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Veneti Z, Fasoulaki V, Kalavros N, Vlachos IS, Delidakis C, Eliopoulos AG. Polycomb-mediated silencing of miR-8 is required for maintenance of intestinal stemness in Drosophila melanogaster. Nat Commun 2024; 15:1924. [PMID: 38429303 PMCID: PMC10907375 DOI: 10.1038/s41467-024-46119-9] [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: 02/28/2023] [Accepted: 02/15/2024] [Indexed: 03/03/2024] Open
Abstract
Balancing maintenance of self-renewal and differentiation is a key property of adult stem cells. The epigenetic mechanisms controlling this balance remain largely unknown. Herein, we report that the Polycomb Repressive Complex 2 (PRC2) is required for maintenance of the intestinal stem cell (ISC) pool in the adult female Drosophila melanogaster. We show that loss of PRC2 activity in ISCs by RNAi-mediated knockdown or genetic ablation of the enzymatic subunit Enhancer of zeste, E(z), results in loss of stemness and precocious differentiation of enteroblasts to enterocytes. Mechanistically, we have identified the microRNA miR-8 as a critical target of E(z)/PRC2-mediated tri-methylation of histone H3 at Lys27 (H3K27me3) and uncovered a dynamic relationship between E(z), miR-8 and Notch signaling in controlling stemness versus differentiation of ISCs. Collectively, these findings uncover a hitherto unrecognized epigenetic layer in the regulation of stem cell specification that safeguards intestinal homeostasis.
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Affiliation(s)
- Zoe Veneti
- Institute of Molecular Biology and Biotechnology, Foundation of Research & Technology Hellas, Heraklion, Greece.
- Medical School, University of Crete, Heraklion, Greece.
| | - Virginia Fasoulaki
- Institute of Molecular Biology and Biotechnology, Foundation of Research & Technology Hellas, Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
| | - Nikolaos Kalavros
- Spatial Technologies Unit, Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ioannis S Vlachos
- Spatial Technologies Unit, Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Christos Delidakis
- Institute of Molecular Biology and Biotechnology, Foundation of Research & Technology Hellas, Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
| | - Aristides G Eliopoulos
- Laboratory of Biology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece.
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
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2
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Hung YH, Capeling M, Villanueva JW, Kanke M, Shanahan MT, Huang S, Cubitt R, Rinaldi VD, Schimenti JC, Spence JR, Sethupathy P. Integrative genome-scale analyses reveal post-transcriptional signatures of early human small intestinal development in a directed differentiation organoid model. BMC Genomics 2023; 24:641. [PMID: 37884859 PMCID: PMC10601309 DOI: 10.1186/s12864-023-09743-1] [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: 07/04/2023] [Accepted: 10/14/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are important post-transcriptional gene regulators controlling cellular lineage specification and differentiation during embryonic development, including the gastrointestinal system. However, miRNA-mediated regulatory mechanisms involved in early embryonic development of human small intestine (SI) remains underexplored. To explore candidate roles for miRNAs in prenatal SI lineage specification in humans, we used a multi-omic analysis strategy in a directed differentiation model that programs human pluripotent stem cells toward the SI lineage. RESULTS We leveraged small RNA-seq to define the changing miRNA landscape, and integrated chromatin run-on sequencing (ChRO-seq) and RNA-seq to define genes subject to significant post-transcriptional regulation across the different stages of differentiation. Small RNA-seq profiling revealed temporal dynamics of miRNA signatures across different developmental events of the model, including definitive endoderm formation, SI lineage specification and SI regional patterning. Our multi-omic, integrative analyses showed further that the elevation of miR-182 and reduction of miR-375 are key events during SI lineage specification. We demonstrated that loss of miR-182 leads to an increase in the foregut master marker SOX2. We also used single-cell analyses in murine adult intestinal crypts to support a life-long role for miR-375 in the regulation of Zfp36l2. Finally, we uncovered opposing roles of SMAD4 and WNT signaling in regulating miR-375 expression during SI lineage specification. Beyond the mechanisms highlighted in this study, we also present a web-based application for exploration of post-transcriptional regulation and miRNA-mediated control in the context of early human SI development. CONCLUSION The present study uncovers a novel facet of miRNAs in regulating prenatal SI development. We leveraged multi-omic, systems biology approaches to discover candidate miRNA regulators associated with early SI developmental events in a human organoid model. In this study, we highlighted miRNA-mediated post-transcriptional regulation relevant to the event of SI lineage specification. The candidate miRNA regulators that we identified for the other stages of SI development also warrant detailed characterization in the future.
