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Patil DT, Odze RD. Barrett's Esophagus and Associated Dysplasia. Gastroenterol Clin North Am 2024; 53:1-23. [PMID: 38280743 DOI: 10.1016/j.gtc.2023.11.002] [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] [Indexed: 01/29/2024]
Abstract
Early detection of dysplasia and effective management are critical steps in halting neoplastic progression in patients with Barrett's esophagus (BE). This review provides a contemporary overview of the BE-related dysplasia, its role in guiding surveillance and management, and discusses emerging diagnostic and therapeutic approaches that might further enhance patient management. Novel, noninvasive techniques for sampling and surveillance, adjunct biomarkers for risk assessment, and their limitations are also discussed.
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Affiliation(s)
- Deepa T Patil
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
| | - Robert D Odze
- Department of Pathology and Lab Medicine, Tufts University School of Medicine, Boston, MA, USA
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2
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Sugano K, Moss SF, Kuipers EJ. Gastric Intestinal Metaplasia: Real Culprit or Innocent Bystander as a Precancerous Condition for Gastric Cancer? Gastroenterology 2023; 165:1352-1366.e1. [PMID: 37652306 DOI: 10.1053/j.gastro.2023.08.028] [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: 03/14/2022] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 09/02/2023]
Abstract
Gastric intestinal metaplasia (GIM), which denotes conversion of gastric mucosa into an intestinal phenotype, can occur in all regions of the stomach, including cardiac, fundic, and pyloric mucosa. Since the earliest description of GIM, its association with gastric cancer of the differentiated (intestinal) type has been a well-recognized concern. Many epidemiologic studies have confirmed GIM to be significantly associated with subsequent gastric cancer development. Helicobacter pylori, the principal etiologic factor for gastric cancer, plays the most important role in predisposing to GIM. Although the role of GIM in the stepwise progression model of gastric carcinogenesis (the so-called "Correa cascade") has come into question recently, we review the scientific evidence that strongly supports this long-standing model and propose a new progression model that builds on the Correa cascade. Eradication of H pylori is the most important method for preventing gastric cancer globally, but the effect of eradication on established GIM, is limited, if any. Endoscopic surveillance for GIM may, therefore, be necessary, especially when there is extensive corpus GIM. Recent advances in image-enhanced endoscopy with integrated artificial intelligence have facilitated the identification of GIM and neoplastic lesions, which will impact preventive strategies in the near future.
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Affiliation(s)
| | - Steven F Moss
- Alpert Medical School of Brown University, Providence, Rhode Island
| | - Ernst J Kuipers
- Erasmus Medical Center, Rotterdam and Minister, Ministry of Health, Welfare, and Sport, Hague, The Netherlands
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3
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Liu M, Fu J, Yang S. Synthesis of Microparticles with Diverse Thermally Responsive Shapes Originated from the Same Janus Liquid Crystalline Microdroplets. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2303106. [PMID: 37495936 DOI: 10.1002/smll.202303106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/14/2023] [Indexed: 07/28/2023]
Abstract
Liquid crystalline elastomer (LCE)-based microparticles that can change shapes in response to external stimuli are of great interest for potential applications such as artificial cells, micro-actuators, micro-valves, and smart drug carriers. Here, the synthesis of LCE microparticles with diverse temperature-dependent anisotropic shapes originated from the same Janus microdroplets is reported. The Janus microdroplets, suspended in an aqueous solution of surfactants, are transformed from microdroplets consisting of a mixture of liquid crystal (LC) monomers, oligomers, silicone oil, and an organic solvent, after the removal of the organic solvent. The molecular alignment of the LC part at the interface, whether planar, homeotropic, or hybrid, is dependent on the choice of the surfactants but not affected by the silicone oil. After polymerization and solvent extraction of the unreacted components, LCE microparticles of various shapes are obtained depending on the concentration and composition of the surfactants, the weight ratio of the LC part to the silicone oil part, and the choice of the extraction solvent. The microparticles that undergo different synthetic pathways show distinct thermally responsive shapes, much like how stem cells differentiate in different environmental conditions.
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Affiliation(s)
- Mingzhu Liu
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
- School of Chemistry, Beihang University, Beijing, 100191, P. R. China
| | - Jiemin Fu
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Shu Yang
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
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4
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Ozen M, Lopez CF. Data-driven structural analysis of small cell lung cancer transcription factor network suggests potential subtype regulators and transition pathways. NPJ Syst Biol Appl 2023; 9:55. [PMID: 37907529 PMCID: PMC10618210 DOI: 10.1038/s41540-023-00316-2] [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: 07/18/2023] [Accepted: 10/12/2023] [Indexed: 11/02/2023] Open
Abstract
Small cell lung cancer (SCLC) is an aggressive disease and challenging to treat due to its mixture of transcriptional subtypes and subtype transitions. Transcription factor (TF) networks have been the focus of studies to identify SCLC subtype regulators via systems approaches. Yet, their structures, which can provide clues on subtype drivers and transitions, are barely investigated. Here, we analyze the structure of an SCLC TF network by using graph theory concepts and identify its structurally important components responsible for complex signal processing, called hubs. We show that the hubs of the network are regulators of different SCLC subtypes by analyzing first the unbiased network structure and then integrating RNA-seq data as weights assigned to each interaction. Data-driven analysis emphasizes MYC as a hub, consistent with recent reports. Furthermore, we hypothesize that the pathways connecting functionally distinct hubs may control subtype transitions and test this hypothesis via network simulations on a candidate pathway and observe subtype transition. Overall, structural analyses of complex networks can identify their functionally important components and pathways driving the network dynamics. Such analyses can be an initial step for generating hypotheses and can guide the discovery of target pathways whose perturbation may change the network dynamics phenotypically.
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Affiliation(s)
- Mustafa Ozen
- Dept. of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Multiscale Modeling Group, SI3, Altos Labs, Redwood City, CA, USA
| | - Carlos F Lopez
- Dept. of Biochemistry, Vanderbilt University, Nashville, TN, USA.
- Multiscale Modeling Group, SI3, Altos Labs, Redwood City, CA, USA.
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5
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Ozen M, Lopez CF. Data-driven structural analysis of Small Cell Lung Cancer transcription factor network suggests potential subtype regulators and transition pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.01.535226. [PMID: 37066351 PMCID: PMC10104011 DOI: 10.1101/2023.04.01.535226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Small Cell Lung Cancer (SCLC) is an aggressive disease and challenging to treat due to its mixture of transcriptional subtypes and subtype transitions. Transcription factor (TF) networks have been the focus of studies to identify SCLC subtype regulators via systems approaches. Yet, their structures, which can provide clues on subtype drivers and transitions, are barely investigated. Here, we analyze the structure of an SCLC TF network by using graph theory concepts and identify its structurally important components responsible for complex signal processing, called hubs. We show that the hubs of the network are regulators of different SCLC subtypes by analyzing first the unbiased network structure and then integrating RNA-seq data as weights assigned to each interaction. Data-driven analysis emphasizes MYC as a hub, consistent with recent reports. Furthermore, we hypothesize that the pathways connecting functionally distinct hubs may control subtype transitions and test this hypothesis via network simulations on a candidate pathway and observe subtype transition. Overall, structural analyses of complex networks can identify their functionally important components and pathways driving the network dynamics. Such analyses can be an initial step for generating hypotheses and can guide the discovery of target pathways whose perturbation may change the network dynamics phenotypically.
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Affiliation(s)
- Mustafa Ozen
- Dept. of Biochemistry, Vanderbilt University, Nashville, TN 37212, USA
- Currently at: Computational Innovation Hub, Multiscale Modeling Group, Altos Labs, Redwood City, CA 94065, USA
| | - Carlos F. Lopez
- Dept. of Biochemistry, Vanderbilt University, Nashville, TN 37212, USA
- Currently at: Computational Innovation Hub, Multiscale Modeling Group, Altos Labs, Redwood City, CA 94065, USA
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6
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Gromowski T, Lukacs-Kornek V, Cisowski J. Current view of liver cancer cell-of-origin and proposed mechanisms precluding its proper determination. Cancer Cell Int 2023; 23:3. [PMID: 36609378 PMCID: PMC9824961 DOI: 10.1186/s12935-022-02843-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/30/2022] [Indexed: 01/09/2023] Open
Abstract
Hepatocellular carcinoma and intrahepatic cholangiocarcinoma are devastating primary liver cancers with increasing prevalence in many parts of the world. Despite intense investigation, many aspects of their biology are still largely obscure. For example, numerous studies have tackled the question of the cell-of-origin of primary liver cancers using different experimental approaches; they have not, however, provided a clear and undisputed answer. Here, we will review the evidence from animal models supporting the role of all major types of liver epithelial cells: hepatocytes, cholangiocytes, and their common progenitor as liver cancer cell-of-origin. Moreover, we will also propose mechanisms that promote liver cancer cell plasticity (dedifferentiation, transdifferentiation, and epithelial-to-mesenchymal transition) which may contribute to misinterpretation of the results and which make the issue of liver cancer cell-of-origin particularly complex.
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Affiliation(s)
- Tomasz Gromowski
- grid.5522.00000 0001 2162 9631Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Veronika Lukacs-Kornek
- grid.10388.320000 0001 2240 3300Institute of Experimental Immunology, University Hospital of the Rheinische Friedrich-Wilhelms-University, Bonn, Germany
| | - Jaroslaw Cisowski
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
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7
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Zyla RE, Kalimuthu SN. Barrett’s Esophagus and Esophageal Adenocarcinoma: A Histopathological Perspective. Thorac Surg Clin 2022; 32:413-424. [DOI: 10.1016/j.thorsurg.2022.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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8
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Souza RF, Spechler SJ. Mechanisms and pathophysiology of Barrett oesophagus. Nat Rev Gastroenterol Hepatol 2022; 19:605-620. [PMID: 35672395 DOI: 10.1038/s41575-022-00622-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/22/2022] [Indexed: 01/10/2023]
Abstract
Barrett oesophagus, in which a metaplastic columnar mucosa that can predispose individuals to cancer development lines a portion of the distal oesophagus, is the only known precursor of oesophageal adenocarcinoma, the incidence of which has increased profoundly over the past several decades. Most evidence suggests that Barrett oesophagus develops from progenitor cells at the oesophagogastric junction that proliferate and undergo epithelial-mesenchymal transition as part of a wound-healing process that replaces oesophageal squamous epithelium damaged by gastroesophageal reflux disease (GERD). GERD also seems to induce reprogramming of key transcription factors in the progenitor cells, resulting in the development of the specialized intestinal metaplasia that is characteristic of Barrett oesophagus, probably through an intermediate step of metaplasia to cardiac mucosa. Genome-wide association studies suggest that patients with GERD who develop Barrett oesophagus might have an inherited predisposition to oesophageal metaplasia and that there is a shared genetic susceptibility to Barrett oesophagus and to several of its risk factors (such as GERD, obesity and cigarette smoking). In this Review, we discuss the mechanisms, pathophysiology, genetic predisposition and cells of origin of Barrett oesophagus, and opine on the clinical implications and future research directions.
