which possessed an effective barrier function and apicobasal cell polarity. Drug transporter P-gp function as well as CYP3A activity and nuclear receptor function were confirmed in the model. We expect our novel monolayer model to be a useful tool for elucidating drug absorption processes in detail, enabling the development of highly absorbable drugs.
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Affiliation(s)
- Kai Tanaka
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., 5-1-1 Tsukiji Chuo-Ku, Tokyo, 104-0045, Japan.
| | - Shigeto Kawai
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., 5-1-1 Tsukiji Chuo-Ku, Tokyo, 104-0045, Japan
| | - Etsuko Fujii
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., 216 Totsuka Totsuka-Ku Yokohama, Kanagawa, 244-8602, Japan
| | - Masumi Yano
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., 216 Totsuka Totsuka-Ku Yokohama, Kanagawa, 244-8602, Japan
| | - Takashi Miyayama
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., 216 Totsuka Totsuka-Ku Yokohama, Kanagawa, 244-8602, Japan
| | - Kiyotaka Nakano
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., 5-1-1 Tsukiji Chuo-Ku, Tokyo, 104-0045, Japan
| | - Kimio Terao
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., 2-1-1 Nihonbashi-Muromachi Chuo-Ku, Tokyo, 103-8324, Japan
| | - Masami Suzuki
- Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka, 412-8513, Japan
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25
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Pikkupeura LM, Bressan RB, Guiu J, Chen Y, Maimets M, Mayer D, Schweiger PJ, Hansen SL, Maciag GJ, Larsen HL, Lõhmussaar K, Pedersen MT, Teves JMY, Bornholdt J, Benes V, Sandelin A, Jensen KB. Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation. SCIENCE ADVANCES 2023; 9:eadf9460. [PMID: 37436997 DOI: 10.1126/sciadv.adf9460] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 06/08/2023] [Indexed: 07/14/2023]
Abstract
During intestinal organogenesis, equipotent epithelial progenitors mature into phenotypically distinct stem cells that are responsible for lifelong maintenance of the tissue. While the morphological changes associated with the transition are well characterized, the molecular mechanisms underpinning the maturation process are not fully understood. Here, we leverage intestinal organoid cultures to profile transcriptional, chromatin accessibility, DNA methylation, and three-dimensional (3D) chromatin conformation landscapes in fetal and adult epithelial cells. We observed prominent differences in gene expression and enhancer activity, which are accompanied by local changes in 3D organization, DNA accessibility, and methylation between the two cellular states. Using integrative analyses, we identified sustained Yes-Associated Protein (YAP) transcriptional activity as a major gatekeeper of the immature fetal state. We found the YAP-associated transcriptional network to be regulated at various levels of chromatin organization and likely to be coordinated by changes in extracellular matrix composition. Together, our work highlights the value of unbiased profiling of regulatory landscapes for the identification of key mechanisms underlying tissue maturation.
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Affiliation(s)
- Laura M Pikkupeura
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen N DK-2200, Denmark
- Bioinformatics Center, Department of Biology, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Raul B Bressan
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen N DK-2200, Denmark
- Novo Nordisk Foundation Center for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Jordi Guiu
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen N DK-2200, Denmark
- Institut d'Investigació Biomèdica de Bellvitge-IDIBELL, L'Hospitalet de Llobregat, 3a planta, Av. Granvia de l'Hospitalet 199, Hospitalet de Llobregat 08908, Spain
| | - Yun Chen
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen N DK-2200, Denmark
- Bioinformatics Center, Department of Biology, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Martti Maimets
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen N DK-2200, Denmark
- Novo Nordisk Foundation Center for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Daniela Mayer
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen N DK-2200, Denmark
- Novo Nordisk Foundation Center for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Pawel J Schweiger
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen N DK-2200, Denmark
- Novo Nordisk Foundation Center for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Stine L Hansen
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen N DK-2200, Denmark
- Novo Nordisk Foundation Center for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Grzegorz J Maciag
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen N DK-2200, Denmark
- Novo Nordisk Foundation Center for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Hjalte L Larsen
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen N DK-2200, Denmark
- Novo Nordisk Foundation Center for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Kadi Lõhmussaar
- Novo Nordisk Foundation Center for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | | | - Joji M Yap Teves
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen N DK-2200, Denmark
- Novo Nordisk Foundation Center for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Jette Bornholdt
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen N DK-2200, Denmark
- Bioinformatics Center, Department of Biology, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | | | - Albin Sandelin
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen N DK-2200, Denmark
- Bioinformatics Center, Department of Biology, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Kim B Jensen
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen N DK-2200, Denmark
- Novo Nordisk Foundation Center for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
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26
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Hansen SL, Larsen HL, Pikkupeura LM, Maciag G, Guiu J, Müller I, Clement DL, Mueller C, Johansen JV, Helin K, Lerdrup M, Jensen KB. An organoid-based CRISPR-Cas9 screen for regulators of intestinal epithelial maturation and cell fate. SCIENCE ADVANCES 2023; 9:eadg4055. [PMID: 37436979 DOI: 10.1126/sciadv.adg4055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 06/08/2023] [Indexed: 07/14/2023]
Abstract
Generation of functionally mature organs requires exquisite control of transcriptional programs governing cell state transitions during development. Despite advances in understanding the behavior of adult intestinal stem cells and their progeny, the transcriptional regulators that control the emergence of the mature intestinal phenotype remain largely unknown. Using mouse fetal and adult small intestinal organoids, we uncover transcriptional differences between the fetal and adult state and identify rare adult-like cells present in fetal organoids. This suggests that fetal organoids have an inherent potential to mature, which is locked by a regulatory program. By implementing a CRISPR-Cas9 screen targeting transcriptional regulators expressed in fetal organoids, we establish Smarca4 and Smarcc1 as important factors safeguarding the immature progenitor state. Our approach demonstrates the utility of organoid models in the identification of factors regulating cell fate and state transitions during tissue maturation and reveals that SMARCA4 and SMARCC1 prevent precocious differentiation during intestinal development.
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Affiliation(s)
- Stine L Hansen
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Hjalte L Larsen
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Laura M Pikkupeura
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Grzegorz Maciag
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Jordi Guiu
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
- Institut d'Investigació Biomèdica de Bellvitge-IDIBELL, 3a planta, Av. Granvia de l'Hospitalet 199, 08908 Hospitalet de Llobregat, Spain
| | - Iris Müller
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Ditte L Clement
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Christina Mueller
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Jens Vilstrup Johansen
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Mads Lerdrup
- The DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Kim B Jensen
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
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27
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Sell T, Klotz C, Fischer MM, Astaburuaga-García R, Krug S, Drost J, Clevers H, Sers C, Morkel M, Blüthgen N. Oncogenic signaling is coupled to colorectal cancer cell differentiation state. J Cell Biol 2023; 222:e202204001. [PMID: 37017636 PMCID: PMC10082329 DOI: 10.1083/jcb.202204001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 12/23/2022] [Accepted: 03/17/2023] [Indexed: 04/06/2023] Open
Abstract
Colorectal cancer progression is intrinsically linked to stepwise deregulation of the intestinal differentiation trajectory. In this process, sequential mutations of APC, KRAS, TP53, and SMAD4 enable oncogenic signaling and establish the hallmarks of cancer. Here, we use mass cytometry of isogenic human colon organoids and patient-derived cancer organoids to capture oncogenic signaling, cell phenotypes, and differentiation states in a high-dimensional single-cell map. We define a differentiation axis in all tumor progression states from normal to cancer. Our data show that colorectal cancer driver mutations shape the distribution of cells along the differentiation axis. In this regard, subsequent mutations can have stem cell promoting or restricting effects. Individual nodes of the cancer cell signaling network remain coupled to the differentiation state, regardless of the presence of driver mutations. We use single-cell RNA sequencing to link the (phospho-)protein signaling network to transcriptomic states with biological and clinical relevance. Our work highlights how oncogenes gradually shape signaling and transcriptomes during tumor progression.
