1
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Yang Y, Li S, Luo L. Responses of organ precursors to correct and incorrect inductive signals. Trends Cell Biol 2024; 34:484-495. [PMID: 37739814 DOI: 10.1016/j.tcb.2023.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/14/2023] [Accepted: 08/31/2023] [Indexed: 09/24/2023]
Abstract
During embryonic development, the inductive molecules produced by local origins normally arrive at their target tissues in a nondirectional, diffusion manner. The target organ precursor cells must correctly interpret these inductive signals to ensure proper specification/differentiation, which is dependent on two prerequisites: (i) obtaining cell-intrinsic competence; and (ii) receiving correct inductive signals while resisting incorrect ones. Gain of intrinsic competence could avoid a large number of misinductions because the incompetent cells are nonresponsive to inductive signals. However, in cases of different precursor cells with similar competence and located in close proximity, resistance to incorrect inductive signals is essential for accurate determination of cell fate. Here we outline the mechanisms of how organ precursors respond to correct and incorrect inductive signals.
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Affiliation(s)
- Yun Yang
- Institute of Development Biology and Regenerative Medicine, Southwest University, Chongqing, China
| | - Shuang Li
- Institute of Development Biology and Regenerative Medicine, Southwest University, Chongqing, China
| | - Lingfei Luo
- Institute of Development Biology and Regenerative Medicine, Southwest University, Chongqing, China; School of Life Sciences, Fudan University, Shanghai, China.
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2
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Yang JC, Zhang YH, Hu B. Gastric organoids: Rise of a latecomer. WORLD CHINESE JOURNAL OF DIGESTOLOGY 2024; 32:182-191. [DOI: 10.11569/wcjd.v32.i3.182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/29/2024]
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3
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Guan X, Liang J, Xiang Y, Li T, Zhong X. BARX1 repressed FOXF1 expression and activated Wnt/β-catenin signaling pathway to drive lung adenocarcinoma. Int J Biol Macromol 2024; 261:129717. [PMID: 38290639 DOI: 10.1016/j.ijbiomac.2024.129717] [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: 09/25/2023] [Revised: 01/01/2024] [Accepted: 01/17/2024] [Indexed: 02/01/2024]
Abstract
BACKGROUND Underlying molecular mechanisms of BARX homeobox 1 (BARX1) in lung adenocarcinoma (LUAD) remain elusive. METHODS Abnormally expressed genes in LUAD tissues were analyzed by RNA-sequencing. CCK-8, colony formation, transwell, and wound healing assays examined proliferation, colony formation, invasion, and migration of LUAD cells, respectively. Electrophoretic mobility shift assay and chromatin immunoprecipitation assay examined the interaction between BARX1 and Forkhead Box F1 (FOXF1). Xenograft mouse model of LUAD was constructed to monitor the growth and metastasis of tumor. RESULTS BARX1 was upregulated, FOXF1 was downregulated in LUAD tissues and cells. There was a negative correlation between BARX1 and FOXF1 expression. BARX1 deficiency limited malignant phenotypes of LUAD cells, including proliferation, invasion, migration and EMT. In vivo, BARX1 knockdown suppressed tumor growth and metastasis in A549-drove xenograft mouse model. BARX1 interacted with FOXF1 promoter and repressed FOXF1 expression. Upregulation of BARX1 promoted the expression of Wnt5a, β-catenin, and phosphorylated-glycogen synthase kinase-3 beta (p-GSK3β), whereas inhibited FOXF1, p-β-catenin, and GSK3β in LUAD cells. BARX1 knockdown caused an opposite result. Rescue assays uncovered that FOXF1 reversed the impact of BARX1 on malignant phenotypes and Wnt/β-catenin of LUAD cells. CONCLUSION BARX1 repressed FOXF1 expression and activated Wnt/β-catenin signaling pathway to drive lung adenocarcinoma.
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Affiliation(s)
- Xiaojiao Guan
- Department of Pathology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Jie Liang
- Department of Thoracic Surgery, The First Hospital of China Medical University, Shenyang 110001, China
| | - Yifan Xiang
- Department of Thoracic Surgery, The First Hospital of China Medical University, Shenyang 110001, China
| | - Tian Li
- School of Basic Medicine, Fourth Military Medical University, Xi'an 710032, China.
| | - Xinwen Zhong
- Department of Thoracic Surgery, The First Hospital of China Medical University, Shenyang 110001, China.
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4
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Contreras-Panta EW, Choi E, Goldenring JR. The Fibroblast Landscape in Stomach Carcinogenesis. Cell Mol Gastroenterol Hepatol 2024; 17:671-678. [PMID: 38342299 PMCID: PMC10957461 DOI: 10.1016/j.jcmgh.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/13/2024]
Abstract
Numerous recent studies using single cell RNA sequencing and spatial transcriptomics have shown the vast cell heterogeneity, including epithelial, immune, and stromal cells, present in the normal human stomach and at different stages of gastric carcinogenesis. Fibroblasts within the metaplastic and dysplastic mucosal stroma represent key contributors to the carcinogenic microenvironment in the stomach. The heterogeneity of fibroblast populations is present in the normal stomach, but plasticity within these populations underlies their alterations in association with both metaplasia and dysplasia. In this review, we summarize and discuss efforts over the past several years to study the fibroblast components in human stomach from normal to metaplasia, dysplasia, and cancer. In the stomach, myofibroblast populations increase during late phase carcinogenesis and are a source of matrix proteins. PDGFRA-expressing telocyte-like cells are present in normal stomach and expand during metaplasia and dysplasia in close proximity with epithelial lineages, likely providing support for both normal and metaplastic progenitor niches. The alterations in fibroblast transcriptional signatures across the stomach carcinogenesis process indicate that fibroblast populations are likely as plastic as epithelial populations during the evolution of carcinogenesis.
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Affiliation(s)
- Ela W Contreras-Panta
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee; Section of Surgical Sciences, Vanderbilt University Medical Center, Nashville, Tennessee; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Eunyoung Choi
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee; Section of Surgical Sciences, Vanderbilt University Medical Center, Nashville, Tennessee; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - James R Goldenring
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee; Section of Surgical Sciences, Vanderbilt University Medical Center, Nashville, Tennessee; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee; Nashville VA Medical Center, Nashville, Tennessee.
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5
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Tsubosaka A, Komura D, Kakiuchi M, Katoh H, Onoyama T, Yamamoto A, Abe H, Seto Y, Ushiku T, Ishikawa S. Stomach encyclopedia: Combined single-cell and spatial transcriptomics reveal cell diversity and homeostatic regulation of human stomach. Cell Rep 2023; 42:113236. [PMID: 37819756 DOI: 10.1016/j.celrep.2023.113236] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/05/2023] [Accepted: 09/24/2023] [Indexed: 10/13/2023] Open
Abstract
The stomach is an important digestive organ with various biological functions. However, because of the complexity of its cellular and glandular composition, its precise cellular biology has yet to be elucidated. In this study, we conducted single-cell RNA sequencing (scRNA-seq) and subcellular-level spatial transcriptomics analysis of the human stomach and constructed the largest dataset to date: a stomach encyclopedia. This dataset consists of approximately 380,000 cells from scRNA-seq and the spatial transcriptome, enabling integrated analyses of transcriptional and spatial information of gastric and metaplastic cells. This analysis identified LEFTY1 as an uncharacterized stem cell marker, which was confirmed through lineage tracing analysis. A wide variety of cell-cell interactions between epithelial and stromal cells, including PDGFRA+BMP4+WNT5A+ fibroblasts, was highlighted in the developmental switch of intestinal metaplasia. Our extensive dataset will function as a fundamental resource in investigations of the stomach, including studies of development, aging, and carcinogenesis.
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Affiliation(s)
- Ayumu Tsubosaka
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku 1130033, Tokyo, Japan
| | - Daisuke Komura
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku 1130033, Tokyo, Japan
| | - Miwako Kakiuchi
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku 1130033, Tokyo, Japan
| | - Hiroto Katoh
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku 1130033, Tokyo, Japan
| | - Takumi Onoyama
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku 1130033, Tokyo, Japan; Division of Gastroenterology and Nephrology, Department of Multidisciplinary Internal Medicine, School of Medicine, Faculty of Medicine, Tottori University, 36-1, Nishicho, Yonago 683-8504, Tottori, Japan
| | - Asami Yamamoto
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku 1130033, Tokyo, Japan
| | - Hiroyuki Abe
- Dpartment of Pathology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku 1130033, Tokyo, Japan
| | - Yasuyuki Seto
- Department of Gastrointestinal Surgery, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-kyu 1130033, Tokyo, Japan
| | - Tetsuo Ushiku
- Dpartment of Pathology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku 1130033, Tokyo, Japan
| | - Shumpei Ishikawa
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku 1130033, Tokyo, Japan; Division of Pathology, National Cancer Center Exploratory Oncology Research & Clinical Trial Center, 6-5-1, Kashiwanoha, Kashiwa 277-8577, Chiba, Japan.