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Affiliation(s)
- Yu-Han Hung
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Meghan Capeling
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan W Villanueva
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Matt Kanke
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Michael T Shanahan
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Sha Huang
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Rebecca Cubitt
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Vera D Rinaldi
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - John C Schimenti
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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Jenike AE, Bunkelman B, Perzel Mandell KA, Oduor CI, Chin D, Mair D, Jenike KM, Kim DH, Bailey JA, Rafailovich MH, Rosenberg AZ, Halushka MK. Expression Microdissection for the Analysis of miRNA in a Single-Cell Type. J Transl Med 2023; 103:100133. [PMID: 36990152 PMCID: PMC10524025 DOI: 10.1016/j.labinv.2023.100133] [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: 10/04/2022] [Revised: 02/19/2023] [Accepted: 03/02/2023] [Indexed: 03/30/2023] Open
Abstract
Cell-specific microRNA (miRNA) expression estimates are important in characterizing the localization of miRNA signaling within tissues. Much of these data are obtained from cultured cells, a process known to significantly alter miRNA expression levels. Thus, our knowledge of in vivo cell miRNA expression estimates is poor. We previously demonstrated expression microdissection-miRNA-sequencing (xMD-miRNA-seq) to acquire in vivo estimates, directly from formalin-fixed tissues, albeit with a limited yield. In this study, we optimized each step of the xMD process, including tissue retrieval, tissue transfer, film preparation, and RNA isolation, to increase RNA yields and ultimately show strong enrichment for in vivo miRNA expression by qPCR array. These method improvements, such as the development of a noncrosslinked ethylene vinyl acetate membrane, resulted in a 23- to 45-fold increase in miRNA yield, depending on the cell type. By qPCR, miR-200a increased by 14-fold in xMD-derived small intestine epithelial cells, with a concurrent 336-fold reduction in miR-143 relative to the matched nondissected duodenal tissue. xMD is now an optimized method to obtain robust in vivo miRNA expression estimates from cells. xMD will allow formalin-fixed tissues from surgical pathology archives to make theragnostic biomarker discoveries.
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Affiliation(s)
- Ana E Jenike
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Brady Bunkelman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kira A Perzel Mandell
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Cliff I Oduor
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, Rhode Island
| | - Deborah Chin
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, Rhode Island
| | - Devin Mair
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Katharine M Jenike
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Deok-Ho Kim
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, Rhode Island
| | - Miriam H Rafailovich
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York
| | - Avi Z Rosenberg
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Marc K Halushka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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Sahoo DK, Martinez MN, Dao K, Gabriel V, Zdyrski C, Jergens AE, Atherly T, Iennarella-Servantez CA, Burns LE, Schrunk D, Volpe DA, Allenspach K, Mochel JP. Canine Intestinal Organoids as a Novel In Vitro Model of Intestinal Drug Permeability: A Proof-of-Concept Study. Cells 2023; 12:cells12091269. [PMID: 37174669 PMCID: PMC10177590 DOI: 10.3390/cells12091269] [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: 03/31/2023] [Revised: 04/20/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
A key component of efforts to identify the biological and drug-specific aspects contributing to therapeutic failure or unexpected exposure-associated toxicity is the study of drug-intestinal barrier interactions. While methods supporting such assessments are widely described for human therapeutics, relatively little information is available for similar evaluations in support of veterinary pharmaceuticals. There is, therefore, a critical need to develop novel approaches for evaluating drug-gut interactions in veterinary medicine. Three-dimensional (3D) organoids can address these difficulties in a reasonably affordable system that circumvents the need for more invasive in vivo assays in live animals. However, a first step in developing such systems is understanding organoid interactions in a 2D monolayer. Given the importance of orally administered medications for meeting the therapeutic need of companion animals, we demonstrate growth conditions under which canine-colonoid-derived intestinal epithelial cells survive, mature, and differentiate into confluent cell systems with high monolayer integrity. We further examine the applicability of this canine-colonoid-derived 2D model to assess the permeability of three structurally diverse, passively absorbed β-blockers (e.g., propranolol, metoprolol, and atenolol). Both the absorptive and secretive apparent permeability (Papp) of these drugs at two different pH conditions were evaluated in canine-colonoid-derived monolayers and compared with that of Caco-2 cells. This proof-of-concept study provides promising preliminary results with regard to the utility of canine-derived organoid monolayers for species-specific assessments of therapeutic drug passive permeability.