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Affiliation(s)
- Rhonda F Souza
- Division of Gastroenterology, Center for Oesophageal Diseases, Baylor University Medical Center, Dallas, TX, USA. .,Center for Oesophageal Research, Baylor Scott & White Research Institute, Dallas, TX, USA.
| | - Stuart J Spechler
- Division of Gastroenterology, Center for Oesophageal Diseases, Baylor University Medical Center, Dallas, TX, USA.,Center for Oesophageal Research, Baylor Scott & White Research Institute, Dallas, TX, USA
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9
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Sadeghi M, Bahrami A, Hasankhani A, Kioumarsi H, Nouralizadeh R, Abdulkareem SA, Ghafouri F, Barkema HW. lncRNA-miRNA-mRNA ceRNA Network Involved in Sheep Prolificacy: An Integrated Approach. Genes (Basel) 2022; 13:genes13081295. [PMID: 35893032 PMCID: PMC9332185 DOI: 10.3390/genes13081295] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 02/06/2023] Open
Abstract
Understanding the molecular pattern of fertility is considered as an important step in breeding of different species, and despite the high importance of the fertility, little success has been achieved in dissecting the interactome basis of sheep fertility. However, the complex mechanisms associated with prolificacy in sheep have not been fully understood. Therefore, this study aimed to use competitive endogenous RNA (ceRNA) networks to evaluate this trait to better understand the molecular mechanisms responsible for fertility. A competitive endogenous RNA (ceRNA) network of the corpus luteum was constructed between Romanov and Baluchi sheep breeds with either good or poor genetic merit for prolificacy using whole-transcriptome analysis. First, the main list of lncRNAs, miRNAs, and mRNA related to the corpus luteum that alter with the breed were extracted, then miRNA−mRNA and lncRNA−mRNA interactions were predicted, and the ceRNA network was constructed by integrating these interactions with the other gene regulatory networks and the protein−protein interaction (PPI). A total of 264 mRNAs, 14 lncRNAs, and 34 miRNAs were identified by combining the GO and KEGG enrichment analyses. In total, 44, 7, 7, and 6 mRNAs, lncRNAs, miRNAs, and crucial modules, respectively, were disclosed through clustering for the corpus luteum ceRNA network. All these RNAs involved in biological processes, namely proteolysis, actin cytoskeleton organization, immune system process, cell adhesion, cell differentiation, and lipid metabolic process, have an overexpression pattern (Padj < 0.01). This study increases our understanding of the contribution of different breed transcriptomes to phenotypic fertility differences and constructed a ceRNA network in sheep (Ovis aries) to provide insights into further research on the molecular mechanism and identify new biomarkers for genetic improvement.
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Affiliation(s)
- Masoumeh Sadeghi
- Environmental Health, Zahedan University of Medical Sciences, Zahedan 98, Iran;
| | - Abolfazl Bahrami
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj 31, Iran; (A.H.); (F.G.)
- Biomedical Center for Systems Biology Science Munich, Ludwig-Maximilians-University, 80333 Munich, Germany
- Correspondence: (A.B.); (R.N.); Tel.: +98-9199300065 (A.B.)
| | - Aliakbar Hasankhani
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj 31, Iran; (A.H.); (F.G.)
| | - Hamed Kioumarsi
- Department of Animal Science Research, Gilan Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Rasht 43, Iran;
| | - Reza Nouralizadeh
- Department of Food and Drug Control, Faculty of Pharmacy, Jundishapour University of Medical Sciences, Ahvaz 63, Iran
- Correspondence: (A.B.); (R.N.); Tel.: +98-9199300065 (A.B.)
| | - Sarah Ali Abdulkareem
- Department of Computer Science, Al-Turath University College, Al Mansour, Baghdad 10011, Iraq;
| | - Farzad Ghafouri
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj 31, Iran; (A.H.); (F.G.)
| | - Herman W. Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N4Z6, Canada;
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10
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Sengupta K, Denkiewicz M, Chiliński M, Szczepińska T, Mollah AF, Korsak S, D'Souza R, Ruan Y, Plewczynski D. Multi-scale phase separation by explosive percolation with single-chromatin loop resolution. Comput Struct Biotechnol J 2022; 20:3591-3603. [PMID: 35860407 PMCID: PMC9283880 DOI: 10.1016/j.csbj.2022.06.063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/28/2022] [Accepted: 06/28/2022] [Indexed: 12/03/2022] Open
Abstract
The 2 m-long human DNA is tightly intertwined into the cell nucleus of the size of 10 μm. The DNA packing is explained by folding of chromatin fiber. This folding leads to the formation of such hierarchical structures as: chromosomal territories, compartments; densely-packed genomic regions known as Topologically Associating Domains (TADs), or Chromatin Contact Domains (CCDs), and loops. We propose models of dynamical human genome folding into hierarchical components in human lymphoblastoid, stem cell, and fibroblast cell lines. Our models are based on explosive percolation theory. The chromosomes are modeled as graphs where CTCF chromatin loops are represented as edges. The folding trajectory is simulated by gradually introducing loops to the graph following various edge addition strategies that are based on topological network properties, chromatin loop frequencies, compartmentalization, or epigenomic features. Finally, we propose the genome folding model - a biophysical pseudo-time process guided by a single scalar order parameter. The parameter is calculated by Linear Discriminant Analysis of chromatin features. We also include dynamics of loop formation by using Loop Extrusion Model (LEM) while adding them to the system. The chromatin phase separation, where fiber folds in 3D space into topological domains and compartments, is observed when the critical number of contacts is reached. We also observe that at least 80% of the loops are needed for chromatin fiber to condense in 3D space, and this is constant through various cell lines. Overall, our in-silico model integrates the high-throughput 3D genome interaction experimental data with the novel theoretical concept of phase separation, which allows us to model event-based time dynamics of chromatin loop formation and folding trajectories.
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Affiliation(s)
- Kaustav Sengupta
- Center of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Michał Denkiewicz
- Center of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Mateusz Chiliński
- Center of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Teresa Szczepińska
- Center of New Technologies, University of Warsaw, Warsaw, Poland
- Centre for Advanced Materials and Technologies, Warsaw University of Technology, Warsaw, Poland
| | - Ayatullah Faruk Mollah
- Center of New Technologies, University of Warsaw, Warsaw, Poland
- Department of Computer Science and Engineering, Aliah University, Kolkata, West Bengal, India
| | - Sevastianos Korsak
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Raissa D'Souza
- Department of Computer Science, University of California, Davis, USA
- The Santa Fe Institute, Santa Fe, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, USA
| | - Dariusz Plewczynski
- Center of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
- Department of Computer Science, University of California, Davis, USA
- The Jackson Laboratory for Genomic Medicine, USA
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11
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Jiang T, Wei F, Xie K. Clinical significance of pancreatic ductal metaplasia. J Pathol 2022; 257:125-139. [PMID: 35170758 DOI: 10.1002/path.5883] [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: 11/21/2021] [Revised: 02/06/2022] [Accepted: 02/14/2022] [Indexed: 11/08/2022]
Abstract
Pancreatic ductal metaplasia (PDM) is the stepwise replacement of differentiated somatic cells with ductal or ductal-like cells in the pancreas. PDM is usually triggered by cellular and environmental insults. PDM development may involve all cell lineages of the pancreas, and acinar cells with the highest plasticity are the major source of PDM. Pancreatic progenitor cells are also involved as cells of origin or transitional intermediates. PDM is heterogeneous at the histological, cellular, and molecular levels and only certain subsets of PDM develop further into pancreatic intraepithelial neoplasia (PanIN) and then pancreatic ductal adenocarcinoma (PDAC). The formation and evolution of PDM is regulated at the cellular and molecular levels through a complex network of signaling pathways. The key molecular mechanisms that drive PDM formation and its progression into PanIN/PDAC remain unclear, but represent key targets for reversing or inhibiting PDM. Alternatively, PDM could be a source of pancreas regeneration, including both exocrine and endocrine components. Cellular aging and apoptosis are obstacles to PDM-to-PanIN progression or pancreas regeneration. Functional identification of the cellular and molecular events driving senescence and apoptosis in PDM and its progression would help not only to restrict the development of PDM into PanIN/PDAC, but may also facilitate pancreatic regeneration. This review systematically assesses recent advances in the understanding of PDM physiology and pathology, with a focus on its implications for enhancing regeneration and prevention of cancer. © 2022 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Tingting Jiang
- Center for Pancreatic Cancer Research, The South China University of Technology School of Medicine, Guangzhou, PR China
- Department of Pathology, The South China University of Technology School of Medicine, Guangzhou, PR China
| | - Fang Wei
- Institute of Digestive Diseases Research, The South China University of Technology School of Medicine, Guangzhou, PR China
| | - Keping Xie
- Center for Pancreatic Cancer Research, The South China University of Technology School of Medicine, Guangzhou, PR China
- Department of Pathology, The South China University of Technology School of Medicine, Guangzhou, PR China
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12
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Caldwell B, Meyer AR, Weis JA, Engevik AC, Choi E. Chief cell plasticity is the origin of metaplasia following acute injury in the stomach mucosa. Gut 2022; 71:1068-1077. [PMID: 34497145 PMCID: PMC8901801 DOI: 10.1136/gutjnl-2021-325310] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/31/2021] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Metaplasia arises from differentiated cell types in response to injury and is considered a precursor in many cancers. Heterogeneous cell lineages are present in the reparative metaplastic mucosa with response to injury, including foveolar cells, proliferating cells and spasmolytic polypeptide-expressing metaplasia (SPEM) cells, a key metaplastic cell population. Zymogen-secreting chief cells are long-lived cells in the stomach mucosa and have been considered the origin of SPEM cells; however, a conflicting paradigm has proposed isthmal progenitor cells as an origin for SPEM. DESIGN Gastric intrinsic factor (GIF) is a stomach tissue-specific gene and exhibits protein expression unique to mature mouse chief cells. We generated a novel chief cell-specific driver mouse allele, GIF-rtTA. GIF-GFP reporter mice were used to validate specificity of GIF-rtTA driver in chief cells. GIF-Cre-RnTnG mice were used to perform lineage tracing during homoeostasis and acute metaplasia development. L635 treatment was used to induce acute mucosal injury and coimmunofluorescence staining was performed for various gastric lineage markers. RESULTS We demonstrated that mature chief cells, rather than isthmal progenitor cells, serve as the predominant origin of SPEM cells during the metaplastic process after acute mucosal injury. Furthermore, we observed long-term label-retaining chief cells at 1 year after the GFP labelling in chief cells. However, only a very small subset of the long-term label-retaining chief cells displayed the reprogramming ability in homoeostasis. In contrast, we identified chief cell-originating SPEM cells as contributing to lineages within foveolar cell hyperplasia in response to the acute mucosal injury. CONCLUSION Our study provides pivotal evidence for cell plasticity and lineage contributions from differentiated gastric chief cells during acute metaplasia development.
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Affiliation(s)
- Brianna Caldwell
- Section of Surgical Sciences and Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Anne R Meyer
- Section of Surgical Sciences and Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jared A Weis
- Department of Biomedical Engineering, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Amy C Engevik
- Section of Surgical Sciences and Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Eunyoung Choi
- Section of Surgical Sciences and Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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13
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Du S, Li Y, Geng Z, Zhang Q, Buhler LH, Gonelle-Gispert C, Wang Y. Engineering Islets From Stem Cells: The Optimal Solution for the Treatment of Diabetes? Front Immunol 2022; 13:869514. [PMID: 35572568 PMCID: PMC9092457 DOI: 10.3389/fimmu.2022.869514] [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: 02/04/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Diabetes is a metabolic disease characterized by insulin deficiency. Bioengineering of stem cells with the aim to restore insulin production and glucose regulation has the potential to cure diabetic patients. In this review, we focus on the recent developments for bioengineering of induced pluripotent stem cells (iPSCs), mesenchymal stem cells (MSCs), embryonic stem cells (ESCs), and pancreatic progenitor cells in view of generating insulin producing and glucose regulating cells for β-cell replacement therapies. Recent clinical trials using islet cells derived from stem cells have been initiated for the transplantation into diabetic patients, with crucial bottlenecks of tumorigenesis, post-transplant survival, genetic instability, and immunogenicity that should be further optimized. As a new approach given high expectations, bioengineered islets from stem cells occupies considerable potential for the future clinical application and addressing the treatment dilemma of diabetes.