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6
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Alvina FB, Chen TCY, Lim HYG, Barker N. Gastric epithelial stem cells in development, homeostasis and regeneration. Development 2023; 150:dev201494. [PMID: 37746871 DOI: 10.1242/dev.201494] [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: 09/26/2023]
Abstract
The stem/progenitor cell pool is indispensable for the development, homeostasis and regeneration of the gastric epithelium, owing to its defining ability to self-renew whilst supplying the various functional epithelial lineages needed to digest food efficiently. A detailed understanding of the intricacies and complexities surrounding the behaviours and roles of these stem cells offers insights, not only into the physiology of gastric epithelial development and maintenance, but also into the pathological consequences following aberrations in stem cell regulation. Here, we provide an insightful synthesis of the existing knowledge on gastric epithelial stem cell biology, including the in vitro and in vivo experimental techniques that have advanced such studies. We highlight the contributions of stem/progenitor cells towards patterning the developing stomach, specification of the differentiated cell lineages and maintenance of the mature epithelium during homeostasis and following injury. Finally, we discuss gaps in our understanding and identify key research areas for future work.
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Affiliation(s)
- Fidelia B Alvina
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore
| | - Tanysha Chi-Ying Chen
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore
| | - Hui Yi Grace Lim
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore
| | - Nick Barker
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117593, Republic of Singapore
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7
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Jeong YS, Eun YG, Lee SH, Kang SH, Yim SY, Kim EH, Noh JK, Sohn BH, Woo SR, Kong M, Nam DH, Jang HJ, Lee HS, Song S, Oh SC, Lee J, Ajani JA, Lee JS. Clinically conserved genomic subtypes of gastric adenocarcinoma. Mol Cancer 2023; 22:147. [PMID: 37674200 PMCID: PMC10481468 DOI: 10.1186/s12943-023-01796-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 05/31/2023] [Indexed: 09/08/2023] Open
Abstract
Gastric adenocarcinoma (GAC) is a lethal disease characterized by genomic and clinical heterogeneity. By integrating 8 previously established genomic signatures for GAC subtypes, we identified 6 clinically and molecularly distinct genomic consensus subtypes (CGSs). CGS1 have the poorest prognosis, very high stem cell characteristics, and high IGF1 expression, but low genomic alterations. CGS2 is enriched with canonical epithelial gene expression. CGS3 and CGS4 have high copy number alterations and low immune reactivity. However, CGS3 and CGS4 differ in that CGS3 has high HER2 activation, while CGS4 has high SALL4 and KRAS activation. CGS5 has the high mutation burden and moderately high immune reactivity that are characteristic of microsatellite instable tumors. Most CGS6 tumors are positive for Epstein Barr virus and show extremely high levels of methylation and high immune reactivity. In a systematic analysis of genomic and proteomic data, we estimated the potential response rate of each consensus subtype to standard and experimental treatments such as radiation therapy, targeted therapy, and immunotherapy. Interestingly, CGS3 was significantly associated with a benefit from chemoradiation therapy owing to its high basal level of ferroptosis. In addition, we also identified potential therapeutic targets for each consensus subtype. Thus, the consensus subtypes produced a robust classification and provide for additional characterizations for subtype-based customized interventions.
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Affiliation(s)
- Yun Seong Jeong
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Unit 1058, Houston, TX, 77030, USA
| | - Young-Gyu Eun
- Department of Biomedical Science and Technology, Graduate School, Kyung Hee University, Seoul, Korea
- Department of Otolaryngology - Head and Neck Surgery, Kyung Hee University Medical Center, Kyung Hee University School of Medicine, Seoul, Korea
| | - Sung Hwan Lee
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Yonsei University College of Medicine, Seoul, Korea
- Division of Hepatobiliary and Pancreas, Department of Surgery, CHA Bundang Medical Center, CHA University, Pocheon, Korea
| | - Sang-Hee Kang
- Department of Surgery, Korea University Guro Hospital, Seoul, Korea
| | - Sun Young Yim
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - Eui Hyun Kim
- Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Korea
| | - Joo Kyung Noh
- Department of Biomedical Science and Technology, Graduate School, Kyung Hee University, Seoul, Korea
| | - Bo Hwa Sohn
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Unit 1058, Houston, TX, 77030, USA
| | - Seon Rang Woo
- Department of Otolaryngology - Head and Neck Surgery, Kyung Hee University Medical Center, Kyung Hee University School of Medicine, Seoul, Korea
| | - Moonkyoo Kong
- Department of Radiation Oncology, Kyung Hee University Medical Center, Kyung Hee University School of Medicine, Seoul, Korea
| | - Deok Hwa Nam
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Unit 1058, Houston, TX, 77030, USA
| | - Hee-Jin Jang
- Systems Onco-Immunology Laboratory, David J. Sugarbaker Division of Thoracic Surgery, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX, USA
| | - Hyun-Sung Lee
- Systems Onco-Immunology Laboratory, David J. Sugarbaker Division of Thoracic Surgery, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX, USA
| | - Shumei Song
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sang Cheul Oh
- Division of Oncology/Hematology, Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - Jeeyun Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jaffer A Ajani
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ju-Seog Lee
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Unit 1058, Houston, TX, 77030, USA.
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8
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Yadav US, Biswas T, Singh PN, Gupta P, Chakraborty S, Delgado I, Zafar H, Capellini TD, Torres M, Bandyopadhyay A. Molecular mechanism of synovial joint site specification and induction in developing vertebrate limbs. Development 2023; 150:dev201335. [PMID: 37272420 PMCID: PMC10323242 DOI: 10.1242/dev.201335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 05/25/2023] [Indexed: 06/06/2023]
Abstract
The vertebrate appendage comprises three primary segments, the stylopod, zeugopod and autopod, each separated by joints. The molecular mechanisms governing the specification of joint sites, which define segment lengths and thereby limb architecture, remain largely unknown. Existing literature suggests that reciprocal gradients of retinoic acid (RA) and fibroblast growth factor (FGF) signaling define the expression domains of the putative segment markers Meis1, Hoxa11 and Hoxa13. Barx1 is expressed in the presumptive joint sites. Our data demonstrate that RA-FGF signaling gradients define the expression domain of Barx1 in the first presumptive joint site. When misexpressed, Barx1 induces ectopic interzone-like structures, and its loss of function partially blocks interzone development. Simultaneous perturbations of RA-FGF signaling gradients result in predictable shifts of Barx1 expression domains along the proximo-distal axis and, consequently, in the formation of repositioned joints. Our data suggest that during early limb bud development in chick, Meis1 and Hoxa11 expression domains are overlapping, whereas the Barx1 expression domain resides within the Hoxa11 expression domain. However, once the interzone is formed, the expression domains are refined and the Barx1 expression domain becomes congruent with the border of these two putative segment markers.
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Affiliation(s)
- Upendra S. Yadav
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
- The Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Tathagata Biswas
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
- The Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Pratik N. Singh
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
- The Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Pankaj Gupta
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
- The Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Soura Chakraborty
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Irene Delgado
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares, CNIC, 28029 Madrid, Spain
| | - Hamim Zafar
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
- The Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
- Department of Computer Science and Engineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Terence D. Capellini
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA
| | - Miguel Torres
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares, CNIC, 28029 Madrid, Spain
| | - Amitabha Bandyopadhyay
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
- The Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
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9
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Huang X, Wang Z, Zhang J, Ni X, Bai G, Cao J, Zhang C, Han Z, Liu T. BARX1 promotes osteosarcoma cell proliferation and invasion by regulating HSPA6 expression. J Orthop Surg Res 2023; 18:211. [PMID: 36927457 PMCID: PMC10018937 DOI: 10.1186/s13018-023-03690-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/08/2023] [Indexed: 03/18/2023] Open
Abstract
Osteosarcoma (OS) is a bone tumour affecting adolescents. Dysregulation of Barx homeobox 1 (BARX1) expression is involved in various cancers, but its function and mechanism in the process of OS are undefined. This study revealed that BARX1 expression is higher in OS tissue than in adjacent normal tissue. Downregulation of BARX1 in OS cells significantly suppressed their proliferation and migration, whereas enforced expression of exogenous BARX1 exerted the opposite effects on OS cells. Subsequently, heat shock 70-kDa protein 6 (HSPA6) expression was clearly increased after BARX1 overexpression in OS cells, as confirmed by RNA sequencing. The dual-luciferase reporter assay confirmed that HSPA6 expression is directly regulated by BARX1. The in vitro assay indicated that silencing HSPA6 expression attenuated OS proliferation and migration induced by BARX1. A dual immunofluorescence labelling assay provided further evidence that BARX1 was overexpressed and associated with HSPA6 overexpression in OS tumour tissue. In conclusion, BARX1 promotes OS cell proliferation and migration by inducing the expression of HSPA6, which plays an oncogenic role in OS. BARX1 and HSPA6 can potentially act as novel therapeutic targets for OS.
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Affiliation(s)
- Xing Huang
- Department of Orthopaedic Oncology, The Second Affiliated Hospital of Naval Medical University, No. 415 Fengyang Road, Huangpu District, Shanghai, 200003, China
| | - Zhenhua Wang
- Department of Laboratory Medicine, Changzheng Hospital, Naval Medical University, No. 415 Fengyang Road, Huangpu District, Shanghai, 200003, China
| | - Jing Zhang
- Department of Orthopaedic Oncology, The Second Affiliated Hospital of Naval Medical University, No. 415 Fengyang Road, Huangpu District, Shanghai, 200003, China
| | - Xiangzhi Ni
- Department of Orthopaedic Oncology, The Second Affiliated Hospital of Naval Medical University, No. 415 Fengyang Road, Huangpu District, Shanghai, 200003, China
| | - Guangjian Bai
- Department of Orthopaedic Oncology, The Second Affiliated Hospital of Naval Medical University, No. 415 Fengyang Road, Huangpu District, Shanghai, 200003, China
| | - Jiashi Cao
- Department of Orthopedics, No. 455 Hospital of Chinese People's Liberation Army, The Navy Medical University, No. 338 Huaihai West Road, Shanghai, 200052, China
| | - Chunlei Zhang
- Department of Orthopedics, Nanjing Hospital of Traditional Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, China.
| | - Zhitao Han
- School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Tielong Liu
- Department of Orthopaedic Oncology, The Second Affiliated Hospital of Naval Medical University, No. 415 Fengyang Road, Huangpu District, Shanghai, 200003, China.