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Affiliation(s)
- Thomas Sell
- Institute of Pathology, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Institute of Biology, Humboldt University of Berlin, Berlin, Germany
| | - Christian Klotz
- Department of Infectious Diseases, Robert Koch-Institute, Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Berlin, Germany
| | - Matthias M. Fischer
- Institute of Pathology, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Institute of Biology, Humboldt University of Berlin, Berlin, Germany
| | - Rosario Astaburuaga-García
- Institute of Pathology, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Institute of Biology, Humboldt University of Berlin, Berlin, Germany
| | - Susanne Krug
- Department of Gastroenterology, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Rheumatology and Infectious Diseases, Clinical Physiology/Nutritional Medicine, Berlin, Germany
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Hans Clevers
- Oncode Institute, Utrecht, Netherlands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, Netherlands
| | - Christine Sers
- Institute of Pathology, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Institute of Biology, Humboldt University of Berlin, Berlin, Germany
- German Cancer Consortium Partner Site Berlin, German Cancer Research Center, Heidelberg, Germany
| | - Markus Morkel
- Institute of Pathology, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium Partner Site Berlin, German Cancer Research Center, Heidelberg, Germany
- Berlin Institute of Health at Charité—Universitätsmedizin Berlin, Bioportal Single Cells, Berlin, Germany
| | - Nils Blüthgen
- Institute of Pathology, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Institute of Biology, Humboldt University of Berlin, Berlin, Germany
- German Cancer Consortium Partner Site Berlin, German Cancer Research Center, Heidelberg, Germany
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28
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Morral C, Ayyaz A, Kuo HC, Fink M, Verginadis I, Daniel AR, Burner DN, Driver LM, Satow S, Hasapis S, Ghinnagow R, Luo L, Ma Y, Attardi LD, Koumenis C, Minn AJ, Wrana JL, Lee CL, Kirsch DG. p53 promotes revival stem cells in the regenerating intestine after severe radiation injury. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.27.538576. [PMID: 37162959 PMCID: PMC10168332 DOI: 10.1101/2023.04.27.538576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Ionizing radiation induces cell death in the gastrointestinal (GI) epithelium by activating p53. However, p53 also prevents animal lethality caused by radiation-induced GI injury. Through single-cell RNA-sequencing of the irradiated mouse intestine, we find that p53 target genes are specifically enriched in stem cells of the regenerating epithelium, including revival stem cells that promote animal survival after GI damage. Accordingly, in mice with p53 deleted specifically in the GI epithelium, ionizing radiation fails to induce revival stem cells. Using intestinal organoids, we show that transient p53 expression is required for the induction of revival stem cells that is controlled by an Mdm2-mediated negative feedback loop. These results suggest that p53 suppresses severe radiation-indued GI injury by promoting intestinal epithelial cell reprogramming. One-Sentence Summary After severe radiation injury to the intestine, transient p53 activity induces revival stem cells to promote regeneration.
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29
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Bala P, Rennhack JP, Aitymbayev D, Morris C, Moyer SM, Duronio GN, Doan P, Li Z, Liang X, Hornick JL, Yurgelun MB, Hahn WC, Sethi NS. Aberrant cell state plasticity mediated by developmental reprogramming precedes colorectal cancer initiation. SCIENCE ADVANCES 2023; 9:eadf0927. [PMID: 36989360 PMCID: PMC10058311 DOI: 10.1126/sciadv.adf0927] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 02/28/2023] [Indexed: 05/12/2023]
Abstract
Cell state plasticity is carefully regulated in adult epithelia to prevent cancer. The aberrant expansion of the normally restricted capability for cell state plasticity in neoplasia is poorly defined. Using genetically engineered and carcinogen-induced mouse models of intestinal neoplasia, we observed that impaired differentiation is a conserved event preceding cancer development. Single-cell RNA sequencing (scRNA-seq) of premalignant lesions from mouse models and a patient with hereditary polyposis revealed that cancer initiates by adopting an aberrant transcriptional state characterized by regenerative activity, marked by Ly6a (Sca-1), and reactivation of fetal intestinal genes, including Tacstd2 (Trop2). Genetic inactivation of Sox9 prevented adenoma formation, obstructed the emergence of regenerative and fetal programs, and restored multilineage differentiation by scRNA-seq. Expanded chromatin accessibility at regeneration and fetal genes upon Apc inactivation was reduced by concomitant Sox9 suppression. These studies indicate that aberrant cell state plasticity mediated by unabated regenerative activity and developmental reprogramming precedes cancer development.
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Affiliation(s)
- Pratyusha Bala
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Jonathan P. Rennhack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Daulet Aitymbayev
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Clare Morris
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sydney M. Moyer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Gina N. Duronio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paul Doan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zhixin Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Xiaoyan Liang
- Department of Gastroenterology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jason L. Hornick
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Matthew B. Yurgelun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - William C. Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Nilay S. Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
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30
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Martinez-Ordoñez A, Duran A, Ruiz-Martinez M, Cid-Diaz T, Zhang X, Han Q, Kinoshita H, Muta Y, Linares JF, Kasashima H, Nakanishi Y, Omar M, Nishimura S, Avila L, Yashiro M, Maeda K, Pannellini T, Pigazzi A, Inghirami G, Marchionni L, Sigal D, Diaz-Meco MT, Moscat J. Hyaluronan driven by epithelial aPKC deficiency remodels the microenvironment and creates a vulnerability in mesenchymal colorectal cancer. Cancer Cell 2023; 41:252-271.e9. [PMID: 36525970 PMCID: PMC9931663 DOI: 10.1016/j.ccell.2022.11.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/17/2022] [Accepted: 11/22/2022] [Indexed: 12/23/2022]
Abstract
Mesenchymal colorectal cancer (mCRC) is microsatellite stable (MSS), highly desmoplastic, with CD8+ T cells excluded to the stromal periphery, resistant to immunotherapy, and driven by low levels of the atypical protein kinase Cs (aPKCs) in the intestinal epithelium. We show here that a salient feature of these tumors is the accumulation of hyaluronan (HA) which, along with reduced aPKC levels, predicts poor survival. HA promotes epithelial heterogeneity and the emergence of a tumor fetal metaplastic cell (TFMC) population endowed with invasive cancer features through a network of interactions with activated fibroblasts. TFMCs are sensitive to HA deposition, and their metaplastic markers have prognostic value. We demonstrate that in vivo HA degradation with a clinical dose of hyaluronidase impairs mCRC tumorigenesis and liver metastasis and enables immune checkpoint blockade therapy by promoting the recruitment of B and CD8+ T cells, including a proportion with resident memory features, and by blocking immunosuppression.
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Affiliation(s)
- Anxo Martinez-Ordoñez
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Angeles Duran
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Marc Ruiz-Martinez
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Tania Cid-Diaz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Xiao Zhang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Qixiu Han
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Hiroto Kinoshita
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Yu Muta
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Juan F Linares
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Hiroaki Kasashima
- Department of Gastroenterological Surgery, Osaka Metropolitan University Graduate School of Medicine, 1-4-3 Asahimachi, Abeno-ku, Osaka City 545-8585, Japan
| | - Yuki Nakanishi
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Mohamed Omar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Sadaaki Nishimura
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Leandro Avila
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Masakazu Yashiro
- Department of Gastroenterological Surgery, Osaka Metropolitan University Graduate School of Medicine, 1-4-3 Asahimachi, Abeno-ku, Osaka City 545-8585, Japan
| | - Kiyoshi Maeda
- Department of Gastroenterological Surgery, Osaka Metropolitan University Graduate School of Medicine, 1-4-3 Asahimachi, Abeno-ku, Osaka City 545-8585, Japan
| | - Tania Pannellini
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Alessio Pigazzi
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Luigi Marchionni
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Darren Sigal
- Division of Hematology-Oncology, Scripps Clinic, La Jolla, CA 92037, USA
| | - Maria T Diaz-Meco
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA.
| | - Jorge Moscat
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA.