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Affiliation(s)
- Suya Du
- Department of Clinical Pharmacy, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yanjiao Li
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhen Geng
- Clinical Immunology Translational Medicine Key Laboratory of Sichuan Province, Center of Organ Transplantation, Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital, Chengdu, China.,Institute of Organ Transplantation, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China.,Chinese Academy of Sciences, Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Qi Zhang
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Leo H Buhler
- Clinical Immunology Translational Medicine Key Laboratory of Sichuan Province, Center of Organ Transplantation, Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital, Chengdu, China.,Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | | | - Yi Wang
- Clinical Immunology Translational Medicine Key Laboratory of Sichuan Province, Center of Organ Transplantation, Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital, Chengdu, China.,Institute of Organ Transplantation, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China.,Chinese Academy of Sciences, Sichuan Translational Medicine Research Hospital, Chengdu, China
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14
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Li X, He J, Xie K. Molecular signaling in pancreatic ductal metaplasia: emerging biomarkers for detection and intervention of early pancreatic cancer. Cell Oncol (Dordr) 2022; 45:201-225. [PMID: 35290607 DOI: 10.1007/s13402-022-00664-x] [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] [Accepted: 02/14/2022] [Indexed: 11/27/2022] Open
Abstract
Pancreatic ductal metaplasia (PDM) is the transformation of potentially various types of cells in the pancreas into ductal or ductal-like cells, which eventually replace the existing differentiated somatic cell type(s). PDM is usually triggered by and manifests its ability to adapt to environmental stimuli and genetic insults. The development of PDM to atypical hyperplasia or dysplasia is an important risk factor for pancreatic intraepithelial neoplasia (PanIN) and pancreatic ductal adenocarcinoma (PDA). Recent studies using genetically engineered mouse models, cell lineage tracing, single-cell sequencing and others have unraveled novel cellular and molecular insights in PDM formation and evolution. Those novel findings help better understand the cellular origins and functional significance of PDM and its regulation at cellular and molecular levels. Given that PDM represents the earliest pathological changes in PDA initiation and development, translational studies are beginning to define PDM-associated cell and molecular biomarkers that can be used to screen and detect early PDA and to enable its effective intervention, thereby truly and significantly reducing the dreadful mortality rate of PDA. This review will describe recent advances in the understanding of PDM biology with a focus on its underlying cellular and molecular mechanisms, and in biomarker discovery with clinical implications for the management of pancreatic regeneration and tumorigenesis.
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Affiliation(s)
- Xiaojia Li
- Center for Pancreatic Cancer Research, The South China University of Technology School of Medicine, Guangzhou, 510006, China
- Department of Pathology, The South China University of Technology School of Medicine, Guangzhou, China
| | - Jie He
- Institute of Digestive Diseases Research, The South China University of Technology School of Medicine, Guangzhou, China
| | - Keping Xie
- Center for Pancreatic Cancer Research, The South China University of Technology School of Medicine, Guangzhou, 510006, China.
- Department of Pathology, The South China University of Technology School of Medicine, Guangzhou, China.
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15
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Kumagai K, Shimizu T, Takai A, Kakiuchi N, Takeuchi Y, Hirano T, Takeda H, Mizuguchi A, Teramura M, Ito T, Iguchi E, Nikaido M, Eso Y, Takahashi K, Ueda Y, Miyamoto SI, Obama K, Ogawa S, Marusawa H, Seno H. Expansion of gastric intestinal metaplasia with copy number aberrations contributes to field cancerization. Cancer Res 2022; 82:1712-1723. [PMID: 35363856 DOI: 10.1158/0008-5472.can-21-1523] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/14/2021] [Accepted: 03/07/2022] [Indexed: 12/09/2022]
Abstract
Intestinal metaplasia (IM) is a risk factor for gastric cancer following infection with Helicobacter pylori. To explore the susceptibility of pure gastric IM to cancer development, we investigated genetic alterations in single IM gastric glands. We isolated 50 single IM or non-IM glands from the inflamed gastric mucosa of 11 patients with intramucosal gastric carcinoma (IGC) and 4 patients without IGC; nineteen single glands in the non-inflamed gastric mucosa of 11 individuals from our cohort and previous dataset were also included as controls. Whole exome sequencing of single glands revealed significantly higher accumulation of somatic mutations in various genes within IM glands compared with non-IM glands. Clonal ordering analysis showed that IM glands expanded to form clusters with shared mutations. Additionally, targeted-capture deep sequencing and copy number (CN) analyses were performed in 96 clustered IM or non-IM gastric glands from 26 patients with IGC. CN analyses were also performed on 41 IGC samples and the Cancer Genome Atlas-Stomach Adenocarcinoma datasets. These analyses revealed that polyclonally expanded IM commonly acquired copy number aberrations (CNA), including amplification of chromosomes 8, 20, and 2. A large portion of clustered IM glands typically consisted of common CNAs rather than other cancer-related mutations. Moreover, the CNA patterns of clustered IM glands were similar to those of IGC, indicative of precancerous conditions. Taken together, these findings suggest that, in the gastric mucosa inflamed with H. pylori infection, IM glands expand via acquisition of CNAs comparable to those of IGC, contributing to field cancerization.
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Affiliation(s)
- Ken Kumagai
- Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
| | | | - Atsushi Takai
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | | | | | - Haruhiko Takeda
- Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
| | - Aya Mizuguchi
- Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
| | - Mari Teramura
- Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
| | - Takahiko Ito
- Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
| | | | | | - Yuji Eso
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ken Takahashi
- Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
| | - Yoshihide Ueda
- Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
| | | | - Kazutaka Obama
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | | | - Hiroshi Seno
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
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16
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Bruno S, Williams RJ, Del Vecchio D. Epigenetic cell memory: The gene's inner chromatin modification circuit. PLoS Comput Biol 2022; 18:e1009961. [PMID: 35385468 PMCID: PMC8985953 DOI: 10.1371/journal.pcbi.1009961] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/24/2022] [Indexed: 12/30/2022] Open
Abstract
Epigenetic cell memory allows distinct gene expression patterns to persist in different cell types despite a common genotype. Although different patterns can be maintained by the concerted action of transcription factors (TFs), it was proposed that long-term persistence hinges on chromatin state. Here, we study how the dynamics of chromatin state affect memory, and focus on a biologically motivated circuit motif, among histones and DNA modifications, that mediates the action of TFs on gene expression. Memory arises from time-scale separation among three circuit’s constituent processes: basal erasure, auto and cross-catalysis, and recruited erasure of modifications. When the two latter processes are sufficiently faster than the former, the circuit exhibits bistability and hysteresis, allowing active and repressed gene states to coexist and persist after TF stimulus removal. The duration of memory is stochastic with a mean value that increases as time-scale separation increases, but more so for the repressed state. This asymmetry stems from the cross-catalysis between repressive histone modifications and DNA methylation and is enhanced by the relatively slower decay rate of the latter. Nevertheless, TF-mediated positive autoregulation can rebalance this asymmetry and even confers robustness of active states to repressive stimuli. More generally, by wiring positively autoregulated chromatin modification circuits under time scale separation, long-term distinct gene expression patterns arise, which are also robust to failure in the regulatory links. Epigenetic cell memory ensures that cells are locked into specialized functions for the life-time of an organism. Phenotype loss is often associated with disease, such as cancer, and also required for artificially reprogramming cells from one type to another. Chromatin state, determined by histone modifications and DNA methylation, has recently appeared as a key mediator of epigenetic cell memory. However, a mechanistic understanding of how the dynamics of chromatin state affect the temporal duration of this memory is lacking. Here, we developed and analyzed a theoretical framework that includes these dynamics in gene regulation. Our results show that when both recruited erasure and auto/cross-catalysis among histone modifications and DNA methylation are sufficiently slower than basal erasure of all modifications, loss of cell memory will occur. Our mathematical formulas show how the parameters capturing these time scales depend on the abundance of methyl-DNA-binding proteins, on writers, erasers, and readers of nucleosome modifications, and on cell division time. With this information, one may design experimental interventions to either enforce phenotypic plasticity or re-lock phenotypes in aberrant cells.
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Affiliation(s)
- Simone Bruno
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Ruth J. Williams
- Department of Mathematics, University of California, San Diego, La Jolla, California, United States of America
| | - Domitilla Del Vecchio
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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17
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Dynamics in Morbidity Markers and Cytological Observations Made in Urine of Schistosoma haematobium-Infected Children: Pre- and Post-Praziquantel Treatment in an Endemic Setting. Med Sci (Basel) 2022; 10:medsci10010014. [PMID: 35225947 PMCID: PMC8883892 DOI: 10.3390/medsci10010014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/04/2022] [Accepted: 02/11/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Schistosomiasis is a neglected tropical disease caused by helminths of the genus Schistosoma. Morbidity markers and cytological observations such as squamous metaplastic cells, inflammatory cells, and hyperkeratotic cells in the urine of S. haematobium-infected children may suggest disease severity. They may also help predict severe forms of clinical presentation, such as bladder cancer in later years, among infected ones who miss out on early detection and treatment. Insights into possible changes in the morbidity markers and cytological observations in the urine of these S. haematobium-infected children before and after treatment would be of high clinical importance. Aim: The aim of this study was to identify changes/dynamics in morbidity markers and cytological abnormalities in the urine deposits of S. haematobium-infected children, pre- and post-praziquantel treatment. Methodology: This was a longitudinal study involving baseline and follow-up sampling among basic school children living in schistosomiasis-endemic communities. Urine samples were collected from 520 children at baseline and examined for S. haematobium ova by microscopy, while urine chemistry analyses were used for the examination of morbidity markers. The cytological analyses involved cytopathological examination of the urine deposits. Children whose urine showed positivity for S. haematobium eggs were treated with a single oral dose of praziquantel (40 mg/kg), after which urine chemistry and cytological analyses were repeated weekly for comparison with baseline, until the eighth week. Results: Morbidity markers such as hematuria, proteinuria, and leukocyturia were detected both at baseline and post-treatment among the infected children (30/520). Hematuria was the predominant parameter (90%, 27/30) detected at baseline, followed by proteinuria (53.3%, 16/30). Leukocyturia was the rarest parameter detected at baseline (13.3%, 4/30). However, almost all these parameters declined gradually post-treatment. Regarding cytological analyses, inflammatory cells were observed most (70.0%, 21/30) at baseline. For hyperkeratotic cells and squamous metaplastic cells, 46.7% and 26.7% were respectively observed at baseline, all of which gradually declined during the weekly follow-ups. Notably, squamous metaplastic cells persisted in all the participants from Week 1 through Week 3 post-treatment, but declined gradually thereafter. Conclusions: Morbidity markers and cytological observations in the children gradually decreased after treatment. Therefore, we continue to recommend routine cytological screening for urogenital schistosomiasis patients at hospitals in S. haematobium-endemic locations using both baseline and follow-up samples to detect these abnormalities early and monitor changes that may be occurring after treatment. Such changes may be useful in assessing treatment progress in infected persons.
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18
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Li S, Xie K. Ductal metaplasia in pancreas. Biochim Biophys Acta Rev Cancer 2022; 1877:188698. [DOI: 10.1016/j.bbcan.2022.188698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/09/2022] [Accepted: 02/09/2022] [Indexed: 02/07/2023]
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19
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Gu W, Wang H, Huang X, Kraiczy J, Singh PNP, Ng C, Dagdeviren S, Houghton S, Pellon-Cardenas O, Lan Y, Nie Y, Zhang J, Banerjee KK, Onufer EJ, Warner BW, Spence J, Scherl E, Rafii S, Lee RT, Verzi MP, Redmond D, Longman R, Helin K, Shivdasani RA, Zhou Q. SATB2 preserves colon stem cell identity and mediates ileum-colon conversion via enhancer remodeling. Cell Stem Cell 2022; 29:101-115.e10. [PMID: 34582804 PMCID: PMC8741647 DOI: 10.1016/j.stem.2021.09.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 07/13/2021] [Accepted: 09/08/2021] [Indexed: 01/09/2023]
Abstract
Adult stem cells maintain regenerative tissue structure and function by producing tissue-specific progeny, but the factors that preserve their tissue identities are not well understood. The small and large intestines differ markedly in cell composition and function, reflecting their distinct stem cell populations. Here we show that SATB2, a colon-restricted chromatin factor, singularly preserves LGR5+ adult colonic stem cell and epithelial identity in mice and humans. Satb2 loss in adult mice leads to stable conversion of colonic stem cells into small intestine ileal-like stem cells and replacement of the colonic mucosa with one that resembles the ileum. Conversely, SATB2 confers colonic properties on the mouse ileum. Human colonic organoids also adopt ileal characteristics upon SATB2 loss. SATB2 regulates colonic identity in part by modulating enhancer binding of the intestinal transcription factors CDX2 and HNF4A. Our study uncovers a conserved core regulator of colonic stem cells able to mediate cross-tissue plasticity in mature intestines.