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10
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Smith RJ, Liang M, Loe AKH, Yung T, Kim JE, Hudson M, Wilson MD, Kim TH. Epigenetic control of cellular crosstalk defines gastrointestinal organ fate and function. Nat Commun 2023; 14:497. [PMID: 36717563 PMCID: PMC9887003 DOI: 10.1038/s41467-023-36228-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 01/20/2023] [Indexed: 02/01/2023] Open
Abstract
Epithelial-mesenchymal signaling in the gastrointestinal system is vital in establishing regional identity during organogenesis and maintaining adult stem cell homeostasis. Although recent work has demonstrated that Wnt ligands expressed by mesenchymal cells are required during gastrointestinal development and stem cell homeostasis, epigenetic mechanisms driving spatiotemporal control of crosstalk remain unknown. Here, we demonstrate that gastrointestinal mesenchymal cells control epithelial fate and function through Polycomb Repressive Complex 2-mediated chromatin bivalency. We find that while key lineage-determining genes possess tissue-specific chromatin accessibility, Polycomb Repressive Complex 2 controls Wnt expression in mesenchymal cells without altering accessibility. We show that reduction of mesenchymal Wnt secretion rescues gastrointestinal fate and proliferation defects caused by Polycomb Repressive Complex 2 loss. We demonstrate that mesenchymal Polycomb Repressive Complex 2 also regulates niche signals to maintain stem cell function in the adult intestine. Our results highlight a broadly permissive chromatin architecture underlying regionalization in mesenchymal cells, then demonstrate further how chromatin architecture in niches can influence the fate and function of neighboring cells.
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Affiliation(s)
- Ryan J Smith
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Minggao Liang
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Adrian Kwan Ho Loe
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Theodora Yung
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Ji-Eun Kim
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Matthew Hudson
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Michael D Wilson
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Tae-Hee Kim
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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11
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Stromal regulation of the intestinal barrier. Mucosal Immunol 2023; 16:221-231. [PMID: 36708806 DOI: 10.1016/j.mucimm.2023.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/27/2022] [Accepted: 01/12/2023] [Indexed: 01/26/2023]
Abstract
The intestinal barrier is a complex structure that allows the absorption of nutrients while ensuring protection against intestinal pathogens and balanced immunity. The development and maintenance of a functional intestinal barrier is a multifactorial process that is only partially understood. Here we review novel findings on the emerging role of mesenchymal cells in this process using insights gained from lineage tracing approaches, Cre-based gene deletion, and single-cell transcriptomics. The current evidence points toward a key organizer role for distinct mesenchymal lineages in intestinal development and homeostasis, regulating both epithelial and immune components of the intestinal barrier. We further discuss recent findings on functional mesenchymal heterogeneity and implications for intestinal regeneration and inflammatory intestinal pathologies.
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12
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Swoboda J, Mittelsdorf P, Chen Y, Weiskirchen R, Stallhofer J, Schüle S, Gassler N. Intestinal Wnt in the transition from physiology to oncology. World J Clin Oncol 2022; 13:168-185. [PMID: 35433295 PMCID: PMC8966512 DOI: 10.5306/wjco.v13.i3.168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 09/07/2021] [Accepted: 02/20/2022] [Indexed: 02/06/2023] Open
Abstract
Adult stem cells are necessary for self-renewal tissues and regeneration after damage. Especially in the intestine, which self-renews every few days, they play a key role in tissue homeostasis. Therefore, complex regulatory mechanisms are needed to prevent hyperproliferation, which can lead in the worst case to carcinogenesis or under-activation of stem cells, which can result in dysfunctional epithelial. One main regulatory signaling pathway is the Wnt/β-catenin signaling pathway. It is a highly conserved pathway, with β-catenin, a transcription factor, as target protein. Translocation of β-catenin from cytoplasm to nucleus activates the transcription of numerous genes involved in regulating stem cell pluripo-tency, proliferation, cell differentiation and regulation of cell death. This review presents a brief overview of the Wnt/β-catenin signaling pathway, the regulatory mechanism of this pathway and its role in intestinal homeostasis. Additionally, this review highlights the molecular mechanisms and the histomorphological features of Wnt hyperactivation. Furthermore, the central role of the Wnt signaling pathway in intestinal carcinogenesis as well as its clinical relevance in colorectal carcinoma are discussed.
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Affiliation(s)
- Julia Swoboda
- Section Pathology, Institute of Forensic Medicine, Jena University Hospital, Jena 07747, Germany
| | - Patrick Mittelsdorf
- Section Pathology, Institute of Forensic Medicine, Jena University Hospital, Jena 07747, Germany
| | - Yuan Chen
- Section Pathology, Institute of Forensic Medicine, Jena University Hospital, Jena 07747, Germany
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry, RWTH University Hospital Aachen, Aachen 52074, Germany
| | - Johannes Stallhofer
- Department of Internal Medicine IV (Gastroenterology, Hepatology, and Infectious Diseases), Jena University Hospital, Jena 07747, Germany
| | - Silke Schüle
- Department of General, Visceral and Vascular Surgery, Jena University Hospital, Jena 07747, Germany
| | - Nikolaus Gassler
- Section Pathology, Institute of Forensic Medicine, Jena University Hospital, Jena 07747, Germany
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13
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Ventx Family and Its Functional Similarities with Nanog: Involvement in Embryonic Development and Cancer Progression. Int J Mol Sci 2022; 23:ijms23052741. [PMID: 35269883 PMCID: PMC8911082 DOI: 10.3390/ijms23052741] [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: 12/28/2021] [Revised: 02/21/2022] [Accepted: 02/27/2022] [Indexed: 12/27/2022] Open
Abstract
The Ventx family is one of the subfamilies of the ANTP (antennapedia) superfamily and belongs to the NK-like (NKL) subclass. Ventx is a homeobox transcription factor and has a DNA-interacting domain that is evolutionarily conserved throughout vertebrates. It has been extensively studied in Xenopus, zebrafish, and humans. The Ventx family contains transcriptional repressors widely involved in embryonic development and tumorigenesis in vertebrates. Several studies have documented that the Ventx family inhibited dorsal mesodermal formation, neural induction, and head formation in Xenopus and zebrafish. Moreover, Ventx2.2 showed functional similarities to Nanog and Barx1, leading to pluripotency and neural-crest migration in vertebrates. Among them, Ventx protein is an orthologue of the Ventx family in humans. Studies have demonstrated that human Ventx was strongly associated with myeloid-cell differentiation and acute myeloid leukemia. The therapeutic potential of Ventx family inhibition in combating cancer progression in humans is discussed. Additionally, we briefly discuss genome evolution, gene duplication, pseudo-allotetraploidy, and the homeobox family in Xenopus.
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14
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Eicher AK, Kechele DO, Sundaram N, Berns HM, Poling HM, Haines LE, Sanchez JG, Kishimoto K, Krishnamurthy M, Han L, Zorn AM, Helmrath MA, Wells JM. Functional human gastrointestinal organoids can be engineered from three primary germ layers derived separately from pluripotent stem cells. Cell Stem Cell 2022; 29:36-51.e6. [PMID: 34856121 PMCID: PMC8741755 DOI: 10.1016/j.stem.2021.10.010] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/22/2021] [Accepted: 10/20/2021] [Indexed: 02/08/2023]
Abstract
Human organoid model systems lack important cell types that, in the embryo, are incorporated into organ tissues during development. We developed an organoid assembly approach starting with cells from the three primary germ layers-enteric neuroglial, mesenchymal, and epithelial precursors-that were derived separately from human pluripotent stem cells (PSCs). From these three cell types, we generated human antral and fundic gastric tissue containing differentiated glands surrounded by layers of smooth muscle containing functional enteric neurons that controlled contractions of the engineered antral tissue. Using this experimental system, we show that human enteric neural crest cells (ENCCs) promote mesenchyme development and glandular morphogenesis of antral stomach organoids. Moreover, ENCCs can act directly on the foregut to promote a posterior fate, resulting in organoids with a Brunner's gland phenotype. Thus, germ layer components that are derived separately from PSCs can be used for tissue engineering to generate complex human organoids.