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31
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Castillo-Azofeifa D, Wald T, Reyes EA, Gallagher A, Schanin J, Vlachos S, Lamarche-Vane N, Bomidi C, Blutt S, Estes MK, Nystul T, Klein OD. A DLG1-ARHGAP31-CDC42 axis is essential for the intestinal stem cell response to fluctuating niche Wnt signaling. Cell Stem Cell 2023; 30:188-206.e6. [PMID: 36640764 PMCID: PMC9922544 DOI: 10.1016/j.stem.2022.12.008] [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: 03/14/2022] [Revised: 10/13/2022] [Accepted: 12/12/2022] [Indexed: 01/15/2023]
Abstract
A central factor in the maintenance of tissue integrity is the response of stem cells to variations in the levels of niche signals. In the gut, intestinal stem cells (ISCs) depend on Wnt ligands for self-renewal and proliferation. Transient increases in Wnt signaling promote regeneration after injury or in inflammatory bowel diseases, whereas constitutive activation of this pathway leads to colorectal cancer. Here, we report that Discs large 1 (Dlg1), although dispensable for polarity and cellular turnover during intestinal homeostasis, is required for ISC survival in the context of increased Wnt signaling. RNA sequencing (RNA-seq) and genetic mouse models demonstrated that DLG1 regulates the cellular response to increased canonical Wnt ligands. This occurs via the transcriptional regulation of Arhgap31, a GTPase-activating protein that deactivates CDC42, an effector of the non-canonical Wnt pathway. These findings reveal a DLG1-ARHGAP31-CDC42 axis that is essential for the ISC response to increased niche Wnt signaling.
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Affiliation(s)
- David Castillo-Azofeifa
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA, USA; Department of Regenerative Medicine, Genentech, Inc., South San Francisco, CA, USA
| | - Tomas Wald
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Efren A Reyes
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA, USA; Department of Pharmaceutical Chemistry and TETRAD Program, University of California, San Francisco, San Francisco, CA, USA
| | - Aaron Gallagher
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Julia Schanin
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Stephanie Vlachos
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Nathalie Lamarche-Vane
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada; Department of Anatomy and Cell Biology, McGill University, Montréal, QC, Canada
| | - Carolyn Bomidi
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Sarah Blutt
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Todd Nystul
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Ophir D Klein
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA, USA; Department of Pediatrics and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA; Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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32
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Chen L, Dupre A, Qiu X, Pellon-Cardenas O, Walton KD, Wang J, Perekatt AO, Hu W, Spence JR, Verzi MP. TGFB1 Induces Fetal Reprogramming and Enhances Intestinal Regeneration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.13.523825. [PMID: 36711781 PMCID: PMC9882197 DOI: 10.1101/2023.01.13.523825] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The adult gut epithelium has a remarkable ability to recover from damage. To achieve cellular therapies aimed at restoring and/or replacing defective gastrointestinal tissue, it is important to understand the natural mechanisms of tissue regeneration. We employed a combination of high throughput sequencing approaches, mouse genetic models, and murine and human organoid models, and identified a role for TGFB signaling during intestinal regeneration following injury. At 2 days following irradiation (IR)-induced damage of intestinal crypts, a surge in TGFB1 expression is mediated by monocyte/macrophage cells at the location of damage. Depletion of macrophages or genetic disruption of TGFB-signaling significantly impaired the regenerative response following irradiation. Murine intestinal regeneration is also characterized by a process where a fetal transcriptional signature is induced during repair. In organoid culture, TGFB1-treatment was necessary and sufficient to induce a transcriptomic shift to the fetal-like/regenerative state. The regenerative response was enhanced by the function of mesenchymal cells, which are also primed for regeneration by TGFB1. Mechanistically, integration of ATAC-seq, scRNA-seq, and ChIP-seq suggest that a regenerative YAP-SOX9 transcriptional circuit is activated in epithelium exposed to TGFB1. Finally, pre-treatment with TGFB1 enhanced the ability of primary epithelial cultures to engraft into damaged murine colon, suggesting promise for the application of the TGFB-induced regenerative circuit in cellular therapy.
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Affiliation(s)
- Lei Chen
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, China
| | - Abigail Dupre
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Xia Qiu
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Oscar Pellon-Cardenas
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Katherine D. Walton
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jianming Wang
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Ansu O. Perekatt
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, NJ, USA
| | - Wenwei Hu
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Jason R. Spence
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI, USA
| | - Michael P. Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
- Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition & Health, Rutgers University, New Brunswick, NJ, USA
- Member of the NIEHS Center for Environmental Exposures and Disease (CEED), Rutgers EOHSI Piscataway, NJ, USA
- Lead Contact
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33
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Imajo M, Hirota A, Tanaka S. Generation of Fetal Intestinal Organoids and Their Maturation into Adult Intestinal Cells. Methods Mol Biol 2023; 2650:133-140. [PMID: 37310629 DOI: 10.1007/978-1-0716-3076-1_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
During embryonic development, the gut tube undergoes massive morphological changes from the simple tube structure composed of the pseudostratified epithelium into the mature intestinal tract composed of the columnar epithelium and characterized by the unique crypt-villus structures. In mice, maturation of fetal gut precursor cells into adult intestinal cells starts around embryonic day (E) 16.5, during which adult intestinal stem cells and their differentiated progenies are generated. In contrast to adult intestinal cells that form budding organoids containing both the crypt-like and villus-like regions, fetal intestinal cells can be cultured as simple spheroid-shaped organoids that show a uniform proliferation pattern. The fetal intestinal spheroids can undergo spontaneous maturation into adult budding organoids that contain intestinal stem cells and differentiated cells, including enterocytes, goblet, enteroendocrine, and Paneth cells, recapitulating intestinal cell maturation in vitro. Here, we provide detailed methods for establishment of fetal intestinal organoids and their differentiation into adult intestinal cells. These methods enable in vitro recapitulation of intestinal development and would be useful to reveal mechanisms that regulate the transition from fetal to adult intestinal cells.
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Affiliation(s)
- Masamichi Imajo
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan.
| | - Akira Hirota
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Shinya Tanaka
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
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34
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Ramadan R, Wouters VM, van Neerven SM, de Groot NE, Garcia TM, Muncan V, Franklin OD, Battle M, Carlson KS, Leach J, Sansom OJ, Boulard O, Chamaillard M, Vermeulen L, Medema JP, Huels DJ. The extracellular matrix controls stem cell specification and crypt morphology in the developing and adult mouse gut. Biol Open 2022; 11:bio059544. [PMID: 36350252 PMCID: PMC9713296 DOI: 10.1242/bio.059544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/22/2022] [Indexed: 11/01/2023] Open
Abstract
The rapid renewal of the epithelial gut lining is fuelled by stem cells that reside at the base of intestinal crypts. The signal transduction pathways and morphogens that regulate intestinal stem cell self-renewal and differentiation have been extensively characterised. In contrast, although extracellular matrix (ECM) components form an integral part of the intestinal stem cell niche, their direct influence on the cellular composition is less well understood. We set out to systematically compare the effect of two ECM classes, the interstitial matrix and the basement membrane, on the intestinal epithelium. We found that both collagen I and laminin-containing cultures allow growth of small intestinal epithelial cells with all cell types present in both cultures, albeit at different ratios. The collagen cultures contained a subset of cells enriched in fetal-like markers. In contrast, laminin increased Lgr5+ stem cells and Paneth cells, and induced crypt-like morphology changes. The transition from a collagen culture to a laminin culture resembled gut development in vivo. The dramatic ECM remodelling was accompanied by a local expression of the laminin receptor ITGA6 in the crypt-forming epithelium. Importantly, deletion of laminin in the adult mouse resulted in a marked reduction of adult intestinal stem cells. Overall, our data support the hypothesis that the formation of intestinal crypts is induced by an increased laminin concentration in the ECM.