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Affiliation(s)
- Wei Gu
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Hua Wang
- Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, 430 E 67th Street, New York, NY, 10065, USA
| | - Xiaofeng Huang
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Judith Kraiczy
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA,Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Pratik N. P. Singh
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA,Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Charles Ng
- Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medicine, 1283 York Avenue, New York, NY, 10065, USA
| | - Sezin Dagdeviren
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Sean Houghton
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Oscar Pellon-Cardenas
- Department of Genetics, Rutgers University, 145 Bevier Road, Piscataway, NJ, 08854, USA
| | - Ying Lan
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Yaohui Nie
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Jiaoyue Zhang
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Kushal K Banerjee
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA,Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Emily J. Onufer
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine, 660 S Euclid Avenue, St. Louis, MO, 63110, USA
| | - Brad W. Warner
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine, 660 S Euclid Avenue, St. Louis, MO, 63110, USA
| | - Jason Spence
- Department of Internal Medicine, University of Michigan, 1500 E Medical Center Drive, Ann Arbor, MI, 48109, USA
| | - Ellen Scherl
- Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medicine, 1283 York Avenue, New York, NY, 10065, USA
| | - Shahin Rafii
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Richard T. Lee
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Michael P. Verzi
- Department of Genetics, Rutgers University, 145 Bevier Road, Piscataway, NJ, 08854, USA
| | - David Redmond
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Randy Longman
- Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medicine, 1283 York Avenue, New York, NY, 10065, USA
| | - Kristian Helin
- Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, 430 E 67th Street, New York, NY, 10065, USA,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen N 2200 Denmark,The Novo Nordisk Foundation for Stem Cell Biology (Danstem), University of Copenhagen, Copenhagen N 2200, Denmark
| | - Ramesh A. Shivdasani
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA,Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Qiao Zhou
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA,Lead Contact ()
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20
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van Roey R, Brabletz T, Stemmler MP, Armstark I. Deregulation of Transcription Factor Networks Driving Cell Plasticity and Metastasis in Pancreatic Cancer. Front Cell Dev Biol 2021; 9:753456. [PMID: 34888306 PMCID: PMC8650502 DOI: 10.3389/fcell.2021.753456] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/27/2021] [Indexed: 12/15/2022] Open
Abstract
Pancreatic cancer is a very aggressive disease with 5-year survival rates of less than 10%. The constantly increasing incidence and stagnant patient outcomes despite changes in treatment regimens emphasize the requirement of a better understanding of the disease mechanisms. Challenges in treating pancreatic cancer include diagnosis at already progressed disease states due to the lack of early detection methods, rapid acquisition of therapy resistance, and high metastatic competence. Pancreatic ductal adenocarcinoma, the most prevalent type of pancreatic cancer, frequently shows dominant-active mutations in KRAS and TP53 as well as inactivation of genes involved in differentiation and cell-cycle regulation (e.g. SMAD4 and CDKN2A). Besides somatic mutations, deregulated transcription factor activities strongly contribute to disease progression. Specifically, transcriptional regulatory networks essential for proper lineage specification and differentiation during pancreas development are reactivated or become deregulated in the context of cancer and exacerbate progression towards an aggressive phenotype. This review summarizes the recent literature on transcription factor networks and epigenetic gene regulation that play a crucial role during tumorigenesis.
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Affiliation(s)
- Ruthger van Roey
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Thomas Brabletz
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Marc P Stemmler
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Isabell Armstark
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
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21
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Clinicopathological variables that correlate with sestamibi positivity in uniglandular parathyroid disease: a retrospective analysis of 378 parathyroid adenomas. Ann Nucl Med 2021; 36:33-42. [PMID: 34580842 DOI: 10.1007/s12149-021-01681-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 09/20/2021] [Indexed: 01/30/2023]
Abstract
PURPOSE Technetium-99 m sestamibi parathyroid scintigraphy (MIBI scan) has been used to localize abnormal glands in patients with primary hyperparathyroidism to guide parathyroidectomy. This series aimed to identify the biochemical and histopathological correlates of MIBI scan findings in patients with parathyroid adenoma. METHODS A total of 378 patients with histologically and biochemically proven parathyroid adenoma were included. The results of MIBI scan, histopathological (gland volume and weight, oxyphil cell ratio), biochemical (blood and 24 h urine calcium, creatinine, glomerular filtration rate, parathormone, alkaline phosphate, and vitamin D3) variables were recorded. A positive uptake on the MIBI scan referred to a localized adenoma. Among histological variables, a cutoff of 30% was applied to define parathyroid adenomas with low (≤ 30%) and high (> 30%) oxyphil cell content. Statistical analyses were performed to assess the relationship among variables. RESULTS MIBI scan localized the adenoma in 306 patients. Parathyroid gland volume and weight, and oxyphil ratio were significantly higher in the MIBI scan-positive group. Among the biochemical variables, only PTH was found to be significantly increased in the MIBI scan-positive group. Binary logistic regression models identified statistically significant cutoffs for the gland volume (1700 mm3), gland weight (1.3 g) and PTH levels (170 pg/mL) that can be used to predict the MIBI scan positivity. CONCLUSION In addition to PTH levels, this series underscored the impact of cellular composition along with the parathyroid gland volume and weight, both of which correlate with sestamibi positivity in patients with benign uniglandular parathyroid disease.
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Cell Transdifferentiation and Reprogramming in Disease Modeling: Insights into the Neuronal and Cardiac Disease Models and Current Translational Strategies. Cells 2021; 10:cells10102558. [PMID: 34685537 PMCID: PMC8533873 DOI: 10.3390/cells10102558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/29/2021] [Accepted: 09/01/2021] [Indexed: 02/07/2023] Open
Abstract
Cell transdifferentiation and reprogramming approaches in recent times have enabled the manipulation of cell fate by enrolling exogenous/artificial controls. The chemical/small molecule and regulatory components of transcription machinery serve as potential tools to execute cell transdifferentiation and have thereby uncovered new avenues for disease modeling and drug discovery. At the advanced stage, one can believe these methods can pave the way to develop efficient and sensitive gene therapy and regenerative medicine approaches. As we are beginning to learn about the utility of cell transdifferentiation and reprogramming, speculations about its applications in translational therapeutics are being largely anticipated. Although clinicians and researchers are endeavoring to scale these processes, we lack a comprehensive understanding of their mechanism(s), and the promises these offer for targeted and personalized therapeutics are scarce. In the present report, we endeavored to provide a detailed review of the original concept, methods and modalities enrolled in the field of cellular transdifferentiation and reprogramming. A special focus is given to the neuronal and cardiac systems/diseases towards scaling their utility in disease modeling and drug discovery.
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23
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Noto CN, Hoft SG, Bockerstett KA, Jackson NM, Ford EL, Vest LS, DiPaolo RJ. IL13 Acts Directly on Gastric Epithelial Cells to Promote Metaplasia Development During Chronic Gastritis. Cell Mol Gastroenterol Hepatol 2021; 13:623-642. [PMID: 34587523 PMCID: PMC8715193 DOI: 10.1016/j.jcmgh.2021.09.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND & AIMS It is well established that chronic inflammation promotes gastric cancer-associated metaplasia, but little is known regarding the mechanisms by which immune cells and cytokines regulate metaplastic cellular changes. The goals of this study were to identify interleukin 13 (IL13)-producing immune cells, determine the gastric epithelial cell response(s) to IL13, and establish the role(s) of IL13 in metaplasia development. METHODS Experiments used an established mouse model of autoimmune gastritis (TxA23), TxA23×Il4ra-/- mice, which develop gastritis but do not express the IL4/IL13-receptor subunit IL4Rα, and TxA23×Il13-Yfp mice, which express yellow fluorescent protein in IL13-producing cells. Flow cytometry was used to measure IL13 secretion and identify IL13-producing immune cells. Mouse and human gastric organoids were cultured with IL13 to determine epithelial cell response(s) to IL13. Single-cell RNA sequencing was performed on gastric epithelial cells from healthy and inflamed mouse stomachs. Mice with gastritis were administered IL13-neutralizing antibodies and stomachs were analyzed by histopathology and immunofluorescence. RESULTS We identified 6 unique subsets of IL13-producing immune cells in the inflamed stomach. Organoid cultures showed that IL13 acts directly on gastric epithelium to induce a metaplastic phenotype. IL4Rα-deficient mice did not progress to metaplasia. Single-cell RNA sequencing determined that gastric epithelial cells from IL4Rα-deficient mice up-regulated inflammatory genes but failed to up-regulate metaplasia-associated transcripts. Neutralization of IL13 significantly reduced and reversed metaplasia development in mice with gastritis. CONCLUSIONS IL13 is made by a variety of immune cell subsets during chronic gastritis and promotes gastric cancer-associated metaplastic epithelial cell changes. Neutralization of IL13 reduces metaplasia severity during chronic gastritis.
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Affiliation(s)
- Christine N Noto
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri
| | - Stella G Hoft
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri
| | - Kevin A Bockerstett
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri
| | - Nicholas M Jackson
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri
| | - Eric L Ford
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri
| | - Luke S Vest
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri
| | - Richard J DiPaolo
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri.
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Spelling Out CICs: A Multi-Organ Examination of the Contributions of Cancer Initiating Cells' Role in Tumor Progression. Stem Cell Rev Rep 2021; 18:228-240. [PMID: 34244971 DOI: 10.1007/s12015-021-10195-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2021] [Indexed: 12/15/2022]
Abstract
Tumor invasion and metastasis remain the leading causes of mortality for patients with cancer despite current treatment strategies. In some cancer types, recurrence is considered inevitable due to the lack of effective anti-metastatic therapies. Recent studies across many cancer types demonstrate a close relationship between cancer-initiating cells (CICs) and metastasis, as well as general cancer progression. First, this review describes CICs' contribution to cancer progression. Then we discuss our recent understanding of mechanisms through which CICs promote tumor invasion and metastasis by examining the role of CICs in each stage. Finally, we examine the current understanding of CICs' contribution to therapeutic resistance and recent developments in CIC-targeting drugs. We believe this understanding is key to advancing anti-CIC clinical therapeutics.
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25
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Barua A, Beygi A, Hatzikirou H. Close to Optimal Cell Sensing Ensures the Robustness of Tissue Differentiation Process: The Avian Photoreceptor Mosaic Case. ENTROPY 2021; 23:e23070867. [PMID: 34356408 PMCID: PMC8303396 DOI: 10.3390/e23070867] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 07/05/2021] [Accepted: 07/05/2021] [Indexed: 12/22/2022]
Abstract
The way that progenitor cell fate decisions and the associated environmental sensing are regulated to ensure the robustness of the spatial and temporal order in which cells are generated towards a fully differentiating tissue still remains elusive. Here, we investigate how cells regulate their sensing intensity and radius to guarantee the required thermodynamic robustness of a differentiated tissue. In particular, we are interested in finding the conditions where dedifferentiation at cell level is possible (microscopic reversibility), but tissue maintains its spatial order and differentiation integrity (macroscopic irreversibility). In order to tackle this, we exploit the recently postulated Least microEnvironmental Uncertainty Principle (LEUP) to develop a theory of stochastic thermodynamics for cell differentiation. To assess the predictive and explanatory power of our theory, we challenge it against the avian photoreceptor mosaic data. By calibrating a single parameter, the LEUP can predict the cone color spatial distribution in the avian retina and, at the same time, suggest that such a spatial pattern is associated with quasi-optimal cell sensing. By means of the stochastic thermodynamics formalism, we find out that thermodynamic robustness of differentiated tissues depends on cell metabolism and cell sensing properties. In turn, we calculate the limits of the cell sensing radius that ensure the robustness of differentiated tissue spatial order. Finally, we further constrain our model predictions to the avian photoreceptor mosaic.
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Affiliation(s)
- Arnab Barua
- Centre for Information Services and High Performance Computing, Technische Universität Dresden, Nöthnitzer Straße 46, 01062 Dresden, Germany; (A.B.); (A.B.)
| | - Alireza Beygi
- Centre for Information Services and High Performance Computing, Technische Universität Dresden, Nöthnitzer Straße 46, 01062 Dresden, Germany; (A.B.); (A.B.)
| | - Haralampos Hatzikirou
- Centre for Information Services and High Performance Computing, Technische Universität Dresden, Nöthnitzer Straße 46, 01062 Dresden, Germany; (A.B.); (A.B.)