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Affiliation(s)
- Alexandra K. Eicher
- College of Medicine, University of Cincinnati, Cincinnati, OH, 45267, USA,Center for Stem Cell and Organoid Medicine (CuSTOM),Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center (CCHMC), Cincinnati, OH, 45229, USA
| | - Daniel O. Kechele
- Center for Stem Cell and Organoid Medicine (CuSTOM),Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center (CCHMC), Cincinnati, OH, 45229, USA
| | - Nambirajan Sundaram
- Center for Stem Cell and Organoid Medicine (CuSTOM),Division of Pediatric General and Thoracic Surgery, Cincinnati Children’s Hospital Medical Center (CCHMC), Cincinnati, OH, 45229, USA
| | - H. Matthew Berns
- Center for Stem Cell and Organoid Medicine (CuSTOM),Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center (CCHMC), Cincinnati, OH, 45229, USA
| | - Holly M. Poling
- Center for Stem Cell and Organoid Medicine (CuSTOM),Division of Pediatric General and Thoracic Surgery, Cincinnati Children’s Hospital Medical Center (CCHMC), Cincinnati, OH, 45229, USA
| | - Lauren E. Haines
- Center for Stem Cell and Organoid Medicine (CuSTOM),Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center (CCHMC), Cincinnati, OH, 45229, USA
| | - J. Guillermo Sanchez
- College of Medicine, University of Cincinnati, Cincinnati, OH, 45267, USA,Center for Stem Cell and Organoid Medicine (CuSTOM),Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center (CCHMC), Cincinnati, OH, 45229, USA
| | - Keishi Kishimoto
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center (CCHMC), Cincinnati, OH, 45229, USA,CuSTOM-RIKEN BDR Collaborative Laboratory, CCHMC, Cincinnati, OH, 45229, USA,Laboratory for Lung Development, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, 650-0047, Japan
| | - Mansa Krishnamurthy
- Center for Stem Cell and Organoid Medicine (CuSTOM),Division of Endocrinology, Cincinnati Children’s Hospital Medical Center (CCHMC), Cincinnati, OH, 45229, USA
| | - Lu Han
- Center for Stem Cell and Organoid Medicine (CuSTOM),Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center (CCHMC), Cincinnati, OH, 45229, USA
| | - Aaron M. Zorn
- Center for Stem Cell and Organoid Medicine (CuSTOM),Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center (CCHMC), Cincinnati, OH, 45229, USA
| | - Michael A. Helmrath
- Center for Stem Cell and Organoid Medicine (CuSTOM),Division of Pediatric General and Thoracic Surgery, Cincinnati Children’s Hospital Medical Center (CCHMC), Cincinnati, OH, 45229, USA
| | - James M. Wells
- Center for Stem Cell and Organoid Medicine (CuSTOM),Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center (CCHMC), Cincinnati, OH, 45229, USA,Division of Endocrinology, Cincinnati Children’s Hospital Medical Center (CCHMC), Cincinnati, OH, 45229, USA,Lead Contact and Corresponding Author,Corresponding Author’s:
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15
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Brosens E, Brouwer RWW, Douben H, van Bever Y, Brooks AS, Wijnen RMH, van IJcken WFJ, Tibboel D, Rottier RJ, de Klein A. Heritability and De Novo Mutations in Oesophageal Atresia and Tracheoesophageal Fistula Aetiology. Genes (Basel) 2021; 12:genes12101595. [PMID: 34680991 PMCID: PMC8535313 DOI: 10.3390/genes12101595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/03/2021] [Accepted: 10/05/2021] [Indexed: 01/12/2023] Open
Abstract
Tracheoesophageal Fistula (TOF) is a congenital anomaly for which the cause is unknown in the majority of patients. OA/TOF is a variable feature in many (often mono-) genetic syndromes. Research using animal models targeting genes involved in candidate pathways often result in tracheoesophageal phenotypes. However, there is limited overlap in the genes implicated by animal models and those found in OA/TOF-related syndromic anomalies. Knowledge on affected pathways in animal models is accumulating, but our understanding on these pathways in patients lags behind. If an affected pathway is associated with both animals and patients, the mechanisms linking the genetic mutation, affected cell types or cellular defect, and the phenotype are often not well understood. The locus heterogeneity and the uncertainty of the exact heritability of OA/TOF results in a relative low diagnostic yield. OA/TOF is a sporadic finding with a low familial recurrence rate. As parents are usually unaffected, de novo dominant mutations seems to be a plausible explanation. The survival rates of patients born with OA/TOF have increased substantially and these patients start families; thus, the detection and a proper interpretation of these dominant inherited pathogenic variants are of great importance for these patients and for our understanding of OA/TOF aetiology.
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Affiliation(s)
- Erwin Brosens
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (H.D.); (Y.v.B.); (A.S.B.); (A.d.K.)
- Correspondence:
| | - Rutger W. W. Brouwer
- Department of Cell Biology, Center for Biomics, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (R.W.W.B.); (W.F.J.v.I.)
| | - Hannie Douben
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (H.D.); (Y.v.B.); (A.S.B.); (A.d.K.)
| | - Yolande van Bever
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (H.D.); (Y.v.B.); (A.S.B.); (A.d.K.)
| | - Alice S. Brooks
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (H.D.); (Y.v.B.); (A.S.B.); (A.d.K.)
| | - Rene M. H. Wijnen
- Department of Pediatric Surgery, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (R.M.H.W.); (D.T.)
| | - Wilfred F. J. van IJcken
- Department of Cell Biology, Center for Biomics, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (R.W.W.B.); (W.F.J.v.I.)
| | - Dick Tibboel
- Department of Pediatric Surgery, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (R.M.H.W.); (D.T.)
| | - Robbert J. Rottier
- Departments of Pediatric Surgery & Cell Biology, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (H.D.); (Y.v.B.); (A.S.B.); (A.d.K.)
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16
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Dakhel S, Davies WIL, Joseph JV, Tomar T, Remeseiro S, Gunhaga L. Chick fetal organ spheroids as a model to study development and disease. BMC Mol Cell Biol 2021; 22:37. [PMID: 34225662 PMCID: PMC8256237 DOI: 10.1186/s12860-021-00374-6] [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: 01/20/2021] [Accepted: 06/08/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Organ culture models have been used over the past few decades to study development and disease. The in vitro three-dimensional (3D) culture system of organoids is well known, however, these 3D systems are both costly and difficult to culture and maintain. As such, less expensive, faster and less complex methods to maintain 3D cell culture models would complement the use of organoids. Chick embryos have been used as a model to study human biology for centuries, with many fundamental discoveries as a result. These include cell type induction, cell competence, plasticity and contact inhibition, which indicates the relevance of using chick embryos when studying developmental biology and disease mechanisms. RESULTS Here, we present an updated protocol that enables time efficient, cost effective and long-term expansion of fetal organ spheroids (FOSs) from chick embryos. Utilizing this protocol, we generated FOSs in an anchorage-independent growth pattern from seven different organs, including brain, lung, heart, liver, stomach, intestine and epidermis. These three-dimensional (3D) structures recapitulate many cellular and structural aspects of their in vivo counterpart organs and serve as a useful developmental model. In addition, we show a functional application of FOSs to analyze cell-cell interaction and cell invasion patterns as observed in cancer. CONCLUSION The establishment of a broad ranging and highly effective method to generate FOSs from different organs was successful in terms of the formation of healthy, proliferating 3D organ spheroids that exhibited organ-like characteristics. Potential applications of chick FOSs are their use in studies of cell-to-cell contact, cell fusion and tumor invasion under defined conditions. Future studies will reveal whether chick FOSs also can be applicable in scientific areas such as viral infections, drug screening, cancer diagnostics and/or tissue engineering.
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Affiliation(s)
- Soran Dakhel
- Umeå Centre for Molecular Medicine, Umeå University, 901 87, Umeå, Sweden.,Wallenberg Centre for Molecular Medicine, Umeå University, 901 87, Umeå, Sweden
| | - Wayne I L Davies
- Umeå Centre for Molecular Medicine, Umeå University, 901 87, Umeå, Sweden
| | - Justin V Joseph
- Umeå Centre for Molecular Medicine, Umeå University, 901 87, Umeå, Sweden
| | - Tushar Tomar
- PamGene International B.V, Wolvenhoek 10, 5211 HH, 's-Hertogenbosch, The Netherlands
| | - Silvia Remeseiro
- Umeå Centre for Molecular Medicine, Umeå University, 901 87, Umeå, Sweden.,Wallenberg Centre for Molecular Medicine, Umeå University, 901 87, Umeå, Sweden
| | - Lena Gunhaga
- Umeå Centre for Molecular Medicine, Umeå University, 901 87, Umeå, Sweden.