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Affiliation(s)
- Rana Ramadan
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Valérie M. Wouters
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Sanne M. van Neerven
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Nina E. de Groot
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Tania Martins Garcia
- Department of Gastroenterology and Hepatology, Tytgat Institute for Intestinal and Liver Research, Amsterdam Gastroenterology Endocrinology and Metabolism, Amsterdam UMC University of Amsterdam, 1015 BK Amsterdam, The Netherlands
| | - Vanessa Muncan
- Department of Gastroenterology and Hepatology, Tytgat Institute for Intestinal and Liver Research, Amsterdam Gastroenterology Endocrinology and Metabolism, Amsterdam UMC University of Amsterdam, 1015 BK Amsterdam, The Netherlands
| | - Olivia D. Franklin
- The Medical College of Wisconsin, Department of Cell Biology, Neurobiology, and Anatomy, Milwaukee, WI 53226, USA
| | - Michelle Battle
- The Medical College of Wisconsin, Department of Cell Biology, Neurobiology, and Anatomy, Milwaukee, WI 53226, USA
| | - Karen Sue Carlson
- The Medical College of Wisconsin, Department of Cell Biology, Neurobiology, and Anatomy, Milwaukee, WI 53226, USA
- The Blood Research Institute of Wisconsin, part of Versiti, and the Medical College of Wisconsin, Department of Internal Medicine, Milwaukee, WI 53226, USA
| | - Joshua Leach
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, G61 1QH, UK
| | - Owen J. Sansom
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, G61 1QH, UK
| | - Olivier Boulard
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 – UMR 8204 – Centre d'Infection et d'Immunité de Lille (CIIL), Université de Lille, 59019 Lille, France
| | - Mathias Chamaillard
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 – UMR 8204 – Centre d'Infection et d'Immunité de Lille (CIIL), Université de Lille, 59019 Lille, France
| | - Louis Vermeulen
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Jan Paul Medema
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - David J. Huels
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
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Kobayashi S, Ogasawara N, Watanabe S, Yoneyama Y, Kirino S, Hiraguri Y, Inoue M, Nagata S, Okamoto-Uchida Y, Kofuji S, Shimizu H, Ito G, Mizutani T, Yamauchi S, Kinugasa Y, Kano Y, Nemoto Y, Watanabe M, Tsuchiya K, Nishina H, Okamoto R, Yui S. Collagen type I-mediated mechanotransduction controls epithelial cell fate conversion during intestinal inflammation. Inflamm Regen 2022; 42:49. [PMID: 36443773 PMCID: PMC9703763 DOI: 10.1186/s41232-022-00237-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/09/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The emerging concepts of fetal-like reprogramming following tissue injury have been well recognized as an important cue for resolving regenerative mechanisms of intestinal epithelium during inflammation. We previously revealed that the remodeling of mesenchyme with collagen fibril induces YAP/TAZ-dependent fate conversion of intestinal/colonic epithelial cells covering the wound bed towards fetal-like progenitors. To fully elucidate the mechanisms underlying the link between extracellular matrix (ECM) remodeling of mesenchyme and fetal-like reprogramming of epithelial cells, it is critical to understand how collagen type I influence the phenotype of epithelial cells. In this study, we utilize collagen sphere, which is the epithelial organoids cultured in purified collagen type I, to understand the mechanisms of the inflammatory associated reprogramming. Resolving the entire landscape of regulatory networks of the collagen sphere is useful to dissect the reprogrammed signature of the intestinal epithelium. METHODS We performed microarray, RNA-seq, and ATAC-seq analyses of the murine collagen sphere in comparison with Matrigel organoid and fetal enterosphere (FEnS). We subsequently cultured human colon epithelium in collagen type I and performed RNA-seq analysis. The enriched genes were validated by gene expression comparison between published gene sets and immunofluorescence in pathological specimens of ulcerative colitis (UC). RESULTS The murine collagen sphere was confirmed to have inflammatory and regenerative signatures from RNA-seq analysis. ATAC-seq analysis confirmed that the YAP/TAZ-TEAD axis plays a central role in the induction of the distinctive signature. Among them, TAZ has implied its relevant role in the process of reprogramming and the ATAC-based motif analysis demonstrated not only Tead proteins, but also Fra1 and Runx2, which are highly enriched in the collagen sphere. Additionally, the human collagen sphere also showed a highly significant enrichment of both inflammatory and fetal-like signatures. Immunofluorescence staining confirmed that the representative genes in the human collagen sphere were highly expressed in the inflammatory region of ulcerative colitis. CONCLUSIONS Collagen type I showed a significant influence in the acquisition of the reprogrammed inflammatory signature in both mice and humans. Dissection of the cell fate conversion and its mechanisms shown in this study can enhance our understanding of how the epithelial signature of inflammation is influenced by the ECM niche.
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Affiliation(s)
- Sakurako Kobayashi
- grid.265073.50000 0001 1014 9130Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510 Japan
| | - Nobuhiko Ogasawara
- grid.265073.50000 0001 1014 9130Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510 Japan
| | - Satoshi Watanabe
- grid.265073.50000 0001 1014 9130Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510 Japan
| | - Yosuke Yoneyama
- grid.265073.50000 0001 1014 9130Institute of Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510 Japan
| | - Sakura Kirino
- grid.265073.50000 0001 1014 9130Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510 Japan
| | - Yui Hiraguri
- grid.265073.50000 0001 1014 9130Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510 Japan
| | - Masami Inoue
- grid.265073.50000 0001 1014 9130Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510 Japan
| | - Sayaka Nagata
- grid.265073.50000 0001 1014 9130Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510 Japan
| | - Yoshimi Okamoto-Uchida
- grid.265073.50000 0001 1014 9130Department of Developmental and Regenerative Biology, Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510 Japan
| | - Satoshi Kofuji
- grid.265073.50000 0001 1014 9130Department of Developmental and Regenerative Biology, Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510 Japan
| | - Hiromichi Shimizu
- grid.265073.50000 0001 1014 9130Center for Stem Cell and Regenerative Medicine, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510 Japan
| | - Go Ito
- grid.265073.50000 0001 1014 9130Advanced Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510 Japan
| | - Tomohiro Mizutani
- grid.265073.50000 0001 1014 9130Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510 Japan
| | - Shinichi Yamauchi
- grid.265073.50000 0001 1014 9130Department of Gastrointestinal Surgery, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510 Japan
| | - Yusuke Kinugasa
- grid.265073.50000 0001 1014 9130Department of Gastrointestinal Surgery, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510 Japan
| | - Yoshihito Kano
- grid.265073.50000 0001 1014 9130Department of Clinical Oncology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510 Japan
| | - Yasuhiro Nemoto
- grid.265073.50000 0001 1014 9130Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510 Japan
| | - Mamoru Watanabe
- grid.265073.50000 0001 1014 9130Advanced Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510 Japan
| | - Kiichiro Tsuchiya
- grid.20515.330000 0001 2369 4728Department of Gastroenterology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8575 Japan
| | - Hiroshi Nishina
- grid.265073.50000 0001 1014 9130Department of Developmental and Regenerative Biology, Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510 Japan
| | - Ryuichi Okamoto
- grid.265073.50000 0001 1014 9130Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510 Japan
| | - Shiro Yui
- grid.265073.50000 0001 1014 9130Center for Stem Cell and Regenerative Medicine, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510 Japan
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36
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Metastatic recurrence in colorectal cancer arises from residual EMP1+ cells. Nature 2022; 611:603-613. [DOI: 10.1038/s41586-022-05402-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 09/30/2022] [Indexed: 11/10/2022]
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Karo-Atar D, Ouladan S, Javkar T, Joumier L, Matheson MK, Merritt S, Westfall S, Rochette A, Gentile ME, Fontes G, Fonseca GJ, Parisien M, Diatchenko L, von Moltke J, Malleshaiah M, Gregorieff A, King IL. Helminth-induced reprogramming of the stem cell compartment inhibits type 2 immunity. J Exp Med 2022; 219:e20212311. [PMID: 35938990 PMCID: PMC9365672 DOI: 10.1084/jem.20212311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 03/23/2022] [Accepted: 07/11/2022] [Indexed: 12/13/2022] Open
Abstract
Enteric helminths form intimate physical connections with the intestinal epithelium, yet their ability to directly alter epithelial stem cell fate has not been resolved. Here we demonstrate that infection of mice with the parasite Heligmosomoides polygyrus bakeri (Hpb) reprograms the intestinal epithelium into a fetal-like state marked by the emergence of Clusterin-expressing revival stem cells (revSCs). Organoid-based studies using parasite-derived excretory-secretory products reveal that Hpb-mediated revSC generation occurs independently of host-derived immune signals and inhibits type 2 cytokine-driven differentiation of secretory epithelial lineages that promote their expulsion. Reciprocally, type 2 cytokine signals limit revSC differentiation and, consequently, Hpb fitness, indicating that helminths compete with their host for control of the intestinal stem cell compartment to promote continuation of their life cycle.