- Mathematics Department, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates
- Correspondence:
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26
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Tata A, Chow RD, Tata PR. Epithelial cell plasticity: breaking boundaries and changing landscapes. EMBO Rep 2021; 22:e51921. [PMID: 34096150 DOI: 10.15252/embr.202051921] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 05/08/2021] [Accepted: 05/18/2021] [Indexed: 12/17/2022] Open
Abstract
Epithelial tissues respond to a wide variety of environmental and genotoxic stresses. As an adaptive mechanism, cells can deviate from their natural paths to acquire new identities, both within and across lineages. Under extreme conditions, epithelial tissues can utilize "shape-shifting" mechanisms whereby they alter their form and function at a tissue-wide scale. Mounting evidence suggests that in order to acquire these alternate tissue identities, cells follow a core set of "tissue logic" principles based on developmental paradigms. Here, we review the terminology and the concepts that have been put forward to describe cell plasticity. We also provide insights into various cell intrinsic and extrinsic factors, including genetic mutations, inflammation, microbiota, and therapeutic agents that contribute to cell plasticity. Additionally, we discuss recent studies that have sought to decode the "syntax" of plasticity-i.e., the cellular and molecular principles through which cells acquire new identities in both homeostatic and malignant epithelial tissues-and how these processes can be manipulated for developing novel cancer therapeutics.
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Affiliation(s)
- Aleksandra Tata
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Ryan D Chow
- Department of Genetics, Systems Biology Institute, Medical Scientist Training Program, Yale University School of Medicine, New Haven, CT, USA
| | - Purushothama Rao Tata
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA.,Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA.,Regeneration Next, Duke University, Durham, NC, USA.,Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
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27
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Molecular mechanisms of transcription factor mediated cell reprogramming: conversion of liver to pancreas. Biochem Soc Trans 2021; 49:579-590. [PMID: 33666218 PMCID: PMC8106502 DOI: 10.1042/bst20200219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/22/2020] [Accepted: 02/01/2021] [Indexed: 12/12/2022]
Abstract
Transdifferentiation is a type of cellular reprogramming involving the conversion of one differentiated cell type to another. This remarkable phenomenon holds enormous promise for the field of regenerative medicine. Over the last 20 years techniques used to reprogram cells to alternative identities have advanced dramatically. Cellular identity is determined by the transcriptional profile which comprises the subset of mRNAs, and therefore proteins, being expressed by a cell at a given point in time. A better understanding of the levers governing transcription factor activity benefits our ability to generate therapeutic cell types at will. One well-established example of transdifferentiation is the conversion of hepatocytes to pancreatic β-cells. This cell type conversion potentially represents a novel therapy in T1D treatment. The identification of key master regulator transcription factors (which distinguish one body part from another) during embryonic development has been central in developing transdifferentiation protocols. Pdx1 is one such example of a master regulator. Ectopic expression of vector-delivered transcription factors (particularly the triumvirate of Pdx1, Ngn3 and MafA) induces reprogramming through broad transcriptional remodelling. Increasingly, complimentary cell culture techniques, which recapitulate the developmental microenvironment, are employed to coax cells to adopt new identities by indirectly regulating transcription factor activity via intracellular signalling pathways. Both transcription factor-based reprogramming and directed differentiation approaches ultimately exploit transcription factors to influence cellular identity. Here, we explore the evolution of reprogramming and directed differentiation approaches within the context of hepatocyte to β-cell transdifferentiation focussing on how the introduction of new techniques has improved our ability to generate β-cells.
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Margres MJ, Rautsaw RM, Strickland JL, Mason AJ, Schramer TD, Hofmann EP, Stiers E, Ellsworth SA, Nystrom GS, Hogan MP, Bartlett DA, Colston TJ, Gilbert DM, Rokyta DR, Parkinson CL. The Tiger Rattlesnake genome reveals a complex genotype underlying a simple venom phenotype. Proc Natl Acad Sci U S A 2021; 118:e2014634118. [PMID: 33468678 PMCID: PMC7848695 DOI: 10.1073/pnas.2014634118] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Variation in gene regulation is ubiquitous, yet identifying the mechanisms producing such variation, especially for complex traits, is challenging. Snake venoms provide a model system for studying the phenotypic impacts of regulatory variation in complex traits because of their genetic tractability. Here, we sequence the genome of the Tiger Rattlesnake, which possesses the simplest and most toxic venom of any rattlesnake species, to determine whether the simple venom phenotype is the result of a simple genotype through gene loss or a complex genotype mediated through regulatory mechanisms. We generate the most contiguous snake-genome assembly to date and use this genome to show that gene loss, chromatin accessibility, and methylation levels all contribute to the production of the simplest, most toxic rattlesnake venom. We provide the most complete characterization of the venom gene-regulatory network to date and identify key mechanisms mediating phenotypic variation across a polygenic regulatory network.
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Affiliation(s)
- Mark J Margres
- Department of Biological Sciences, Clemson University, Clemson, SC 29634;
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Jason L Strickland
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
- Department of Biology, University of South Alabama, Mobile, AL 36688
| | - Andrew J Mason
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Tristan D Schramer
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Erich P Hofmann
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Erin Stiers
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Schyler A Ellsworth
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Gunnar S Nystrom
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Michael P Hogan
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Daniel A Bartlett
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Timothy J Colston
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC 29634;
- Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC 29634
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29
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Rosa L, Lobos-González L, Muñoz-Durango N, García P, Bizama C, Gómez N, González X, Wichmann IA, Saavedra N, Guevara F, Villegas J, Arrese M, Ferreccio C, Kalergis AM, Miquel JF, Espinoza JA, Roa JC. Evaluation of the chemopreventive potentials of ezetimibe and aspirin in a novel mouse model of gallbladder preneoplasia. Mol Oncol 2020; 14:2834-2852. [PMID: 33326125 PMCID: PMC7607176 DOI: 10.1002/1878-0261.12766] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/04/2020] [Accepted: 06/14/2020] [Indexed: 12/24/2022] Open
Abstract
Gallbladder stones (cholecystolithiasis) are the main risk factor for gallbladder cancer (GBC), a lethal biliary malignancy with poor survival rates worldwide. Gallbladder stones are thought to damage the gallbladder epithelium and trigger chronic inflammation. Preneoplastic lesions that arise in such an inflammatory microenvironment can eventually develop into invasive carcinoma, through mechanisms that are not fully understood. Here, we developed a novel gallbladder preneoplasia mouse model through the administration of two lithogenic diets (a low‐ or a high‐cholesterol diet) in wild‐type C57BL/6 mice over a period of 9 months. Additionally, we evaluated the chemopreventive potentials of the anti‐inflammatory drug aspirin and the cholesterol absorption inhibitor ezetimibe. Both lithogenic diets induced early formation of gallbladder stones, together with extensive inflammatory changes and widespread induction of metaplasia, an epithelial adaptation to tissue injury. Dysplastic lesions were presented only in mice fed with high‐cholesterol diet (62.5%) in late stages (9th month), and no invasive carcinoma was observed at any stage. The cholesterol absorption inhibitor ezetimibe inhibited gallbladder stone formation and completely prevented the onset of metaplasia and dysplasia in both lithogenic diets, whereas aspirin partially reduced metaplasia development only in the low‐cholesterol diet setting. This model recapitulates several of the structural and inflammatory findings observed in human cholecystolithiasic gallbladders, making it relevant for the study of gallbladder carcinogenesis. In addition, our results suggest that the use of cholesterol absorption inhibitors and anti‐inflammatory drugs can be evaluated as chemopreventive strategies to reduce the burden of GBC among high‐risk populations.
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Affiliation(s)
- Lorena Rosa
- Doctorado en Ciencias mención Biología Celular y Molecular Aplicada, Universidad de La Frontera, Temuco, Chile.,Departamento de Patología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Lorena Lobos-González
- Centro de Medicina Regenerativa, Facultad de Medicina-Clínica Alemana, Universidad del Desarrollo, Santiago, Chile.,Advanced Center for Chronic Diseases (ACCDiS), Santiago, Chile
| | - Natalia Muñoz-Durango
- Millennium Institute of Immunology and Immunotherapy (IMII), Santiago, Chile.,Departmento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Patricia García
- Departamento de Patología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carolina Bizama
- Departamento de Patología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Natalia Gómez
- Departamento de Patología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Ximena González
- Departamento de Patología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Ignacio A Wichmann
- Advanced Center for Chronic Diseases (ACCDiS), Santiago, Chile.,Departamento de Hematología-Oncología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Nicolás Saavedra
- Departamento de Ciencias Básicas, Centro de Biología Molecular y Farmacogenética, BIOREN, Universidad de La Frontera, Temuco, Chile
| | | | - Jaime Villegas
- Fundación Ciencia & Vida, Santiago, Chile.,Centro de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Marco Arrese
- Departamento de Gastroenterología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Catterina Ferreccio
- Advanced Center for Chronic Diseases (ACCDiS), Santiago, Chile.,Departamento de Salud Publica, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alexis M Kalergis
- Millennium Institute of Immunology and Immunotherapy (IMII), Santiago, Chile.,Departmento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.,Departmento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Juan Francisco Miquel
- Departamento de Gastroenterología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jaime A Espinoza
- SciLifeLab, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Juan C Roa
- Departamento de Patología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
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30
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Abdalla EA, Id‐Lahoucine S, Cánovas A, Casellas J, Schenkel FS, Wood BJ, Baes CF. Discovering lethal alleles across the turkey genome using a transmission ratio distortion approach. Anim Genet 2020; 51:876-889. [PMID: 33006154 PMCID: PMC7702127 DOI: 10.1111/age.13003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2020] [Indexed: 12/23/2022]
Abstract
Deviation from Mendelian inheritance expectations (transmission ratio distortion, TRD) has been observed in several species, including the mouse and humans. In this study, TRD was characterized in the turkey genome using both allelic (specific- and unspecific-parent TRD) and genotypic (additive- and dominance-TRD) parameterizations within a Bayesian framework. In this study, we evaluated TRD for 23 243 genotyped Turkeys across 56 393 autosomal SNPs. The analyses included 500 sires, 2013 dams and 11 047 offspring (trios). Three different haplotype sliding windows of 4, 10 and 20 SNPs were used across the autosomal chromosomes. Based on the genotypic parameterizations, 14 haplotypes showed additive and dominance TRD effects highlighting regions with a recessive TRD pattern. In contrast, the allelic model uncovered 12 haplotype alleles with the allelic TRD pattern which showed an underrepresentation of heterozygous offspring in addition to the absence of homozygous animals. For regions with the allelic pattern, only one particular region showed a parent-specific TRD where the penetrance was high via the dam, but low via the sire. The gene set analysis uncovered several gene ontology functional terms, Reactome pathways and several Medical Subject Headings that showed significant enrichment of genes associated with TRD. Many of these gene ontology functional terms (e.g. mitotic spindle assembly checkpoint, DRM complex and Aneuploidy), Reactome pathways (e.g. Mismatch repair) and Medical Subject Headings (e.g. Adenosine monophosphate) are known to be related to fertility, embryo development and lethality. The results of this study revealed potential novel candidate lethal haplotypes, functional terms and pathways that may enhance breeding programs in Turkeys through reducing mortality and improving reproduction rate.