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17
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Jiang T, Li Y, Motsinger-Reif AA. Knockoff boosted tree for model-free variable selection. Bioinformatics 2021; 37:976-983. [PMID: 32966559 DOI: 10.1093/bioinformatics/btaa770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 08/17/2020] [Accepted: 09/09/2020] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION The recently proposed knockoff filter is a general framework for controlling the false discovery rate (FDR) when performing variable selection. This powerful new approach generates a 'knockoff' of each variable tested for exact FDR control. Imitation variables that mimic the correlation structure found within the original variables serve as negative controls for statistical inference. Current applications of knockoff methods use linear regression models and conduct variable selection only for variables existing in model functions. Here, we extend the use of knockoffs for machine learning with boosted trees, which are successful and widely used in problems where no prior knowledge of model function is required. However, currently available importance scores in tree models are insufficient for variable selection with FDR control. RESULTS We propose a novel strategy for conducting variable selection without prior model topology knowledge using the knockoff method with boosted tree models. We extend the current knockoff method to model-free variable selection through the use of tree-based models. Additionally, we propose and evaluate two new sampling methods for generating knockoffs, namely the sparse covariance and principal component knockoff methods. We test and compare these methods with the original knockoff method regarding their ability to control type I errors and power. In simulation tests, we compare the properties and performance of importance test statistics of tree models. The results include different combinations of knockoffs and importance test statistics. We consider scenarios that include main-effect, interaction, exponential and second-order models while assuming the true model structures are unknown. We apply our algorithm for tumor purity estimation and tumor classification using Cancer Genome Atlas (TCGA) gene expression data. Our results show improved discrimination between difficult-to-discriminate cancer types. AVAILABILITY AND IMPLEMENTATION The proposed algorithm is included in the KOBT package, which is available at https://cran.r-project.org/web/packages/KOBT/index.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Tao Jiang
- Department of Statistics, Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA
| | - Yuanyuan Li
- Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC 27709, USA
| | - Alison A Motsinger-Reif
- Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC 27709, USA
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18
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Sun G, Ge Y, Zhang Y, Yan L, Wu X, Ouyang W, Wang Z, Ding B, Zhang Y, Long G, Liu M, Shi R, Zhou H, Chen Z, Ye Z. Transcription Factors BARX1 and DLX4 Contribute to Progression of Clear Cell Renal Cell Carcinoma via Promoting Proliferation and Epithelial-Mesenchymal Transition. Front Mol Biosci 2021; 8:626328. [PMID: 34124141 PMCID: PMC8188704 DOI: 10.3389/fmolb.2021.626328] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 05/06/2021] [Indexed: 11/29/2022] Open
Abstract
Dysregulation of transcription factors contributes to the carcinogenesis and progression of cancers. However, their roles in clear cell renal cell carcinoma remain largely unknown. This study aimed to evaluate the clinical significance of TFs and investigate their potential molecular mechanisms in ccRCC. Data were accessed from the cancer genome atlas kidney clear cell carcinoma cohort. Bioinformatics algorithm was used in copy number alterations mutations, and differentially expressed TFs’ analysis. Univariate and multivariate Cox regression analyses were performed to identify clinically significant TFs and construct a six-TF prognostic panel. TFs’ expression was validated in human tissues. Gene set enrichment analysis (GSEA) was utilized to find enriched cancer hallmark pathways. Functional experiments were conducted to verify the cancer-promoting effect of BARX homeobox 1 (BARX1) and distal-less homeobox 4 (DLX4) in ccRCC, and Western blot was performed to explore their downstream pathways. As for results, many CNAs and mutations were identified in transcription factor genes. TFs were differentially expressed in ccRCC. An applicable predictive panel of six-TF genes was constructed to predict the overall survival for ccRCC patients, and its diagnostic efficiency was evaluated by the area under the curve (AUC). BARX1 and DLX4 were associated with poor prognosis, and they could promote the proliferation and migration of ccRCC. In conclusion, the six-TF panel can be used as a prognostic biomarker for ccRCC patients. BARX1 and DLX4 play oncogenic roles in ccRCC via promoting proliferation and epithelial–mesenchymal transition. They have the potential to be novel therapeutic targets for ccRCC.
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Affiliation(s)
- Guoliang Sun
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Institute of Urology, Wuhan, China.,Department of Urology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yue Ge
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Institute of Urology, Wuhan, China
| | - Yangjun Zhang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Institute of Urology, Wuhan, China
| | - Libin Yan
- Department of Urology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaoliang Wu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Institute of Urology, Wuhan, China
| | - Wei Ouyang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Institute of Urology, Wuhan, China
| | - Zhize Wang
- Department of Urology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Beichen Ding
- Department of Urology, First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yucong Zhang
- Department of Geriatric, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Gongwei Long
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Institute of Urology, Wuhan, China
| | - Man Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Institute of Urology, Wuhan, China
| | - Runlin Shi
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Zhou
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Institute of Urology, Wuhan, China
| | - Zhiqiang Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Institute of Urology, Wuhan, China
| | - Zhangqun Ye
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Institute of Urology, Wuhan, China
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19
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Sankoda N, Tanabe W, Tanaka A, Shibata H, Woltjen K, Chiba T, Haga H, Sakai Y, Mandai M, Yamamoto T, Yamada Y, Uemoto S, Kawaguchi Y. Epithelial expression of Gata4 and Sox2 regulates specification of the squamous-columnar junction via MAPK/ERK signaling in mice. Nat Commun 2021; 12:560. [PMID: 33495473 PMCID: PMC7835245 DOI: 10.1038/s41467-021-20906-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 12/24/2020] [Indexed: 12/12/2022] Open
Abstract
The squamous-columnar junction (SCJ) is a boundary consisting of precisely positioned transitional epithelium between the squamous and columnar epithelium. Transitional epithelium is a hotspot for precancerous lesions, and is therefore clinically important; however, the origins and physiological properties of transitional epithelium have not been fully elucidated. Here, by using mouse genetics, lineage tracing, and organoid culture, we examine the development of the SCJ in the mouse stomach, and thus define the unique features of transitional epithelium. We find that two transcription factors, encoded by Sox2 and Gata4, specify primitive transitional epithelium into squamous and columnar epithelium. The proximal-distal segregation of Sox2 and Gata4 expression establishes the boundary of the unspecified transitional epithelium between committed squamous and columnar epithelium. Mechanistically, Gata4-mediated expression of the morphogen Fgf10 in the distal stomach and Sox2-mediated Fgfr2 expression in the proximal stomach induce the intermediate regional activation of MAPK/ERK, which prevents the differentiation of transitional epithelial cells within the SCJ boundary. Our results have implications for tissue regeneration and tumorigenesis, which are related to the SCJ.
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Affiliation(s)
- Nao Sankoda
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
- Department of Surgery, Kyoto University Graduate School of Medicine, Kyoto, 606-8507, Japan
- Division of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
| | - Wataru Tanabe
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
- Department of Gastroenterology, Kyoto University Graduate School of Medicine, Kyoto, 606-8507, Japan
| | - Akito Tanaka
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
| | - Hirofumi Shibata
- Department of Otolaryngology, Gifu University Graduate School of Medicine, Gifu, 501-1194, Japan
| | - Knut Woltjen
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, 606-8501, Japan
| | - Tsutomu Chiba
- Department of Gastroenterology, Kyoto University Graduate School of Medicine, Kyoto, 606-8507, Japan
| | - Hironori Haga
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, 606-8507, Japan
| | - Yoshiharu Sakai
- Department of Surgery, Kyoto University Graduate School of Medicine, Kyoto, 606-8507, Japan
| | - Masaki Mandai
- Department of Gynecology and Obstetrics, Kyoto University Hospital, Kyoto, 606-8507, Japan
| | - Takuya Yamamoto
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
- AMED-CREST, AMED 1-7-1 Otemachi, Chiyodaku, Tokyo, 100-0004, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
- Medical-risk Avoidance Based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto, 606-8507, Japan
| | - Yasuhiro Yamada
- Division of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
- AMED-CREST, AMED 1-7-1 Otemachi, Chiyodaku, Tokyo, 100-0004, Japan
| | - Shinji Uemoto
- Department of Surgery, Kyoto University Graduate School of Medicine, Kyoto, 606-8507, Japan
| | - Yoshiya Kawaguchi
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan.
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20
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Marderstein AR, Davenport ER, Kulm S, Van Hout CV, Elemento O, Clark AG. Leveraging phenotypic variability to identify genetic interactions in human phenotypes. Am J Hum Genet 2021; 108:49-67. [PMID: 33326753 DOI: 10.1016/j.ajhg.2020.11.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/23/2020] [Indexed: 12/13/2022] Open
Abstract
Although thousands of loci have been associated with human phenotypes, the role of gene-environment (GxE) interactions in determining individual risk of human diseases remains unclear. This is partly because of the severe erosion of statistical power resulting from the massive number of statistical tests required to detect such interactions. Here, we focus on improving the power of GxE tests by developing a statistical framework for assessing quantitative trait loci (QTLs) associated with the trait means and/or trait variances. When applying this framework to body mass index (BMI), we find that GxE discovery and replication rates are significantly higher when prioritizing genetic variants associated with the variance of the phenotype (vQTLs) compared to when assessing all genetic variants. Moreover, we find that vQTLs are enriched for associations with other non-BMI phenotypes having strong environmental influences, such as diabetes or ulcerative colitis. We show that GxE effects first identified in quantitative traits such as BMI can be used for GxE discovery in disease phenotypes such as diabetes. A clear conclusion is that strong GxE interactions mediate the genetic contribution to body weight and diabetes risk.
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Affiliation(s)
- Andrew R Marderstein
- Tri-Institutional Program in Computational Biology & Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Department of Computational Biology, Cornell University, Ithaca, NY 14850, USA
| | - Emily R Davenport
- Department of Biology, Huck Institutes of the Life Sciences, Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Scott Kulm
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | | | - Olivier Elemento
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
| | - Andrew G Clark
- Department of Computational Biology, Cornell University, Ithaca, NY 14850, USA.
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21
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Sprangers J, Zaalberg IC, Maurice MM. Organoid-based modeling of intestinal development, regeneration, and repair. Cell Death Differ 2021; 28:95-107. [PMID: 33208888 PMCID: PMC7852609 DOI: 10.1038/s41418-020-00665-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 02/07/2023] Open
Abstract
The intestinal epithelium harbors a remarkable adaptability to undergo injury-induced repair. A key part of the regenerative response is the transient reprogramming of epithelial cells into a fetal-like state, which drives uniform proliferation, tissue remodeling, and subsequent restoration of the homeostatic state. In this review, we discuss how Wnt and YAP signaling pathways control the intestinal repair response and the transitioning of cell states, in comparison with the process of intestinal development. Furthermore, we highlight how organoid-based applications have contributed to the characterization of the mechanistic principles and key players that guide these developmental and regenerative events.