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Affiliation(s)
- Danielle Karo-Atar
- Department of Microbiology and Immunology, Meakins-Christie Laboratories, Research Institute of McGill University Health Centre, Montreal, Quebec, Canada
- McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, Quebec, Canada
- McGill Regenerative Medicine Network, Montreal, Quebec, Canada
| | - Shaida Ouladan
- Department of Pathology, McGill University and Cancer Research Program, Research Institute of McGill University Health Centre, Montreal, Quebec, Canada
- McGill Regenerative Medicine Network, Montreal, Quebec, Canada
| | - Tanvi Javkar
- Department of Pathology, McGill University and Cancer Research Program, Research Institute of McGill University Health Centre, Montreal, Quebec, Canada
- McGill Regenerative Medicine Network, Montreal, Quebec, Canada
| | - Loick Joumier
- Division of Systems Biology, Montreal Clinical Research Institute, Montreal, QC, Canada
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, Quebec, Canada
| | | | - Sydney Merritt
- Department of Microbiology and Immunology, Meakins-Christie Laboratories, Research Institute of McGill University Health Centre, Montreal, Quebec, Canada
| | - Susan Westfall
- Department of Microbiology and Immunology, Meakins-Christie Laboratories, Research Institute of McGill University Health Centre, Montreal, Quebec, Canada
| | - Annie Rochette
- Department of Pathology, McGill University and Cancer Research Program, Research Institute of McGill University Health Centre, Montreal, Quebec, Canada
- McGill Regenerative Medicine Network, Montreal, Quebec, Canada
| | - Maria E. Gentile
- Department of Microbiology and Immunology, Meakins-Christie Laboratories, Research Institute of McGill University Health Centre, Montreal, Quebec, Canada
| | - Ghislaine Fontes
- Department of Microbiology and Immunology, Meakins-Christie Laboratories, Research Institute of McGill University Health Centre, Montreal, Quebec, Canada
| | - Gregory J. Fonseca
- McGill University Health Centre, Meakins-Christie Laboratories, Department of Medicine, Division of Quantitative Life Sciences, Montreal, Quebec, Canada
| | - Marc Parisien
- Department of Human Genetics, Allen Edwards Centre for Pain Research, McGill University, Montreal, Quebec, Canada
| | - Luda Diatchenko
- Department of Human Genetics, Allen Edwards Centre for Pain Research, McGill University, Montreal, Quebec, Canada
| | | | - Mohan Malleshaiah
- Division of Systems Biology, Montreal Clinical Research Institute, Montreal, QC, Canada
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, Quebec, Canada
- McGill Regenerative Medicine Network, Montreal, Quebec, Canada
| | - Alex Gregorieff
- Department of Pathology, McGill University and Cancer Research Program, Research Institute of McGill University Health Centre, Montreal, Quebec, Canada
- McGill Regenerative Medicine Network, Montreal, Quebec, Canada
| | - Irah L. King
- Department of Microbiology and Immunology, Meakins-Christie Laboratories, Research Institute of McGill University Health Centre, Montreal, Quebec, Canada
- McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, Quebec, Canada
- McGill Regenerative Medicine Network, Montreal, Quebec, Canada
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38
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Álvarez-Varela A, Novellasdemunt L, Barriga FM, Hernando-Momblona X, Cañellas-Socias A, Cano-Crespo S, Sevillano M, Cortina C, Stork D, Morral C, Turon G, Slebe F, Jiménez-Gracia L, Caratù G, Jung P, Stassi G, Heyn H, Tauriello DVF, Mateo L, Tejpar S, Sancho E, Stephan-Otto Attolini C, Batlle E. Mex3a marks drug-tolerant persister colorectal cancer cells that mediate relapse after chemotherapy. NATURE CANCER 2022; 3:1052-1070. [PMID: 35773527 DOI: 10.1038/s43018-022-00402-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Colorectal cancer (CRC) patient-derived organoids predict responses to chemotherapy. Here we used them to investigate relapse after treatment. Patient-derived organoids expand from highly proliferative LGR5+ tumor cells; however, we discovered that lack of optimal growth conditions specifies a latent LGR5+ cell state. This cell population expressed the gene MEX3A, is chemoresistant and regenerated the organoid culture after treatment. In CRC mouse models, Mex3a+ cells contributed marginally to metastatic outgrowth; however, after chemotherapy, Mex3a+ cells produced large cell clones that regenerated the disease. Lineage-tracing analysis showed that persister Mex3a+ cells downregulate the WNT/stem cell gene program immediately after chemotherapy and adopt a transient state reminiscent to that of YAP+ fetal intestinal progenitors. In contrast, Mex3a-deficient cells differentiated toward a goblet cell-like phenotype and were unable to resist chemotherapy. Our findings reveal that adaptation of cancer stem cells to suboptimal niche environments protects them from chemotherapy and identify a candidate cell of origin of relapse after treatment in CRC.
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Affiliation(s)
- Adrián Álvarez-Varela
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Laura Novellasdemunt
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Francisco M Barriga
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xavier Hernando-Momblona
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Adrià Cañellas-Socias
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Sara Cano-Crespo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marta Sevillano
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Carme Cortina
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Diana Stork
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Clara Morral
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Gemma Turon
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Felipe Slebe
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Laura Jiménez-Gracia
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ginevra Caratù
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Peter Jung
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Partner site Munich, Institute of Pathology, Ludwig Maximilian University, Munich, Germany
| | - Giorgio Stassi
- Department of Surgical Oncological and Stomatological Sciences, University of Palermo, Palermo, Italy
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Daniele V F Tauriello
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Lidia Mateo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Sabine Tejpar
- Molecular Digestive Oncology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Elena Sancho
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Camille Stephan-Otto Attolini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.
- ICREA, Barcelona, Spain.
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39
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TROP2 Represents a Negative Prognostic Factor in Colorectal Adenocarcinoma and Its Expression Is Associated with Features of Epithelial–Mesenchymal Transition and Invasiveness. Cancers (Basel) 2022; 14:cancers14174137. [PMID: 36077674 PMCID: PMC9454662 DOI: 10.3390/cancers14174137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/09/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Colorectal cancer (CRC) is one of the most common cancers worldwide. While the systemic treatment of CRC is based on chemotherapy, subsequent therapeutic options are far less effective. Trophoblast cell surface antigen 2 (TROP2) is highly expressed in many carcinomas, including CRC, where its expression correlates with a poor prognosis. Anti-TROP2-targeted therapy was approved for the treatment of breast and urothelial carcinomas. We aimed to determine whether TROP2 is a suitable target for the treatment of CRC. We demonstrated that TROP2 expression in CRC correlates with lymph node metastasis and poor tumor differentiation. An analysis of mouse tumor models, patient-derived organoids, and tumor cells revealed that TROP2 expression is associated with features related to epithelial–mesenchymal transition and invasiveness. Our results suggest that TROP2 targeting may be a promising approach, especially in the early phase of treatment. Abstract Trophoblastic cell surface antigen 2 (TROP2) is a membrane glycoprotein overexpressed in many solid tumors with a poor prognosis, including intestinal neoplasms. In our study, we show that TROP2 is expressed in preneoplastic lesions, and its expression is maintained in most colorectal cancers (CRC). High TROP2 positivity correlated with lymph node metastases and poor tumor differentiation and was a negative prognostic factor. To investigate the role of TROP2 in intestinal tumors, we analyzed two mouse models with conditional disruption of the adenomatous polyposis coli (Apc) tumor-suppressor gene, human adenocarcinoma samples, patient-derived organoids, and TROP2-deficient tumor cells. We found that Trop2 is produced early after Apc inactivation and its expression is associated with the transcription of genes involved in epithelial–mesenchymal transition, the regulation of migration, invasiveness, and extracellular matrix remodeling. A functionally similar group of genes was also enriched in TROP2-positive cells from human CRC samples. To decipher the driving mechanism of TROP2 expression, we analyzed its promoter. In human cells, this promoter was activated by β-catenin and additionally by the Yes1-associated transcriptional regulator (YAP). The regulation of TROP2 expression by active YAP was verified by YAP knockdown in CRC cells. Our results suggest a possible link between aberrantly activated Wnt/β-catenin signaling, YAP, and TROP2 expression.