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Affiliation(s)
- E. A. Abdalla
- Centre for Genetic Improvement of Livestock, Department of Animal BiosciencesUniversity of GuelphGuelphONN1G 2W1Canada
| | - S. Id‐Lahoucine
- Centre for Genetic Improvement of Livestock, Department of Animal BiosciencesUniversity of GuelphGuelphONN1G 2W1Canada
| | - A. Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal BiosciencesUniversity of GuelphGuelphONN1G 2W1Canada
| | - J. Casellas
- Departament de Ciència Animal i dels AlimentsUniversitat Autònoma de BarcelonaBellaterra08193Spain
| | - F. S. Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal BiosciencesUniversity of GuelphGuelphONN1G 2W1Canada
| | - B. J. Wood
- Centre for Genetic Improvement of Livestock, Department of Animal BiosciencesUniversity of GuelphGuelphONN1G 2W1Canada
- Hybrid TurkeysC‐650 Riverbend Drive, Suite CKitchenerONN2K 3S2Canada
- School of Veterinary ScienceUniversity of QueenslandGattonQld4343Australia
| | - C. F. Baes
- Centre for Genetic Improvement of Livestock, Department of Animal BiosciencesUniversity of GuelphGuelphONN1G 2W1Canada
- Institute of Genetics, Vetsuisse FacultyUniversity of BernBern3001Switzerland
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31
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Cai Q, Shi P, Yuan Y, Peng J, Ou X, Zhou W, Li J, Su T, Lin L, Cai S, He Y, Xu J. Inflammation-Associated Senescence Promotes Helicobacter pylori-Induced Atrophic Gastritis. Cell Mol Gastroenterol Hepatol 2020; 11:857-880. [PMID: 33161156 PMCID: PMC7859172 DOI: 10.1016/j.jcmgh.2020.10.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND & AIMS The association between cellular senescence and Helicobacter pylori-induced atrophic gastritis is not clear. Here, we explore the role of cellular senescence in H pylori-induced atrophic gastritis and the underlying mechanism. METHODS C57BL/6J mice were infected with H pylori for biological and mechanistic studies in vivo. Gastric precancerous lesions from patients and mouse models were collected and analyzed using senescence-associated beta-galactosidase, Sudan Black B, and immunohistochemical staining to analyze senescent cells, signaling pathways, and H pylori infection. Chromatin immunoprecipitation, luciferase reporter assays, and other techniques were used to explore the underlying mechanism in vitro. RESULTS Gastric mucosa atrophy was highly associated with cellular senescence. H pylori promoted gastric epithelial cell senescence in vitro and in vivo in a manner that depended on C-X-C motif chemokine receptor 2 (CXCR2) signaling. Interestingly, H pylori infection not only up-regulated the expression of CXCR2 ligands, C-X-C motif chemokine ligands 1 and 8, but also transcriptionally up-regulated the expression of CXCR2 via the nuclear factor-κB subunit 1 directly. In addition, CXCR2 formed a positive feedback loop with p53 to continually enhance senescence. Pharmaceutical inhibition of CXCR2 in an H pylori-infected mouse model attenuated mucosal senescence and atrophy, and delayed further precancerous lesion progression. CONCLUSIONS Our study showed a new mechanism of H pylori-induced atrophic gastritis through CXCR2-mediated cellular senescence. Inhibition of CXCR2 signaling is suggested as a potential preventive therapy for targeting H pylori-induced atrophic gastritis. GEO data set accession numbers: GSE47797 and GSE3556.
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Affiliation(s)
- Qinbo Cai
- Center of Gastrointestinal Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Center for Diagnosis and Treatment of Gastric Cancer, Sun Yat-sen University, Guangdong, China; Laboratory of General Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Peng Shi
- Center of Gastrointestinal Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Center for Diagnosis and Treatment of Gastric Cancer, Sun Yat-sen University, Guangdong, China; Laboratory of General Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yujie Yuan
- Center of Gastrointestinal Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Center for Diagnosis and Treatment of Gastric Cancer, Sun Yat-sen University, Guangdong, China
| | - Jianjun Peng
- Center of Gastrointestinal Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Center for Diagnosis and Treatment of Gastric Cancer, Sun Yat-sen University, Guangdong, China
| | - Xinde Ou
- Center of Gastrointestinal Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Center for Diagnosis and Treatment of Gastric Cancer, Sun Yat-sen University, Guangdong, China; Laboratory of General Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wen Zhou
- Center of Gastrointestinal Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Center for Diagnosis and Treatment of Gastric Cancer, Sun Yat-sen University, Guangdong, China; Laboratory of General Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jin Li
- Center of Gastrointestinal Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Center for Diagnosis and Treatment of Gastric Cancer, Sun Yat-sen University, Guangdong, China; Center for Digestive Disease, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China; Laboratory of General Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Taiqiang Su
- Center of Gastrointestinal Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Center for Diagnosis and Treatment of Gastric Cancer, Sun Yat-sen University, Guangdong, China; Center for Digestive Disease, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China; Laboratory of General Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Liangliang Lin
- Center of Gastrointestinal Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Center for Diagnosis and Treatment of Gastric Cancer, Sun Yat-sen University, Guangdong, China
| | - Shirong Cai
- Center of Gastrointestinal Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Center for Diagnosis and Treatment of Gastric Cancer, Sun Yat-sen University, Guangdong, China
| | - Yulong He
- Center of Gastrointestinal Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Center for Diagnosis and Treatment of Gastric Cancer, Sun Yat-sen University, Guangdong, China; Center for Digestive Disease, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China.
| | - Jianbo Xu
- Center of Gastrointestinal Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China; Center for Diagnosis and Treatment of Gastric Cancer, Sun Yat-sen University, Guangdong, China.
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Bínová E, Bína D, Nohýnková E. DNA content in Acanthamoeba during two stress defense reactions: Encystation, pseudocyst formation and cell cycle. Eur J Protistol 2020; 77:125745. [PMID: 33218872 DOI: 10.1016/j.ejop.2020.125745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/22/2020] [Accepted: 10/19/2020] [Indexed: 12/01/2022]
Abstract
During environmental stress, the vegetative cells of the facultative pathogenic amoeba Acanthamoeba castellanii reversibly differentiate into resistant dormant stages, namely, cysts or pseudocysts. The type of resistant stage depends on the nature and duration of the stressor. Cell differentiation is accompanied by changes in morphology and cellular metabolism. Moreover, cell differentiation is also expected to be closely linked to the regulation of the cell cycle and, thus, to cellular DNA content. While the existence of the resistant stages in A. castellanii is well known, there is no consensus regarding the relationship between differentiation and cell cycle progression. In the present work, we used flow cytometry analysis to explore the changes in the DNA content during Acanthamoeba encystation and pseudocyst formation. Our results strongly indicate that A. castellanii enters encystation from the G2 phase of the cell cycle. In contrast, differentiation into pseudocysts can begin in the G1 and G2 phases. In addition, we present a phylogenetic analysis and classification of the main cell cycle regulators, namely, cyclin-dependent kinases and cyclins that are found in the genome of A. castellanii.
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Affiliation(s)
- Eva Bínová
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University, Studnickova 7, 128 00 Prague 2, Czech Republic
| | - David Bína
- Faculty of Science, University of South Bohemia, Branišovská 1760 and The Czech Academy of Sciences, Biology Centre, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Eva Nohýnková
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University, Studnickova 7, 128 00 Prague 2, Czech Republic.
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33
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De N, Nandi M, Banik S, Roy S. Bi-stability of the master gene regulatory network of the common dendritic precursor cell: Implications for cell differentiation. IUBMB Life 2020; 72:2225-2232. [PMID: 32790022 DOI: 10.1002/iub.2355] [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: 05/24/2020] [Accepted: 07/10/2020] [Indexed: 11/08/2022]
Abstract
In cell lineage commitment decisions, a gene regulatory network (GRN) consisting of a limited number of transcription factors forms the regulatory pivot. Myeloid lineage dendritic cells or DCs are specialized cells having the antigen-presenting ability and are of immense importance in immune surveillance. In this report, we analyze the GRN that governs the lineage commitment of Common DC Progenitor (CDP) cells to conventional dendritic cells (cDC) and plasmacytoid dendritic cells (pDC). We have analyzed the quantitative behavior of the master regulatory circuit of CDP that governs the lineage commitment. Simulations showed that the GRN displays a bi-stable behavior within a range of parameter values. Several transcription factors, PU.1, IRF8, Flt3, and Stat3, whose concentrations vary significantly in the two steady states, appear to be the key players. We hypothesize that the two stable steady states are precursors of cDC and pDC, and the variation of concentration of these key transcription factors in the two states may be responsible for early events in lineage commitment.
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Affiliation(s)
- Nayan De
- Department of Biophysics, Bose Institute, Kolkata, India
| | - Mintu Nandi
- Department of Chemistry, University of Calcutta, Kolkata, India
| | - Suman Banik
- Department of Chemistry, Bose Institute, Kolkata, India
| | - Siddhartha Roy
- Department of Biophysics, Bose Institute, Kolkata, India
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34
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Camacho JP, Obaíd M, Bustos C, Calderón W, Lombardi JJ, Subiabre R, Guler K, Correa F. Squamous Cell Carcinoma as a Result of Likely Industrial Grade Ruptured Poly Implant Prosthèse Silicone Buttock Implants. Aesthet Surg J Open Forum 2020; 2:ojaa030. [PMID: 33791653 PMCID: PMC7671286 DOI: 10.1093/asjof/ojaa030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Poly Implant Prosthèse (PIP) implants were withdrawn from the market in 2010 due to the use of a nonmedical grade silicone filler. In 2012, the French medical authorities and the International Confederation of Societies of Plastic, Reconstructive and Aesthetic Surgery recommended the extraction of PIP implants. However, during the duration of this scandal, each country in the world did not agree with a uniform procedure, and this rule was not implemented in its entirety. Although laboratory test results on PIP implants were negative for cytotoxicity and genotoxicity, there are many reports in the literature of several complications associated with PIP implants, including high rupture rates and the fact that they are 3 to 5 times more likely to produce local tissue reactions. On the other hand, the development of more strange and worse prognosis complications, such as the development of squamous carcinoma associated with the use of silicone implants (not necessarily related to PIP implants), is less known. To date, only 6 cases have been reported, and all are related to breast augmentation. The authors made the first report of primary gluteal squamous cell cancer related to rupture and delayed removal of PIP silicone buttock implants. Level of Evidence: 5
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Affiliation(s)
- Juan P Camacho
- Department of Plastic and Reconstructive Surgery and the Department of Pathology, Hospital del Salvador, Santiago, Chile
| | - Miguel Obaíd
- Department of Plastic and Reconstructive Surgery and the Department of Pathology, Hospital del Salvador, Santiago, Chile
| | - Camilo Bustos
- Department of Plastic and Reconstructive Surgery and the Department of Pathology, Hospital del Salvador, Santiago, Chile
| | - Wilfredo Calderón
- Department of Plastic and Reconstructive Surgery and the Department of Pathology, Hospital del Salvador, Santiago, Chile
| | - Juan J Lombardi
- Department of Plastic and Reconstructive Surgery and the Department of Pathology, Hospital del Salvador, Santiago, Chile
| | - Rodrigo Subiabre
- Department of Plastic and Reconstructive Surgery and the Department of Pathology, Hospital del Salvador, Santiago, Chile
| | - Kenneth Guler
- Department of Plastic and Reconstructive Surgery and the Department of Pathology, Hospital del Salvador, Santiago, Chile
| | - Francisca Correa
- Department of Plastic and Reconstructive Surgery and the Department of Pathology, Hospital del Salvador, Santiago, Chile
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Vasilyev NV, Topolnitsky EB, Borodina YA, Molodykh VS, Lyutikova PO, Maltseva AA, Garcheva AS. [Biphasic (dedifferentiated) osteosarcoma of the lung in the light of current ideas on biphasic tumors]. Arkh Patol 2020; 82:56-61. [PMID: 32096492 DOI: 10.17116/patol20208201156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The paper presents a case of biphasic (dedifferentiated) osteosarcoma arising primarily on the lung, which has not previously encountered in the literature. It provides a detailed description of its clinical, instrumental, and morphological pattern. It also analyzes the literature on the study of primary pulmonary osteosarcoma and extraskeletal osteosarcoma with high-grade transformation. This clinical case is a clear example of classic biphasic sarcoma interpreted in the context of the phenomenon of biphasic tumors. Their most important aspects (terminology, morphology, biological behavior, and a mechanism of dedifferentiation) are highlighted; the key characteristics of biphasic sarcomas are listed.