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Affiliation(s)
- Joep Sprangers
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Irene C Zaalberg
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Madelon M Maurice
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
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22
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Loe AKH, Rao-Bhatia A, Kim JE, Kim TH. Mesenchymal Niches for Digestive Organ Development, Homeostasis, and Disease. Trends Cell Biol 2020; 31:152-165. [PMID: 33349527 DOI: 10.1016/j.tcb.2020.11.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 02/08/2023]
Abstract
Mesenchymal-epithelial crosstalk plays a crucial role in organ development and stem cell function. However, the identity of the mesenchymal cells involved in this exchange was unclear. Recent significant advances in single-cell transcriptomics have defined the heterogeneity of these mesenchymal niches. By combining multiomic profiling, animal models, and organoid culture, new studies have not only demonstrated the roles of diverse mesenchymal cell populations but also defined the mechanisms underlying their regulation of niche signals. Focusing on several digestive organs, we describe how similar and diverse mesenchymal cell populations promote organ development and maintain proper stem cell activity, and how the heterogeneity of mesenchymal niches is altered in digestive diseases such as inflammation and cancer.
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Affiliation(s)
- Adrian Kwan Ho Loe
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Abilasha Rao-Bhatia
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ji-Eun Kim
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Tae-Hee Kim
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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23
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Grzymkowski J, Wyatt B, Nascone-Yoder N. The twists and turns of left-right asymmetric gut morphogenesis. Development 2020; 147:147/19/dev187583. [PMID: 33046455 DOI: 10.1242/dev.187583] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Many organs develop left-right asymmetric shapes and positions that are crucial for normal function. Indeed, anomalous laterality is associated with multiple severe birth defects. Although the events that initially orient the left-right body axis are beginning to be understood, the mechanisms that shape the asymmetries of individual organs remain less clear. Here, we summarize new evidence challenging century-old ideas about the development of stomach and intestine laterality. We compare classical and contemporary models of asymmetric gut morphogenesis and highlight key unanswered questions for future investigation.
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Affiliation(s)
- Julia Grzymkowski
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
| | - Brent Wyatt
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
| | - Nanette Nascone-Yoder
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
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24
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Chang CA, Di Donato N, Hackmann K, Argiropoulos B, Ferreira P, Innes AM, Thomas MA. Congenital hiatal hernia segregating with a duplication in 9q22.31q22.32 in two families. Am J Med Genet A 2020; 182:3040-3047. [PMID: 33026187 DOI: 10.1002/ajmg.a.61898] [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: 05/06/2020] [Revised: 07/30/2020] [Accepted: 09/02/2020] [Indexed: 11/12/2022]
Abstract
Congenital hiatal hernia (HH) is a rare congenital defect and is often described on a sporadic basis, but familial cases have also been reported. The mechanism of development is not well understood, and to our knowledge no specific genetic factors have been implicated to date. We report on seven individuals from two families with 9q22 duplication, who have variably associated features including congenital HH in four individuals. One family had an 1.09 Mb 9q22 duplication, and the other family had an overlapping 2.73 Mb 9q22 duplication. We review the genes in this region and discuss BARX1 (BarH-like homeobox gene 1) as a gene of interest.
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Affiliation(s)
- Caitlin A Chang
- The Department of Medical Genetics, Cumming School of Medicine, Calgary, Alberta, Canada
| | - Nataliya Di Donato
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Karl Hackmann
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Bob Argiropoulos
- The Department of Medical Genetics, Cumming School of Medicine, Calgary, Alberta, Canada.,Cytogenetics Laboratory South, Alberta Precision Laboratories, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Patrick Ferreira
- The Department of Pediatrics, Division of Medical Genetics, Alberta Children's Hospital, Calgary, Alberta, Canada
| | - A Micheil Innes
- The Department of Medical Genetics, Cumming School of Medicine, Calgary, Alberta, Canada.,The Department of Pediatrics, Division of Medical Genetics, Alberta Children's Hospital, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Mary Ann Thomas
- The Department of Medical Genetics, Cumming School of Medicine, Calgary, Alberta, Canada.,Cytogenetics Laboratory South, Alberta Precision Laboratories, Calgary, Alberta, Canada.,The Department of Pediatrics, Division of Medical Genetics, Alberta Children's Hospital, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
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25
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Liu S, Song A, Zhou X, Huo Z, Yao S, Yang B, Liu Y, Wang Y. ceRNA network development and tumour-infiltrating immune cell analysis of metastatic breast cancer to bone. J Bone Oncol 2020; 24:100304. [PMID: 32760644 PMCID: PMC7393400 DOI: 10.1016/j.jbo.2020.100304] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/09/2020] [Accepted: 07/10/2020] [Indexed: 12/18/2022] Open
Abstract
PURPOSE Advanced breast cancer commonly metastasises to bone; however, the molecular mechanisms underlying the affinity for breast cancer cells to bone remains unclear. Thus, we developed nomograms based on a competing endogenous RNA (ceRNA) network and analysed tumour-infiltrating immune cells to elucidate the molecular pathways that may predict prognosis in patients with breast cancer. METHODS We obtained the RNA expression profile of 1091 primary breast cancer samples included in The Cancer Genome Atlas database, 58 of which were from patients with bone metastasis. We analysed the differential RNA expression patterns between breast cancer with and without bone metastasis and developed a ceRNA network. Cibersort was employed to differentiate between immune cell types based on tumour transcripts. Nomograms were then established based on the ceRNA network and immune cell analysis. The value of prognostic factors was evaluated by Kaplan-Meier survival analysis and a Cox proportional risk model. RESULTS We found significant differences in long non-coding RNAs (lncRNAs), 18 microRNAs (miRNAs), and 20 messenger RNAs (mRNAs) between breast cancer with and without bone metastasis, which were used to construct a ceRNA network. We found that the protein-coding genes GJB3, CAMMV, PTPRZ1, and FBN3 were significantly differentially expressed by Kaplan-Meier analysis. We also observed significant differences in the abundance of plasma cell and follicular helper T cell populations between the two groups. In addition, the proportion of mast cells, gamma delta T cells, and plasma cells differed depending on disease location and stage. Our analysis showed that a high proportion of follicular helper T cells and a low proportion of eosinophils promoted survival and that DLX6-AS1, Wnt6, and GABBR2 expression may be associated with bone metastasis in breast cancer. CONCLUSIONS We developed a bioinformatic tool for exploring the molecular mechanisms of bone metastasis in patients with breast cancer and identified factors that may predict the occurrence of bone metastasis.
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Key Words
- AIC, Akaike information criterion
- AUC, Area under curve
- Bone metastasis
- Breast cancer
- DE, Differentially expressed
- DEmRNA, differentially expressed messenger RNA
- EMT, epithelial-mesenchymal transition
- ER, estrogen receptor
- FPKM, fragments per kilobase per million mapped reads
- GO, Gene ontology
- HER2, human epidermal growth factor receptor 2
- Immune infiltration
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- Nomogram
- PCC, Pearson correlation coefficient
- Prognosis
- ROC curve, receiver operating characteristic curve
- Runx2, runt related transcription factor 2
- TCGA, The Cancer Genome Atlas
- TNM, Tumor, Node, Metastases
- ceRNA network
- ceRNA, competing endogenous RNA
- lncRNA, long non-coding RNA
- mRNA, messenger RNA
- miRNA, microRNA
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Affiliation(s)
- Shuzhong Liu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - An Song
- Department of Endocrinology, Key Laboratory of Endocrinology, National Health and Family Planning Commission, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Xi Zhou
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Zhen Huo
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Siyuan Yao
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Bo Yang
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Corresponding authors at: Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan Wangfujing, Beijing 100730, China.
| | - Yong Liu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Corresponding authors at: Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan Wangfujing, Beijing 100730, China.
| | - Yipeng Wang
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Corresponding authors at: Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan Wangfujing, Beijing 100730, China.
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26
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McCarthy N, Kraiczy J, Shivdasani RA. Cellular and molecular architecture of the intestinal stem cell niche. Nat Cell Biol 2020; 22:1033-1041. [PMID: 32884148 DOI: 10.1038/s41556-020-0567-z] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/29/2020] [Indexed: 12/23/2022]
Abstract
Intestinal stem and progenitor cells replicate and differentiate in distinct compartments, influenced by Wnt, BMP, and other subepithelial cues. The cellular sources of these signals were long obscure because intestinal mesenchyme was insufficiently characterised. In this Review, we discuss how recent mRNA profiles of mouse and human intestinal submucosa, coupled with fine-resolution microscopy and gene and cell disruptions, reveal a coherent picture of an organised tissue carrying cells with distinct molecular properties and functions.
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Affiliation(s)
- Neil McCarthy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Judith Kraiczy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Ramesh A Shivdasani
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, USA.