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40
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Wu L, Tian X, Du H, Liu X, Wu H. Bioinformatics Analysis of LGR4 in Colon Adenocarcinoma as Potential Diagnostic Biomarker, Therapeutic Target and Promoting Immune Cell Infiltration. Biomolecules 2022; 12:biom12081081. [PMID: 36008975 PMCID: PMC9406187 DOI: 10.3390/biom12081081] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/31/2022] [Accepted: 08/01/2022] [Indexed: 12/24/2022] Open
Abstract
Colon adenocarcinoma is one of the tumors with the highest mortality rate, and tumorigenesis or development of colon adenocarcinoma is the major reason leading to patient death. However, the molecular mechanism and biomarker to predict tumor progression are currently unclear. With the goal of understanding the molecular mechanism and tumor progression, we utilized the TCGA database to identify differentially expressed genes. After identifying the differentially expressed genes among colon adenocarcinoma tissues with different expression levels of LGR4 and normal tissue, protein–protein interaction, gene ontology, pathway enrichment, gene set enrichment analysis, and immune cell infiltration analysis were conducted. Here, the top 10 hub genes, i.e., ALB, F2, APOA2, CYP1A1, SPRR2B, APOA1, APOB, CYP3A4, SST, and GCG, were identified, and relative correlation analysis was conducted. Kaplan–Meier analysis revealed that higher expression of LGR4 correlates with overall survival of colon adenocarcinoma patients, although expression levels of LGR4 in normal tissues are higher than in tumor tissues. Further functional analysis demonstrated that higher expression of LGR4 in colon adenocarcinoma may be linked to up-regulate metabolism-related pathways, for example, the cholesterol biosynthesis pathway. These results were confirmed by gene set enrichment analysis. Immune cell infiltration analysis clearly showed that the infiltration percentage of T cells was significantly higher than other immune cells, and TIMER analysis revealed a positive correlation between T-cell infiltration and LGR4 expression. Finally, COAD cancer cells, Caco-2, were employed to be incubated with squalene and 25-hydroxycholesterol-3-sulfate, and relative experimental results confirmed that the cholesterol biosynthesis pathway involved in modulating the proliferation of COAD tumorigenesis. Our investigation revealed that LGR4 can be an emerging diagnostic and prognostic biomarker for colon adenocarcinoma by affecting metabolism-related pathways.
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Affiliation(s)
- Lijuan Wu
- Department of Gastroenterology, the First Affiliated Hospital, College of Clinical Medicine of Henan University of Science and Technology, Luoyang 471003, China
- Correspondence: (L.W.); (H.W.)
| | - Xiaoxiao Tian
- Department of Gastroenterology, the First Affiliated Hospital, College of Clinical Medicine of Henan University of Science and Technology, Luoyang 471003, China
| | - Hao Du
- Department of Orthopedic, the First Affiliated Hospital, College of Clinical Medicine of Henan University of Science and Technology, Luoyang 471003, China
| | - Xiaomin Liu
- Department of Gastroenterology, the First Affiliated Hospital, College of Clinical Medicine of Henan University of Science and Technology, Luoyang 471003, China
| | - Haigang Wu
- School of Life Sciences, Henan University, Kaifeng 475000, China
- Correspondence: (L.W.); (H.W.)
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41
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Gil Vazquez E, Nasreddin N, Valbuena GN, Mulholland EJ, Belnoue-Davis HL, Eggington HR, Schenck RO, Wouters VM, Wirapati P, Gilroy K, Lannagan TR, Flanagan DJ, Najumudeen AK, Omwenga S, McCorry AM, Easton A, Koelzer VH, East JE, Morton D, Trusolino L, Maughan T, Campbell AD, Loughrey MB, Dunne PD, Tsantoulis P, Huels DJ, Tejpar S, Sansom OJ, Leedham SJ. Dynamic and adaptive cancer stem cell population admixture in colorectal neoplasia. Cell Stem Cell 2022; 29:1213-1228.e8. [PMID: 35931031 PMCID: PMC9592560 DOI: 10.1016/j.stem.2022.07.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/01/2022] [Accepted: 07/19/2022] [Indexed: 12/13/2022]
Abstract
Intestinal homeostasis is underpinned by LGR5+ve crypt-base columnar stem cells (CBCs), but following injury, dedifferentiation results in the emergence of LGR5-ve regenerative stem cell populations (RSCs), characterized by fetal transcriptional profiles. Neoplasia hijacks regenerative signaling, so we assessed the distribution of CBCs and RSCs in mouse and human intestinal tumors. Using combined molecular-morphological analysis, we demonstrate variable expression of stem cell markers across a range of lesions. The degree of CBC-RSC admixture was associated with both epithelial mutation and microenvironmental signaling disruption and could be mapped across disease molecular subtypes. The CBC-RSC equilibrium was adaptive, with a dynamic response to acute selective pressure, and adaptability was associated with chemoresistance. We propose a fitness landscape model where individual tumors have equilibrated stem cell population distributions along a CBC-RSC phenotypic axis. Cellular plasticity is represented by position shift along this axis and is influenced by cell-intrinsic, extrinsic, and therapeutic selective pressures.
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Affiliation(s)
- Ester Gil Vazquez
- Wellcome Centre Human Genetics, Roosevelt Drive, University of Oxford, Oxford, UK
| | - Nadia Nasreddin
- Wellcome Centre Human Genetics, Roosevelt Drive, University of Oxford, Oxford, UK
| | - Gabriel N. Valbuena
- Wellcome Centre Human Genetics, Roosevelt Drive, University of Oxford, Oxford, UK
| | - Eoghan J. Mulholland
- Wellcome Centre Human Genetics, Roosevelt Drive, University of Oxford, Oxford, UK
| | | | - Holly R. Eggington
- Wellcome Centre Human Genetics, Roosevelt Drive, University of Oxford, Oxford, UK
| | - Ryan O. Schenck
- Wellcome Centre Human Genetics, Roosevelt Drive, University of Oxford, Oxford, UK
| | - Valérie M. Wouters
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Meibergdreef 9, 1105 Amsterdam, the Netherlands,Oncode Institute, Meibergdreef 9, 1105 Amsterdam, the Netherlands
| | - Pratyaksha Wirapati
- Swiss Institute for Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | | | | | | | | | - Sulochana Omwenga
- Wellcome Centre Human Genetics, Roosevelt Drive, University of Oxford, Oxford, UK
| | - Amy M.B. McCorry
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, UK
| | - Alistair Easton
- Department of Oncology, Old Road Campus Research Building, Roosevelt Drive, University of Oxford, Oxford, UK
| | - Viktor H. Koelzer
- Department of Pathology and Molecular Pathology, University and University Hospital Zürich, Rämistrasse 100, 8006 Zürich, Switzerland
| | - James E. East
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, and Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Dion Morton
- Academic Department of Surgery, University of Birmingham, Birmingham, UK
| | - Livio Trusolino
- Candiolo Cancer Institute FPO IRCCS, 10060 Candiolo, Torino, Italy
| | - Timothy Maughan
- Department of Oncology, Old Road Campus Research Building, Roosevelt Drive, University of Oxford, Oxford, UK
| | | | - Maurice B. Loughrey
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, UK
| | - Philip D. Dunne
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, UK
| | - Petros Tsantoulis
- University of Geneva and Department of Oncology, Hôpitaux Universitaires de Genève, Geneva, Switzerland
| | - David J. Huels
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Meibergdreef 9, 1105 Amsterdam, the Netherlands,Oncode Institute, Meibergdreef 9, 1105 Amsterdam, the Netherlands
| | - Sabine Tejpar
- Molecular Digestive Oncology Unit, KU Leuven, Leuven, Belgium
| | - Owen J. Sansom
- Cancer Research UK Beatson Institute, Glasgow, UK,Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Glasgow, UK
| | - Simon J. Leedham
- Wellcome Centre Human Genetics, Roosevelt Drive, University of Oxford, Oxford, UK,Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, and Oxford NIHR Biomedical Research Centre, Oxford, UK,Corresponding author
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42
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Ribosome impairment regulates intestinal stem cell identity via ZAKɑ activation. Nat Commun 2022; 13:4492. [PMID: 35918345 PMCID: PMC9345940 DOI: 10.1038/s41467-022-32220-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 07/21/2022] [Indexed: 11/09/2022] Open
Abstract
The small intestine is a rapidly proliferating organ that is maintained by a small population of Lgr5-expressing intestinal stem cells (ISCs). However, several Lgr5-negative ISC populations have been identified, and this remarkable plasticity allows the intestine to rapidly respond to both the local environment and to damage. However, the mediators of such plasticity are still largely unknown. Using intestinal organoids and mouse models, we show that upon ribosome impairment (driven by Rptor deletion, amino acid starvation, or low dose cyclohexamide treatment) ISCs gain an Lgr5-negative, fetal-like identity. This is accompanied by a rewiring of metabolism. Our findings suggest that the ribosome can act as a sensor of nutrient availability, allowing ISCs to respond to the local nutrient environment. Mechanistically, we show that this phenotype requires the activation of ZAKɑ, which in turn activates YAP, via SRC. Together, our data reveals a central role for ribosome dynamics in intestinal stem cells, and identify the activation of ZAKɑ as a critical mediator of stem cell identity. Intestinal stem cells are responsible for replenishing cells within the high-turnover intestinal epithelium. Here they show that ribosome dynamics affect intestinal stem cell identity through a mechanism that is triggered by changes in nutrient availability.