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Affiliation(s)
- N V Vasilyev
- Tomsk National Research Medical Center, Tomsk, Russia
| | - E B Topolnitsky
- Tomsk Regional Clinical Hospital, Tomsk, Russia; Siberian State Medical University, Tomsk, Russia
| | - Yu A Borodina
- Tomsk Regional Clinical Hospital, Tomsk, Russia; Siberian State Medical University, Tomsk, Russia
| | | | | | - A A Maltseva
- Siberian State Medical University, Tomsk, Russia
| | - A S Garcheva
- Tomsk Regional Clinical Hospital, Tomsk, Russia; Tomsk Regional Prosectorium, Tomsk, Russia
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Thiagalingam S. Epigenetic memory in development and disease: Unraveling the mechanism. Biochim Biophys Acta Rev Cancer 2020; 1873:188349. [PMID: 31982403 DOI: 10.1016/j.bbcan.2020.188349] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 01/22/2020] [Accepted: 01/22/2020] [Indexed: 01/14/2023]
Abstract
Epigenetic memory is an essential process of life that governs the inheritance of predestined functional characteristics of normal cells and the newly acquired properties of cells affected by cancer and other diseases from parental to progeny cells. Unraveling the molecular basis of epigenetic memory dictated by protein and RNA factors in conjunction with epigenetic marks that are erased and re-established during embryogenesis/development during the formation of somatic, stem and disease cells will have far reaching implications to our understanding of embryogenesis/development and various diseases including cancer. While there has been enormous progress made, there are still gaps in knowledge which includes, the identity of unique epigenetic memory factors (EMFs) and epigenome coding enzymes/co-factors/scaffolding proteins involved in the assembly of defined "epigenetic memorysomes" and the epigenome marks that constitute collections of gene specific epigenetic memories corresponding to specific cell types and physiological conditions. A better understanding of the molecular basis for epigenetic memory will play a central role in improving diagnostics and prognostics of disease states and aid the development of targeted therapeutics of complex diseases.
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Affiliation(s)
- Sam Thiagalingam
- Department of Medicine (Biomedical Genetics Section and Cancer Center), Department of Pathology & Laboratory Medicine, Department of Pharmacology & Experimental Therapeutics, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, United States of America.
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Schallenberg S, Bork J, Essakly A, Alakus H, Buettner R, Hillmer AM, Bruns C, Schroeder W, Zander T, Loeser H, Gebauer F, Quaas A. Loss of the SWI/SNF-ATPase subunit members SMARCF1 (ARID1A), SMARCA2 (BRM), SMARCA4 (BRG1) and SMARCB1 (INI1) in oesophageal adenocarcinoma. BMC Cancer 2020; 20:12. [PMID: 31906887 PMCID: PMC6945480 DOI: 10.1186/s12885-019-6425-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 12/03/2019] [Indexed: 12/15/2022] Open
Abstract
Background The SWI/SNF complex is an important chromatin remodeler, commonly dysregulated in cancer, with an estimated mutation frequency of 20%. ARID1A is the most frequently mutated subunit gene. Almost nothing is known about the other familiar members of the SWI/SNF complexes, SMARCA2 (BRM), SMARCA4 (BRG1) and SMARCB1 (INI1), in oesophageal adenocarcinoma (EAC). Methods We analysed a large cohort of 685 patients with EAC. We used four different antibodies to detect a loss-of-protein of ARID1A BRM, BRG1 and INI1 by immunohistochemistry and correlated these findings with molecular and clinical data. Results Loss of ARID1A, BRG1, BRM and INI1 was observed in 10.4, 3.4, 9.9 and 2% of EAC. We found a co-existing protein loss of ARID1A and BRM in 9.9% and of ARID1A and BRG1 in 2.2%. Patients with loss of ARID1A and TP53 wildtype EACs showed a shortened overall survival compared with AIRDA1A-positive tumours [median overall survival was 60.1 months (95%CI 1.2–139.9 months)] in patients with ARIDA-1A expression and 26.2 months (95%CI 3.7–19.1 months) in cases of ARIDA-1A loss (p = 0.044). Tumours with loss or expression of ARID1A and TP53 loss were not associated with a difference in survival. Only one tumour revealed high microsatellite instability (MSI-H) with concomitant ARID1A loss. All other ARID1A loss-EACs were microsatellite-stable (MSS). No predictive relevance was seen for SWI/SNF-complex alterations and simultaneous amplification of different genes (PIK3CA, KRAS, c-MYC, MET, GATA6, ERBB2). Conclusion Our work describes, for the first time, loss of one of the SWI/SNF ATPase subunit proteins in a large number of adenocarcinomas of the oesophagus. Several papers discuss possible therapeutic interventions for tumours showing a loss of function of the SWI/SNF complex, such as PARP inhibitors or PI3K and AKT inhibitors. Future studies will be needed to show whether SWI/SNF complex-deficient EACs may benefit from personalized therapy.
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Affiliation(s)
- Simon Schallenberg
- Institute of Pathology, University of Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
| | - Julian Bork
- Institute of Pathology, University of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
| | - Ahlem Essakly
- Institute of Pathology, University of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
| | - Hakan Alakus
- Department of General, Visceral and Cancer Surgery, University of Cologne, Cologne, Germany
| | - Reinhard Buettner
- Institute of Pathology, University of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
| | - Axel M Hillmer
- Institute of Pathology, University of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
| | - Christiane Bruns
- Department of General, Visceral and Cancer Surgery, University of Cologne, Cologne, Germany
| | - Wolfgang Schroeder
- Department of General, Visceral and Cancer Surgery, University of Cologne, Cologne, Germany
| | - Thomas Zander
- Department I of Internal Medicine, Center for Integrated Oncology (CIO)University of Cologne, Cologne, Germany
| | - Heike Loeser
- Institute of Pathology, University of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
| | - Florian Gebauer
- Department of General, Visceral and Cancer Surgery, University of Cologne, Cologne, Germany
| | - Alexander Quaas
- Institute of Pathology, University of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
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Abstract
Regenerative processes that maintain the function of the gastrointestinal (GI) epithelium are critical for health and survival of multicellular organisms. In insects and vertebrates, intestinal stem cells (ISCs) regenerate the GI epithelium. ISC function is regulated by intrinsic, local, and systemic stimuli to adjust regeneration to tissue demands. These control mechanisms decline with age, resulting in significant perturbation of intestinal homeostasis. Processes that lead to this decline have been explored intensively in Drosophila melanogaster in recent years and are now starting to be characterized in mammalian models. This review presents a model for age-related regenerative decline in the fly intestine and discusses recent findings that start to establish molecular mechanisms of age-related decline of mammalian ISC function.
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Affiliation(s)
- Heinrich Jasper
- Immunology Discovery, Genentech, Inc., South San Francisco, California 94080, USA;
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39
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Microfluidic models of physiological or pathological flow shear stress for cell biology, disease modeling and drug development. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.06.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Que J, Garman KS, Souza RF, Spechler SJ. Pathogenesis and Cells of Origin of Barrett's Esophagus. Gastroenterology 2019; 157:349-364.e1. [PMID: 31082367 PMCID: PMC6650338 DOI: 10.1053/j.gastro.2019.03.072] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 03/22/2019] [Accepted: 03/25/2019] [Indexed: 02/06/2023]
Abstract
In patients with Barrett's esophagus (BE), metaplastic columnar mucosa containing epithelial cells with gastric and intestinal features replaces esophageal squamous mucosa damaged by gastroesophageal reflux disease. This condition is estimated to affect 5.6% of adults in the United States, and is a major risk factor for esophageal adenocarcinoma. Despite the prevalence and importance of BE, its pathogenesis is incompletely understood and there are disagreements over the cells of origin. We review mechanisms of BE pathogenesis, including transdifferentiation and transcommitment, and discuss potential cells of origin, including basal cells of the squamous epithelium, cells of esophageal submucosal glands and their ducts, cells of the proximal stomach, and specialized populations of cells at the esophagogastric junction (residual embryonic cells and transitional basal cells). We discuss the concept of metaplasia as a wound-healing response, and how cardiac mucosa might be the precursor of the intestinal metaplasia of BE. Finally, we discuss shortcomings in current diagnostic criteria for BE that have important clinical implications.
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Affiliation(s)
- Jianwen Que
- Division of Digestive and Liver Diseases and Center for Human Development, Department of Medicine, Columbia University, New York, New York.
| | - Katherine S. Garman
- Division of Gastroenterology, Department of Medicine, Duke University School of Medicine. Durham, NC
| | - Rhonda F. Souza
- Center for Esophageal Diseases, Department of Medicine, Baylor University Medical Center at Dallas, and Center for Esophageal Research, Department of Medicine, Baylor Scott & White Research Institute, Dallas, TX
| | - Stuart Jon Spechler
- Center for Esophageal Diseases, Department of Medicine, Baylor University Medical Center at Dallas, Dallas, Texas; Center for Esophageal Research, Department of Medicine, Baylor Scott & White Research Institute, Dallas, Texas.
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Mukaisho KI, Kanai S, Kushima R, Nakayama T, Hattori T, Sugihara H. Barretts's carcinogenesis. Pathol Int 2019; 69:319-330. [PMID: 31290583 PMCID: PMC6851828 DOI: 10.1111/pin.12804] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 03/22/2019] [Indexed: 12/14/2022]
Abstract
Barrett's esophagus is considered a precancerous lesion of esophageal adenocarcinoma (EAC). Long‐segment Barrett's esophagus, which is generally associated with intestinal metaplasia, has a higher rate of carcinogenesis than short‐segment Barrett's esophagus, which is mainly composed of cardiac‐type mucosa. However, a large number of cases reportedly develop EAC from the cardiac‐type mucosa which has the potential to involve intestinal phenotypes. There is no consensus regarding whether the definition of Barrett's epithelium should include intestinal metaplasia. Basic researches using rodent models have provided information regarding the origins of Barrett's epithelium. Nevertheless, it remains unclear whether differentiated gastric columnar epithelium or stratified esophageal squamous epithelium undergo transdifferentiation into the intestinal‐type columnar epithelium, transcommittment into the columnar epithelium, or whether the other pathways exist. Reflux of duodenal fluid including bile acids into the stomach may occur when an individual lies down after eating, which could cause the digestive juices to collect in the fornix of the stomach. N‐nitroso‐bile acids are produced with nitrites that are secreted from the salivary glands, and bile acids can drive expression of pro‐inflammatory cytokines via EGFR or the NF‐κB pathway. These steps may contribute significantly to carcinogenesis.
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Affiliation(s)
- Ken-Ichi Mukaisho
- Division of Molecular and Diagnostic Pathology, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
| | - Shunpei Kanai
- Division of Molecular and Diagnostic Pathology, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
| | - Ryoji Kushima
- Division of Diagnostic Pathology, Shiga University of Medical Science Hospital, Otsu, Japan
| | - Takahisa Nakayama
- Division of Molecular and Diagnostic Pathology, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
| | - Takanori Hattori
- Division of Molecular and Diagnostic Pathology, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
| | - Hiroyuki Sugihara
- Division of Molecular and Diagnostic Pathology, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
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Peters Y, Al-Kaabi A, Shaheen NJ, Chak A, Blum A, Souza RF, Di Pietro M, Iyer PG, Pech O, Fitzgerald RC, Siersema PD. Barrett oesophagus. Nat Rev Dis Primers 2019; 5:35. [PMID: 31123267 DOI: 10.1038/s41572-019-0086-z] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Barrett oesophagus (BE), the only known histological precursor of oesophageal adenocarcinoma (EAC), is a condition in which the squamous epithelium of the oesophagus is replaced by columnar epithelium as an adaptive response to gastro-oesophageal reflux. EAC has one of the fastest rising incidences of cancers in Western countries and has a dismal prognosis. BE is usually detected during endoscopic examination, and diagnosis is confirmed by the histological presence of intestinal metaplasia. Advances in genomics and transcriptomics have improved our understanding of the pathogenesis and malignant progression of intestinal metaplasia. As the majority of EAC cases are diagnosed in individuals without a known history of BE, screening for BE could potentially decrease disease-related mortality. Owing to the pre-malignant nature of BE, endoscopic surveillance of patients with BE is imperative for early detection and treatment of dysplasia to prevent further progression to invasive EAC. Developments in endoscopic therapy have resulted in a major shift in the treatment of patients with BE who have dysplasia or early EAC, from surgical resection to endoscopic resection and ablation. In addition to symptom control by optimization of lifestyle and pharmacological therapy with proton pump inhibitors, chemopreventive strategies based on NSAIDs and statins are currently being investigated for BE management.