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Affiliation(s)
- Dipak Kumar Sahoo
- Department of Veterinary Clinical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Marilyn N Martinez
- Office of New Animal Drug Evaluation, Center for Veterinary Medicine, Food and Drug Administration, Rockville, MD 20852, USA
| | - Kimberly Dao
- 3D Health Solutions, Iowa State University, Ames, IA 50011, USA
| | - Vojtech Gabriel
- Department of Biomedical Sciences, SMART Pharmacology, Iowa State University, Ames, IA 50011, USA
| | - Christopher Zdyrski
- 3D Health Solutions, Iowa State University, Ames, IA 50011, USA
- Department of Biomedical Sciences, SMART Pharmacology, Iowa State University, Ames, IA 50011, USA
| | - Albert E Jergens
- Department of Veterinary Clinical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Todd Atherly
- 3D Health Solutions, Iowa State University, Ames, IA 50011, USA
| | | | - Laura E Burns
- Veterinary Diagnostic Laboratory, Iowa State University, Ames, IA 50011, USA
| | - Dwayne Schrunk
- Veterinary Diagnostic Laboratory, Iowa State University, Ames, IA 50011, USA
| | - Donna A Volpe
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20852, USA
| | - Karin Allenspach
- Department of Veterinary Clinical Sciences, Iowa State University, Ames, IA 50011, USA
- 3D Health Solutions, Iowa State University, Ames, IA 50011, USA
| | - Jonathan P Mochel
- 3D Health Solutions, Iowa State University, Ames, IA 50011, USA
- Department of Biomedical Sciences, SMART Pharmacology, Iowa State University, Ames, IA 50011, USA
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Li L, Ma M, Duan T, Sui X. The critical roles and therapeutic implications of tuft cells in cancer. Front Pharmacol 2022; 13:1047188. [PMID: 36569325 PMCID: PMC9780677 DOI: 10.3389/fphar.2022.1047188] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
Tuft cells are solitary chemosensory epithelial cells with microvilli at the top, which are found in hollow organs such as the gastrointestinal tract, pancreas, and lungs. Recently, an increasing number of studies have revealed the chemotactic abilities and immune function of the tuft cells, and numerous efforts have been devoted to uncovering the role of tuft cells in tumors. Notably, accumulating evidence has shown that the specific genes (POU2F3, DCLK1) expressed in tuft cells are involved in vital processes related with carcinogenesis and cancer development. However, the interaction between the tuft cells and cancer remains to be further elucidated. Here, based on an introduction of biological functions and specific markers of the tuft cells, we have summarized the functional roles and potential therapeutic implications of tuft cells in cancers, including pancreatic cancer, lung cancer, gastric cancer, colon cancer, and liver cancer, which is in the hope of inspiring the future research in validating tuft cells as novel strategies for cancer therapies.
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Affiliation(s)
- Lin Li
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China
| | - Mengmeng Ma
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China
| | - Ting Duan
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China,*Correspondence: Ting Duan, ; Xinbing Sui,
| | - Xinbing Sui
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China,Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou, China,*Correspondence: Ting Duan, ; Xinbing Sui,
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