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27
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Han L, Chaturvedi P, Kishimoto K, Koike H, Nasr T, Iwasawa K, Giesbrecht K, Witcher PC, Eicher A, Haines L, Lee Y, Shannon JM, Morimoto M, Wells JM, Takebe T, Zorn AM. Single cell transcriptomics identifies a signaling network coordinating endoderm and mesoderm diversification during foregut organogenesis. Nat Commun 2020; 11:4158. [PMID: 32855417 PMCID: PMC7453027 DOI: 10.1038/s41467-020-17968-x] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 07/24/2020] [Indexed: 12/12/2022] Open
Abstract
Visceral organs, such as the lungs, stomach and liver, are derived from the fetal foregut through a series of inductive interactions between the definitive endoderm (DE) and the surrounding splanchnic mesoderm (SM). While DE patterning is fairly well studied, the paracrine signaling controlling SM regionalization and how this is coordinated with epithelial identity is obscure. Here, we use single cell transcriptomics to generate a high-resolution cell state map of the embryonic mouse foregut. This identifies a diversity of SM cell types that develop in close register with the organ-specific epithelium. We infer a spatiotemporal signaling network of endoderm-mesoderm interactions that orchestrate foregut organogenesis. We validate key predictions with mouse genetics, showing the importance of endoderm-derived signals in mesoderm patterning. Finally, leveraging these signaling interactions, we generate different SM subtypes from human pluripotent stem cells (hPSCs), which previously have been elusive. The single cell data can be explored at: https://research.cchmc.org/ZornLab-singlecell. The fetal murine foregut develops into visceral organs via interactions between the mesoderm and endoderm, but how is unclear. Here, the authors use single cell RNAseq to show a diversity in organ specific splanchnic mesoderm cell-types, infer a signalling network governing organogenesis and use this to differentiate human pluripotent stem cells.
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Affiliation(s)
- Lu Han
- Center for Stem Cell and Organoid Medicine (CuSTOM), Perinatal Institute, Division of Developmental Biology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - Praneet Chaturvedi
- Center for Stem Cell and Organoid Medicine (CuSTOM), Perinatal Institute, Division of Developmental Biology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - Keishi Kishimoto
- Center for Stem Cell and Organoid Medicine (CuSTOM), Perinatal Institute, Division of Developmental Biology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA.,Laboratory for Lung Development, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, 650-0047, Japan.,CuSTOM-RIKEN BDR Collaborative Laboratory, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | - Hiroyuki Koike
- CuSTOM, Division of Gastroenterology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - Talia Nasr
- Center for Stem Cell and Organoid Medicine (CuSTOM), Perinatal Institute, Division of Developmental Biology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - Kentaro Iwasawa
- CuSTOM, Division of Gastroenterology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - Kirsten Giesbrecht
- CuSTOM, Division of Gastroenterology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - Phillip C Witcher
- Center for Stem Cell and Organoid Medicine (CuSTOM), Perinatal Institute, Division of Developmental Biology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - Alexandra Eicher
- Center for Stem Cell and Organoid Medicine (CuSTOM), Perinatal Institute, Division of Developmental Biology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - Lauren Haines
- Center for Stem Cell and Organoid Medicine (CuSTOM), Perinatal Institute, Division of Developmental Biology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - Yarim Lee
- Center for Stem Cell and Organoid Medicine (CuSTOM), Perinatal Institute, Division of Developmental Biology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - John M Shannon
- Division of Pulmonary Biology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - Mitsuru Morimoto
- Laboratory for Lung Development, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, 650-0047, Japan.,CuSTOM-RIKEN BDR Collaborative Laboratory, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | - James M Wells
- Center for Stem Cell and Organoid Medicine (CuSTOM), Perinatal Institute, Division of Developmental Biology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - Takanori Takebe
- CuSTOM, Division of Gastroenterology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - Aaron M Zorn
- Center for Stem Cell and Organoid Medicine (CuSTOM), Perinatal Institute, Division of Developmental Biology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA. .,CuSTOM-RIKEN BDR Collaborative Laboratory, Cincinnati Children's Hospital, Cincinnati, OH, USA.
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28
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Raad S, David A, Que J, Faure C. Genetic Mouse Models and Induced Pluripotent Stem Cells for Studying Tracheal-Esophageal Separation and Esophageal Development. Stem Cells Dev 2020; 29:953-966. [PMID: 32515280 PMCID: PMC9839344 DOI: 10.1089/scd.2020.0075] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Esophagus and trachea arise from a common origin, the anterior foregut tube. The compartmentalization process of the foregut into the esophagus and trachea is still poorly understood. Esophageal atresia/tracheoesophageal fistula (EA/TEF) is one of the most common gastrointestinal congenital defects with an incidence rate of 1 in 2,500 births. EA/TEF is linked to the disruption of the compartmentalization process of the foregut tube. In EA/TEF patients, other organ anomalies and disorders have also been reported. Over the last two decades, animal models have shown the involvement of multiple signaling pathways and transcription factors in the development of the esophagus and trachea. Use of induced pluripotent stem cells (iPSCs) to understand organogenesis has been a valuable tool for mimicking gastrointestinal and respiratory organs. This review focuses on the signaling mechanisms involved in esophageal development and the use of iPSCs to model and understand it.
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Affiliation(s)
- Suleen Raad
- Esophageal Development and Engineering Laboratory, Sainte-Justine Research Centre, Montreal, Quebec, Canada
| | - Anu David
- Esophageal Development and Engineering Laboratory, Sainte-Justine Research Centre, Montreal, Quebec, Canada
| | - Jianwen Que
- Division of Digestive and Liver Diseases, Department of Medicine, Center for Human Development, Columbia University, New York, New York, USA
| | - Christophe Faure
- Esophageal Development and Engineering Laboratory, Sainte-Justine Research Centre, Montreal, Quebec, Canada.,Esophageal Atresia Clinic and Division of Pediatric Gastroenterology Hepatology and Nutrition, CHU Sainte Justine, Université de Montréal, Montréal, Quebec, Canada.,Address correspondence to: Dr. Christophe Faure, Division of Pediatric Gastroenterology, Sainte-Justine Hospital, 3715 Côte Sainte Catherine, Montreal H3T1C5, Quebec, Canada
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29
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Zhang Y, Que J. BMP Signaling in Development, Stem Cells, and Diseases of the Gastrointestinal Tract. Annu Rev Physiol 2020; 82:251-273. [PMID: 31618602 DOI: 10.1146/annurev-physiol-021119-034500] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The bone morphogenetic protein (BMP) pathway is essential for the morphogenesis of multiple organs in the digestive system. Abnormal BMP signaling has also been associated with disease initiation and progression in the gastrointestinal (GI) tract and associated organs. Recent studies using animal models, tissue organoids, and human pluripotent stem cells have significantly expanded our understanding of the roles played by BMPs in the development and homeostasis of GI organs. It is clear that BMP signaling regulates GI function and disease progression that involve stem/progenitor cells and inflammation in a tissue-specific manner. In this review we discuss these new findings with a focus on the esophagus, stomach, and intestine.
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Affiliation(s)
- Yongchun Zhang
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, New York, NY 10032, USA; .,Columbia Center for Human Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Jianwen Que
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, New York, NY 10032, USA; .,Columbia Center for Human Development, Columbia University Medical Center, New York, NY 10032, USA
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30
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Min S, Kim S, Cho SW. Gastrointestinal tract modeling using organoids engineered with cellular and microbiota niches. Exp Mol Med 2020; 52:227-237. [PMID: 32103122 PMCID: PMC7062772 DOI: 10.1038/s12276-020-0386-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/21/2019] [Accepted: 12/27/2019] [Indexed: 02/08/2023] Open
Abstract
The recent emergence of organoid technology has attracted great attention in gastroenterology because the gastrointestinal (GI) tract can be recapitulated in vitro using organoids, enabling disease modeling and mechanistic studies. However, to more precisely emulate the GI microenvironment in vivo, several neighboring cell types and types of microbiota need to be integrated into GI organoids. This article reviews the recent progress made in elucidating the crosstalk between GI organoids and components of their microenvironment. We outline the effects of stromal cells (such as fibroblasts, neural cells, immune cells, and vascular cells) on the gastric and intestinal epithelia of organoids. Because of the important roles that microbiota play in the physiology and function of the GI tract, we also highlight interactions between organoids and commensal, symbiotic, and pathogenic microorganisms and viruses. GI organoid models that contain niche components will provide new insight into gastroenterological pathophysiology and disease mechanisms.
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Affiliation(s)
- Sungjin Min
- Department of Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Suran Kim
- Department of Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Seung-Woo Cho
- Department of Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.
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31
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Single cell and genetic analyses reveal conserved populations and signaling mechanisms of gastrointestinal stromal niches. Nat Commun 2020; 11:334. [PMID: 31953387 PMCID: PMC6969052 DOI: 10.1038/s41467-019-14058-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 12/14/2019] [Indexed: 12/12/2022] Open
Abstract
Stomach and intestinal stem cells are located in discrete niches called the isthmus and crypt, respectively. Recent studies have demonstrated a surprisingly conserved role for Wnt signaling in gastrointestinal development. Although intestinal stromal cells secrete Wnt ligands to promote stem cell renewal, the source of stomach Wnt ligands is still unclear. Here, by performing single cell analysis, we identify gastrointestinal stromal cell populations with transcriptome signatures that are conserved between the stomach and intestine. In close proximity to epithelial cells, these perictye-like cells highly express telocyte and pericyte markers as well as Wnt ligands, and they are enriched for Hh signaling. By analyzing mice activated for Hh signaling, we show a conserved mechanism of GLI2 activation of Wnt ligands. Moreover, genetic inhibition of Wnt secretion in perictye-like stromal cells or stromal cells more broadly demonstrates their essential roles in gastrointestinal regeneration and development, respectively, highlighting a redundancy in gastrointestinal stem cell niches.