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43
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Development and characterization of human fetal female reproductive tract organoids to understand Müllerian duct anomalies. Proc Natl Acad Sci U S A 2022; 119:e2118054119. [PMID: 35858415 PMCID: PMC9335258 DOI: 10.1073/pnas.2118054119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Müllerian ducts are paired tubular structures that give rise to most of the female reproductive organs. Any abnormalities in the development and differentiation of these ducts lead to anatomical defects in the female reproductive tract organs categorized as Müllerian duct anomalies. Due to the limited access to fetal tissues, little is understood of human reproductive tract development and the associated anomalies. Although organoids represent a powerful model to decipher human development and disease, such organoids from fetal reproductive organs are not available. Here, we developed organoids from human fetal fallopian tubes and uteri and compared them with their adult counterparts. Our results demonstrate that human fetal reproductive tract epithelia do not express some of the typical markers of adult reproductive tract epithelia. Furthermore, fetal organoids are grossly, histologically, and proteomically different from adult organoids. While external supplementation of WNT ligands or activators in culture medium is an absolute requirement for the adult reproductive tract organoids, fetal organoids are able to grow in WNT-deficient conditions. We also developed decellularized tissue scaffolds from adult human fallopian tubes and uteri. Transplantation of fetal organoids onto these scaffolds led to the regeneration of the adult fallopian tube and uterine epithelia. Importantly, suppression of Wnt signaling, which is altered in patients with Müllerian duct anomalies, inhibits the regenerative ability of human fetal organoids and causes severe anatomical defects in the mouse reproductive tract. Thus, our fetal organoids represent an important platform to study the underlying basis of human female reproductive tract development and diseases.
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44
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Zhao L, Song W, Chen YG. Mesenchymal-epithelial interaction regulates gastrointestinal tract development in mouse embryos. Cell Rep 2022; 40:111053. [PMID: 35830795 DOI: 10.1016/j.celrep.2022.111053] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 03/31/2022] [Accepted: 06/14/2022] [Indexed: 01/10/2023] Open
Abstract
After gut tube patterning in early embryos, the cellular and molecular changes of developing stomach and intestine remain largely unknown. Here, combining single-cell RNA sequencing and spatial RNA sequencing, we construct a spatiotemporal transcriptomic landscape of the mouse stomach and intestine during embryonic days E9.5-E15.5. Several subpopulations are identified, including Lox+ stomach mesenchyme, Aldh1a3+ small-intestinal mesenchyme, and Adamdec1+ large-intestinal mesenchyme. The regionalization and heterogeneity of both the epithelium and the mesenchyme can be traced back to E9.5. The spatiotemporal distributions of cell clusters and the mesenchymal-epithelial interaction analysis indicate that a coordinated development of the epithelium and mesenchyme contribute to the stomach regionalization, intestine segmentation, and villus formation. Using the gut tube-derived organoids, we find that the cell fate of the foregut and hindgut can be switched by the regional niche factors, including fibroblast growth factors (FGFs) and retinoic acid (RA). This work lays a foundation for further dissection of the mechanisms governing this process.
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Affiliation(s)
- Lianzheng Zhao
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wanlu Song
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ye-Guang Chen
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; Guangzhou Laboratory, Guangzhou, China.
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45
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Lenárt S, Lenárt P, Knopfová L, Kotasová H, Pelková V, Sedláková V, Vacek O, Pokludová J, Čan V, Šmarda J, Souček K, Hampl A, Beneš P. TACSTD2 upregulation is an early reaction to lung infection. Sci Rep 2022; 12:9583. [PMID: 35688908 PMCID: PMC9185727 DOI: 10.1038/s41598-022-13637-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 05/18/2022] [Indexed: 11/16/2022] Open
Abstract
TACSTD2 encodes a transmembrane glycoprotein Trop2 commonly overexpressed in carcinomas. While the Trop2 protein was discovered already in 1981 and first antibody–drug conjugate targeting Trop2 were recently approved for cancer therapy, the physiological role of Trop2 is still not fully understood. In this article, we show that TACSTD2/Trop2 expression is evolutionarily conserved in lungs of various vertebrates. By analysis of publicly available transcriptomic data we demonstrate that TACSTD2 level consistently increases in lungs infected with miscellaneous, but mainly viral pathogens. Single cell and subpopulation based transcriptomic data revealed that the major source of TACSTD2 transcript are lung epithelial cells and their progenitors and that TACSTD2 is induced directly in lung epithelial cells following infection. Increase in TACSTD2 expression may represent a mechanism to maintain/restore epithelial barrier function and contribute to regeneration process in infected/damaged lungs.
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Affiliation(s)
- Sára Lenárt
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
| | - Peter Lenárt
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic.,Faculty of Science, Research Centre for Toxic Compounds in the Environment, Masaryk University, Brno, Czech Republic.,Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Lucia Knopfová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Hana Kotasová
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic.,Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Vendula Pelková
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Veronika Sedláková
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Ondřej Vacek
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic.,Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Jana Pokludová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
| | - Vladimír Čan
- Department of Surgery, University Hospital Brno, Brno, Czech Republic
| | - Jan Šmarda
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
| | - Karel Souček
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic.,Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Aleš Hampl
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic.,Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Petr Beneš
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic. .,International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic.
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46
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Hamdy MS, Elbehairi SEI, Shati AA, Abd-Rabboh HSM, Alfaifi MY, Fawy KF, Ibrahium HA, Alamri S, Awwad NS. Cytotoxic Potential of Bio-Silica Conjugate with Different Sizes of Silver Nanoparticles for Cancer Cell Death. MATERIALS 2022; 15:ma15124074. [PMID: 35744132 PMCID: PMC9229810 DOI: 10.3390/ma15124074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/30/2022] [Accepted: 06/02/2022] [Indexed: 02/01/2023]
Abstract
Well-defined silver nanoparticles were doped into bio-based amorphous silica (Ag-b-SiO2) with different silver contents (from 2 to 20 wt%) by a solvent-free procedure. The four as-synthetized samples were hydrogenated at 300 °C to ensure the formation of zero-valent Ag nanoparticles. The prepared samples were characterized by X-ray powder diffraction (XRD), elemental analysis, N2 sorption measurements, scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS), and high-resolution transmission electron microscopy (HR-TEM). The characterization data confirmed the formation of well-defined zero-valent silver nanoparticles in the range of 3-10 nm in the low-loading samples, while in high-loading samples, bulky particles of silver in the range of 200-500 nm were formed. The in vitro cytotoxic activities of the Ag-b-SiO2 samples were tested against the tumor cell lines of breast (MCF-7), liver (HepG2), and colon (HCT 116) over a concentration range of 0.01 to 1000 g. The prepared samples exhibited a wide range of cytotoxic activities against cancer cells. An inverse relationship was observed between the silver nanoparticles' size and the cytotoxic activity, while a direct relationship between the silver nanoparticles' size and the apoptotic cell death was noticed.