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Affiliation(s)
- Yonne Peters
- Department of Gastroenterology and Hepatology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Ali Al-Kaabi
- Department of Gastroenterology and Hepatology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Nicholas J Shaheen
- Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Amitabh Chak
- Division of Gastroenterology and Liver Diseases, Case Western Reserve University, Cleveland, OH, USA
| | - Andrew Blum
- Division of Gastroenterology and Liver Diseases, Case Western Reserve University, Cleveland, OH, USA
| | - Rhonda F Souza
- Department of Medicine and the Center for Esophageal Diseases, Baylor University Medical Center at Dallas and the Center for Esophageal Research, Baylor Scott and White Research Institute, Dallas, TX, USA
| | | | - Prasad G Iyer
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Oliver Pech
- Department of Gastroenterology, St John of God Hospital, Regensburg, Germany
| | | | - Peter D Siersema
- Department of Gastroenterology and Hepatology, Radboud University Medical Center, Nijmegen, Netherlands.
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Layer-by-layer assembly as a robust method to construct extracellular matrix mimic surfaces to modulate cell behavior. Prog Polym Sci 2019. [DOI: 10.1016/j.progpolymsci.2019.02.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Chen B, Yu J, Lu L, Dong F, Zhou F, Tao X, Sun E. Upregulated forkhead-box A3 elevates the expression of forkhead-box A1 and forkhead-box A2 to promote metastasis in esophageal cancer. Oncol Lett 2019; 17:4351-4360. [PMID: 30944629 DOI: 10.3892/ol.2019.10078] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 02/04/2019] [Indexed: 11/06/2022] Open
Abstract
Esophageal cancer (EC) is one of the most lethal cancers currently known. Members of the forkhead-box A (FOXA) family, including FOXA1 and FOXA2, have been reported to regulate EC progression. However, the role of FOXA3, which is another FOXA member, has not yet been investigated. In the present study, public dataset analyses and immunohistochemistry of 96 samples from patients with EC were performed to determine the potential roles of FOXA3 in EC. The results revealed that FOXA3 was significantly upregulated in EC tumor tissues and Barrett's esophagus tissues. In addition, FOXA3 upregulation was positively associated with tumor invasion, distant metastasis, tumor-node-metastasis stage and shorter overall survival in patients with EC, and multivariate analysis identified FOXA3 as an independent prognostic marker. In vitro experiments demonstrated that the migratory and invasive abilities of EC109 and EC9706 cell lines were inhibited following FOXA3 knockdown. Notably, FOXA3 expression levels were positively correlated with FOXA1 and FOXA2 expression levels according to The Cancer Genome Atlas dataset analysis. Furthermore, FOXA3 knockdown decreased the expression levels of FOXA1 and FOXA2 in EC109 and EC9706 cell lines. Conversely, FOXA1 or FOXA2 overexpression compensated for the effects of FOXA3 knockdown on the migratory and invasive capacities of EC cells. In conclusion, the present study demonstrated that FOXA3 upregulation in EC cells promoted metastasis through regulation of other FOXA members.
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Affiliation(s)
- Bing Chen
- Department of Pathology, School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Jiegen Yu
- Department of Management Science, School of Humanities and Management, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Linming Lu
- Department of Pathology, School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Fangyuan Dong
- Department of Pathology, School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Fangfang Zhou
- Department of Pathology, School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Xiangxiang Tao
- Department of Pathology, School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Entao Sun
- Department of Health Inspection and Quarantine, School of Laboratory Medicine, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
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Su TT. Cellular plasticity, caspases and autophagy; that which does not kill us, well, makes us different. Open Biol 2018; 8:rsob.180157. [PMID: 30487302 PMCID: PMC6282069 DOI: 10.1098/rsob.180157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 10/30/2018] [Indexed: 02/07/2023] Open
Abstract
The ability to regenerate is a fundamental requirement for tissue homeostasis. Regeneration draws on three sources of cells. First and best-studied are dedicated stem/progenitor cells. Second, existing cells may proliferate to compensate for the lost cells of the same type. Third, a different cell type may change fate to compensate for the lost cells. This review focuses on regeneration of the third type and will discuss the contributions by post-transcriptional mechanisms including the emerging evidence for cell-autonomous and non-lethal roles of cell death pathways.
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Affiliation(s)
- Tin Tin Su
- Department of Molecular, Cellular and Developmental Biology, 347 UCB, University of Colorado, Boulder, CO 80309-0347, USA .,University of Colorado Comprehensive Cancer Center, Anschutz Medical Campus, 13001 E. 17th Pl., Aurora, CO 80045, USA
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46
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Lumelsky N, O'Hayre M, Chander P, Shum L, Somerman MJ. Autotherapies: Enhancing Endogenous Healing and Regeneration. Trends Mol Med 2018; 24:919-930. [PMID: 30213702 DOI: 10.1016/j.molmed.2018.08.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/09/2018] [Accepted: 08/17/2018] [Indexed: 12/31/2022]
Abstract
The promise of tissue engineering and regenerative medicine to reduce the burden of disease and improve quality of life are widely acknowledged. Traditional tissue engineering and regenerative medicine approaches rely on generation of tissue constructs in vitro for subsequent transplantation or injection of exogenously manipulated cells into a host. While promising, few such therapies have succeeded in clinical practice. Here, we propose that recent advances in stem cell and developmental biology, immunology, bioengineering, and material sciences, position us to develop a new generation of in vivo regenerative medicine therapies, which we term autotherapies. Autotherapies are strategies based on optimizing endogenous tissue responses and capitalizing on manipulation of stem cell niches and endogenous tissue microenvironments to enhance tissue healing and regeneration.
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Affiliation(s)
- Nadya Lumelsky
- National Institute of Dental and Craniofacial Research, National Institutes of Health, 6701 Democracy Blvd., Bethesda, MD 20892-4878, USA.
| | - Morgan O'Hayre
- National Institute of Dental and Craniofacial Research, National Institutes of Health, 6701 Democracy Blvd., Bethesda, MD 20892-4878, USA
| | - Preethi Chander
- National Institute of Dental and Craniofacial Research, National Institutes of Health, 6701 Democracy Blvd., Bethesda, MD 20892-4878, USA
| | - Lillian Shum
- National Institute of Dental and Craniofacial Research, National Institutes of Health, 6701 Democracy Blvd., Bethesda, MD 20892-4878, USA
| | - Martha J Somerman
- National Institute of Dental and Craniofacial Research, National Institutes of Health, 6701 Democracy Blvd., Bethesda, MD 20892-4878, USA
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Kanematsu A. Regenerative medicine for urological tissues: Updated review 2018. Int J Urol 2018; 25:788-791. [PMID: 30066462 DOI: 10.1111/iju.13762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/12/2018] [Indexed: 01/10/2023]
Abstract
The focus of the present review on regenerative medicine is limited; first, on a few human clinical trials carried out thus far in the urology field, and second, on more basic but important biological progress that regenerative medicine has brought us. Clinical trials for the bladder, urethra and urethral sphincter have been carried out thus far. Reconstruction with autologous cell-seeded biomaterial failed in patients in need of bladder augmentation. The strategy succeeded for urethral reconstruction in patients who might not have required this approach. Sphincter function improvement was attained by cell therapy, but did not equal the conventional standard therapy - the artificial sphincter. The radical progress in regenerative medicine is reported in more basic stem cell technology. The strategy to induce therapeutic cells from inducible pluripotent stem cells has shed novel light on developmental biology. In vitro creation of novel kidney tissue from inducible pluripotent stem cells has been attained. Other kinds of therapeutic cells could also be induced from the inducible pluripotent stem cells. Research should be encouraged to fill the gap between patient needs and what current regenerative medicine can attain.
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Affiliation(s)
- Akihiro Kanematsu
- Department of Urology, Hyogo College of Medicine, Nishinomiya, Hyogo, Japan
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48
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Abstract
This review has provided a summary of the biology of goblet cell metaplasia in CLE as it pertains to BE. Goblet cells are terminally differentiated nonproliferative cells that have many overlapping histochemical characteristics with mucinous columnar cells and pseudogoblet cells. There is an abundance of evidence that suggests that use of goblet cells as a biomarker of BE, and its progression to malignancy, is problematic. Some of these limitations include the fact that the background non-goblet epithelium in most patients with CLE is biologically intestinalized and contains molecular abnormalities similar to goblet cell CLE, goblet cells fluctuate with time and decrease in number with progression of neoplasia, and pathologists have problems with interpretation, and distinction, of goblet cells from other types of cells in the esophagus. Sampling error results in sensitivity and specificity issues that limit its positive predictive value. Goblet cells are fewest in number in the same population of patients with CLE that are hardest to detect endoscopically (i.e., those with short or ultrashort CLE). Nevertheless, the risk of cancer in patients with short-segment BE, a condition difficult to distinguish from the stomach, is very low regardless of the presence or absence of goblet cells so it is unclear what the role of goblet cells is in these patients as a biomarker. Nevertheless, if the answer to the following question, "Would you as a gastroenterologist recommend surveillance for a patient with clear endoscopic evidence of CLE, particularly if it is ≥ 3 cm in length, but in which goblet cells were not reported to be present by the pathologist," is yes, then the US requirement for goblet cells as part of the criteria for "BE" is superfluous.
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Abstract
Over the past two decades, evidence has accumulated to challenge the traditional view that cardiac mucosa, which is comprised exclusively of mucus glands, is the normal lining of the most proximal portion of the stomach (the gastric cardia). There is now considerable evidence to suggest that cardiac mucosa develops as a GERD-induced, squamous-to-columnar esophageal metaplasia in some, if not all, cases. Although cardiac mucosa lacks the goblet cells commonly required for a histologic diagnosis of intestinal metaplasia, cardiac mucosa has many molecular features of an intestinal-type mucosa, and appears to be the precursor of intestinal metaplasia with goblet cells. In apparently normal individuals, cardiac mucosa is commonly found in a narrow band, less than 3 mm in extent, on the columnar side of the squamo-columnar junction at the end of the esophagus. A greater extent of cardiac mucosa can be found in GERD patients, and the magnitude of that extent appears to be an index of GERD severity. Presently, the risk of adenocarcinoma imposed by cardiac mucosa is not clear, but appears to be far less than that of intestinal metaplasis with goblet cells. The British Society of Gastroenterology accepts an esophagus lined by cardiac mucosa as a "Barrett's esophagus". However, if one defines Barrett's esophagus as a metaplasia that predisposes to cancer, then only intestinal metaplasia clearly fulfills that criterion at this time. Well-designed, prospective studies are needed to establish the malignant potential of cardiac mucosa.
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Liver-enriched Genes are Associated with the Prognosis of Patients with Hepatocellular Carcinoma. Sci Rep 2018; 8:11197. [PMID: 30046116 PMCID: PMC6060164 DOI: 10.1038/s41598-018-29237-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 06/29/2018] [Indexed: 02/07/2023] Open
Abstract
Tissue-enriched genes are highly expressed in one particular tissue type and represent distinct physiological processes. The dynamic profile of tissue-enriched genes during tumorigenesis and progression remains largely unstudied. Here, we identified tissue-enriched genes from 12 tissue types based on RNA sequencing data from the Cancer Genome Atlas (TCGA), and found that the liver had the largest number of such genes among the 12 tissue types. The characteristics of liver-enriched genes were further investigated. Most liver-enriched genes were downregulated and metabolism-related genes, which were associated with pathological stage and dedifferentiation in patients with hepatocellular carcinoma (HCC). Hypermethylation might be a mechanism underlying the downregulation of liver-enriched genes. We constructed a liver-enriched gene set and demonstrated that it is associated with the prognosis of the patients with HCC both in the TCGA cohort and the Gene Expression Omnibus (GEO) datasets. Moreover, we discovered that the degree of the dissimilarity between tumors and normal tissues was correlated with the prognosis of patients with HCC and the biological behaviours of the tumors. These results will help identify prognostic biomarkers of patients with HCC, and enhance our understanding of the molecular mechanisms of hepatocarcinogenesis and progression.
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