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Affiliation(s)
- Mohamed S. Hamdy
- Department of Chemistry, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia; (M.S.H.); (H.S.M.A.-R.); (K.F.F.)
| | - Serag Eldin I. Elbehairi
- Department of Biology, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia; (S.E.I.E.); (A.A.S.); (M.Y.A.); (H.A.I.); (S.A.)
| | - Ali A. Shati
- Department of Biology, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia; (S.E.I.E.); (A.A.S.); (M.Y.A.); (H.A.I.); (S.A.)
| | - Hisham S. M. Abd-Rabboh
- Department of Chemistry, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia; (M.S.H.); (H.S.M.A.-R.); (K.F.F.)
| | - Mohammad Y. Alfaifi
- Department of Biology, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia; (S.E.I.E.); (A.A.S.); (M.Y.A.); (H.A.I.); (S.A.)
| | - Khaled F. Fawy
- Department of Chemistry, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia; (M.S.H.); (H.S.M.A.-R.); (K.F.F.)
| | - Hala A. Ibrahium
- Department of Biology, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia; (S.E.I.E.); (A.A.S.); (M.Y.A.); (H.A.I.); (S.A.)
| | - Saad Alamri
- Department of Biology, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia; (S.E.I.E.); (A.A.S.); (M.Y.A.); (H.A.I.); (S.A.)
| | - Nasser S. Awwad
- Department of Chemistry, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia; (M.S.H.); (H.S.M.A.-R.); (K.F.F.)
- Correspondence:
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47
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Liu CY, Girish N, Gomez ML, Dubé PE, Washington MK, Simons BD, Polk DB. Transitional Anal Cells Mediate Colonic Re-epithelialization in Colitis. Gastroenterology 2022; 162:1975-1989. [PMID: 35227778 PMCID: PMC9402284 DOI: 10.1053/j.gastro.2022.02.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 01/14/2023]
Abstract
BACKGROUND & AIMS Epithelial wound healing is compromised and represents an unleveraged therapeutic target in inflammatory bowel disease (IBD). Intestinal epithelial cells exhibit plasticity that facilitates dedifferentiation and repair during the response to injury. However, it is not known whether epithelial cells of a neighboring organ can be activated to mediate re-epithelialization in acute colitis. Histological findings of a permanent squamous tissue structure in the distal colon in human IBD could suggest diverse cellular origins of repair-associated epithelium. Here, we tested whether skin-like cells from the anus mediate colonic re-epithelialization in murine colitis. METHODS We studied dextran sulfate sodium-induced colitis and interleukin 10-deficient colitis in transgenic mice. We performed lineage tracing, 3-dimensional (3D) imaging, single-cell transcriptomics, and biophysical modeling to map squamous cell fates and to identify squamous cell types involved in colonic repair. RESULTS In acute and chronic colitis, we found a large squamous epithelium, called squamous neo-epithelium of the colon (SNEC), near the anorectal junction. Neighboring squamous cells of the anus rapidly migrate into the ulcerated colon and establish this permanent epithelium of crypt-like morphology. These squamous cells derive from a small unique transition zone, distal to the border of colonic and anal epithelium, that resists colitic injury. The cells of this zone have a pre-loaded program of colonic differentiation and further upregulate key aspects of colonic epithelium during repair. CONCLUSION Transitional anal cells represent unique reserve cells capable of rebuilding epithelial structures in the colon after colitis. Further study of these cells could reveal novel approaches to direct mucosal healing in inflammation and disease.
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Affiliation(s)
- Cambrian Y Liu
- Division of Pediatric Gastroenterology and Nutrition, The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California; Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Nandini Girish
- Division of Pediatric Gastroenterology and Nutrition, The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California; Department of Pediatrics, Division of Gastroenterology, Hepatology, and Nutrition, Rady Children's Hospital San Diego, University of California San Diego, San Diego, California
| | - Marie L Gomez
- Division of Pediatric Gastroenterology and Nutrition, The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California; Department of Pediatrics, Department of Biochemistry and Molecular Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - Philip E Dubé
- Division of Pediatric Gastroenterology and Nutrition, The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California
| | - M Kay Washington
- Department of Pathology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Benjamin D Simons
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom; Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, United Kingdom; Wellcome Trust/Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - D Brent Polk
- Division of Pediatric Gastroenterology and Nutrition, The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California; Department of Pediatrics, Division of Gastroenterology, Hepatology, and Nutrition, Rady Children's Hospital San Diego, University of California San Diego, San Diego, California; Department of Pediatrics, Department of Biochemistry and Molecular Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California.
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48
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Singh PNP, Madha S, Leiter AB, Shivdasani RA. Cell and chromatin transitions in intestinal stem cell regeneration. Genes Dev 2022; 36:684-698. [PMID: 35738677 PMCID: PMC9296007 DOI: 10.1101/gad.349412.122] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 06/06/2022] [Indexed: 11/25/2022]
Abstract
The progeny of intestinal stem cells (ISCs) dedifferentiate in response to ISC attrition. The precise cell sources, transitional states, and chromatin remodeling behind this activity remain unclear. In the skin, stem cell recovery after injury preserves an epigenetic memory of the damage response; whether similar memories arise and persist in regenerated ISCs is not known. We addressed these questions by examining gene activity and open chromatin at the resolution of single Neurog3-labeled mouse intestinal crypt cells, hence deconstructing forward and reverse differentiation of the intestinal secretory (Sec) lineage. We show that goblet, Paneth, and enteroendocrine cells arise by multilineage priming in common precursors, followed by selective access at thousands of cell-restricted cis-elements. Selective ablation of the ISC compartment elicits speedy reversal of chromatin and transcriptional features in large fractions of precursor and mature crypt Sec cells without obligate cell cycle re-entry. ISC programs decay and reappear along a cellular continuum lacking discernible discrete interim states. In the absence of gross tissue damage, Sec cells simply reverse their forward trajectories, without invoking developmental or other extrinsic programs, and starting chromatin identities are effectively erased. These findings identify strikingly plastic molecular frameworks in assembly and regeneration of a self-renewing tissue.
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Affiliation(s)
- Pratik N P Singh
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Shariq Madha
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Andrew B Leiter
- Division of Gastroenterology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Ramesh A Shivdasani
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
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49
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p53 wild-type colorectal cancer cells that express a fetal gene signature are associated with metastasis and poor prognosis. Nat Commun 2022; 13:2866. [PMID: 35606354 PMCID: PMC9126967 DOI: 10.1038/s41467-022-30382-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/29/2022] [Indexed: 12/14/2022] Open
Abstract
Current therapy against colorectal cancer (CRC) is based on DNA-damaging agents that remain ineffective in a proportion of patients. Whether and how non-curative DNA damage-based treatment affects tumor cell behavior and patient outcome is primarily unstudied. Using CRC patient-derived organoids (PDO)s, we show that sublethal doses of chemotherapy (CT) does not select previously resistant tumor populations but induces a quiescent state specifically to TP53 wildtype (WT) cancer cells, which is linked to the acquisition of a YAP1-dependent fetal phenotype. Cells displaying this phenotype exhibit high tumor-initiating and metastatic activity. Nuclear YAP1 and fetal traits are present in a proportion of tumors at diagnosis and predict poor prognosis in patients carrying TP53 WT CRC tumors. We provide data indicating the higher efficacy of CT together with YAP1 inhibitors for eradication of therapy resistant TP53 WT cancer cells. Together these results identify fetal conversion as a useful biomarker for patient prognosis and therapy prescription. The failure of chemotherapy in colorectal cancer is currently unclear. Here, the authors show that upon sub-lethal dose of chemotherapy wild-type p53 colorectal cancers acquire a quiescence-like phenotype and a YAP-dependent fetal-like intestinal stem cell state associated with a higher metastatic activity and poor prognosis in patients.
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50
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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: 26] [Impact Index Per Article: 13.0] [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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