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32
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Early chromatin shaping predetermines multipotent vagal neural crest into neural, neuronal and mesenchymal lineages. Nat Cell Biol 2019; 21:1504-1517. [PMID: 31792380 PMCID: PMC7188519 DOI: 10.1038/s41556-019-0428-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 10/28/2019] [Indexed: 01/28/2023]
Abstract
The enteric nervous system (ENS) predominantly originates from vagal neural crest cells (VNC) that emerge from the caudal hindbrain, invade the foregut and populate the gastrointestinal tract. However, the gene regulatory network (GRN) orchestrating the early specification of VNC remains unknown. Using an EdnrB enhancer, we generated a comprehensive temporal map of the chromatin and transcriptional landscape of VNC in the avian model, revealing three VNC cell clusters (neural, neurogenic and mesenchymal), each predetermined epigenetically prior to neural tube delamination. We identify and functionally validate regulatory cores (Sox10/Tfap2B/SoxB/Hbox) mediating each programme and elucidate their combinatorial activities with other spatiotemporally-specific transcription factors (bHLH/NR). Our global deconstruction of the VNC-GRN in vivo sheds light on critical early regulatory mechanisms that may influence the divergent neural phenotypes in enteric neuropathies.
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33
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Pickett MA, Naturale VF, Feldman JL. A Polarizing Issue: Diversity in the Mechanisms Underlying Apico-Basolateral Polarization In Vivo. Annu Rev Cell Dev Biol 2019; 35:285-308. [PMID: 31461314 DOI: 10.1146/annurev-cellbio-100818-125134] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Polarization along an apico-basolateral axis is a hallmark of epithelial cells and is essential for their selective barrier and transporter functions, as well as for their ability to provide mechanical resiliency to organs. Loss of polarity along this axis perturbs development and is associated with a wide number of diseases. We describe three steps involved in polarization: symmetry breaking, polarity establishment, and polarity maintenance. While the proteins involved in these processes are highly conserved among epithelial tissues and species, the execution of these steps varies widely and is context dependent. We review both theoretical principles underlying these steps and recent work demonstrating how apico-basolateral polarity is established in vivo in different tissues, highlighting how developmental and physiological contexts play major roles in the execution of the epithelial polarity program.
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Affiliation(s)
- Melissa A Pickett
- Department of Biology, Stanford University, Stanford, California 94305, USA;
| | - Victor F Naturale
- Department of Biology, Stanford University, Stanford, California 94305, USA;
| | - Jessica L Feldman
- Department of Biology, Stanford University, Stanford, California 94305, USA;
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34
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Argyrou A, Legaki E, Koutserimpas C, Gazouli M, Papaconstantinou I, Gkiokas G, Karamanolis G. Polymorphisms of the BARX1 and ADAMTS17 Locus Genes in Individuals With Gastroesophageal Reflux Disease. J Neurogastroenterol Motil 2019; 25:436-441. [PMID: 31048564 PMCID: PMC6657930 DOI: 10.5056/jnm18183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 02/01/2019] [Accepted: 04/07/2019] [Indexed: 12/13/2022] Open
Abstract
Background/Aims Gastroesophageal reflux disease (GERD) represents a common condition having a substantial impact on the patients’ quality of life, as well as the health system. According to many studies, the BARX1 and ADAMTS17 genes have been suggested as genetic risk loci for the development of GERD and its complications. The purpose of this study is to investigate the potential association between GERD and BARX1 and ADAMTS17 polymorphisms. Methods The present is a prospective cohort study of 160 GERD patients and 180 healthy control subjects of Greek origin, examined for BARX1 and ADAMTS17 polymorphisms (rs11789015 and rs4965272) and a potential correlation to GERD. Results The rs11789015 AG and GG genotypes were found to be significantly associated with GERD (P = 0.032; OR, 1.65; 95% CI, 1.06–2.57 and P = 0.033; OR, 3.00; 95% CI, 1.15–7.82, respectively), as well as the G allele (P = 0.007; OR, 1.60; 95% CI, 1.14–2.24). Concerning the rs4965272, only the GG genotype was significantly associated with GERD (P = 0.035; OR, 3.42; 95% CI, 1.06–11.05). Conclusions This is a study investigating the potential correlation between BARX1 and ADAMTS17 polymorphisms and the development of GERD, showing a considerable association between both polymorphisms and the disease. This finding suggests that esophageal differentiation or altered regulation on microfibrils in the cell environment could be implicated as possible mechanisms in the pathogenesis of GERD.
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Affiliation(s)
- Alexandra Argyrou
- Department of Basic Medical Sciences, Laboratory of Biology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Evangelia Legaki
- Department of Basic Medical Sciences, Laboratory of Biology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Christos Koutserimpas
- 2nd Department of General Surgery, "Sismanoglio General Hospital of Athens, Athens, Greece
| | - Maria Gazouli
- Department of Basic Medical Sciences, Laboratory of Biology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Ioannis Papaconstantinou
- 2nd Department of Surgery, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - George Gkiokas
- 2nd Department of Surgery, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - George Karamanolis
- Gastroenterology Unit, 2nd Department of Surgery, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
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35
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Fadista J, Skotte L, Geller F, Bybjerg-Grauholm J, Gørtz S, Romitti PA, Caggana M, Kay DM, Matsson H, Boyd HA, Hougaard DM, Nordenskjöld A, Mills JL, Melbye M, Feenstra B. Genome-wide meta-analysis identifies BARX1 and EML4-MTA3 as new loci associated with infantile hypertrophic pyloric stenosis. Hum Mol Genet 2019; 28:332-340. [PMID: 30281099 PMCID: PMC6322072 DOI: 10.1093/hmg/ddy347] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/24/2018] [Indexed: 01/15/2023] Open
Abstract
Infantile hypertrophic pyloric stenosis (IHPS) is a disorder of young infants with a population incidence of ∼2/1000 live births, caused by hypertrophy of the pyloric sphincter smooth muscle. Reported genetic loci associated with IHPS explain only a minor proportion of IHPS risk. To identify new risk loci, we carried out a genome-wide meta-analysis on 1395 surgery-confirmed cases and 4438 controls, with replication in a set of 2427 cases and 2524 controls. We identified and replicated six independent genomic loci associated with IHPS risk at genome wide significance (P < 5 × 10-8), including novel associations with two single nucleotide polymorphisms (SNPs). One of these SNPs, rs6736913 [odds ratio (OR) = 2.32; P = 3.0 × 10-15], is a low frequency missense variant in EML4 at 2p21. The second SNP, rs1933683 (OR = 1.34; P = 3.1 × 10-9) is 1 kb downstream of BARX1 at 9q22.32, an essential gene for stomach formation in embryogenesis. Using the genome-wide complex trait analysis method, we estimated the IHPS SNP heritability to be 30%, and using the linkage disequilibrium score regression method, we found support for a previously reported genetic correlation of IHPS with lipid metabolism. By combining the largest collection of IHPS cases to date (3822 cases), with results generalized across populations of different ancestry, we elucidate novel mechanistic avenues of IHPS disease architecture.
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Affiliation(s)
- João Fadista
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark.,Department of Clinical Sciences, Lund University Diabetes Centre, Malmö, Sweden
| | - Line Skotte
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jonas Bybjerg-Grauholm
- Department of Congenital Disorders, Danish Center for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - Sanne Gørtz
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Paul A Romitti
- Department of Epidemiology, College of Public Health, The University of Iowa, Iowa City, IA, USA
| | - Michele Caggana
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Denise M Kay
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Hans Matsson
- Department of Women's and Children's Health, and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Heather A Boyd
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - David M Hougaard
- Department of Congenital Disorders, Danish Center for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - Agneta Nordenskjöld
- Department of Women's and Children's Health, and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Pediatric Surgery, Astrid Lindgren Children´s Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - James L Mills
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Mads Melbye
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.,Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
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36
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Chen J, Lau BT, Andor N, Grimes SM, Handy C, Wood-Bouwens C, Ji HP. Single-cell transcriptome analysis identifies distinct cell types and niche signaling in a primary gastric organoid model. Sci Rep 2019; 9:4536. [PMID: 30872643 PMCID: PMC6418230 DOI: 10.1038/s41598-019-40809-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 02/22/2019] [Indexed: 12/18/2022] Open
Abstract
The diverse cellular milieu of the gastric tissue microenvironment plays a critical role in normal tissue homeostasis and tumor development. However, few cell culture model can recapitulate the tissue microenvironment and intercellular signaling in vitro. We used a primary tissue culture system to generate a murine p53 null gastric tissue model containing both epithelium and mesenchymal stroma. To characterize the microenvironment and niche signaling, we used single cell RNA sequencing (scRNA-Seq) to determine the transcriptomes of 4,391 individual cells. Based on specific markers, we identified epithelial cells, fibroblasts and macrophages in initial tissue explants during organoid formation. The majority of macrophages were polarized towards wound healing and tumor promotion M2-type. During the course of time, the organoids maintained both epithelial and fibroblast lineages with the features of immature mouse gastric stomach. We detected a subset of cells in both lineages expressing Lgr5, one of the stem cell markers. We examined the lineage-specific Wnt signaling activation, and identified that Rspo3 was specifically expressed in the fibroblast lineage, providing an endogenous source of the R-spondin to activate Wnt signaling. Our studies demonstrate that this primary tissue culture system enables one to study gastric tissue niche signaling and immune response in vitro.
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Affiliation(s)
- Jiamin Chen
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Billy T Lau
- Stanford Genome Technology Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Noemi Andor
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Susan M Grimes
- Stanford Genome Technology Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Christine Handy
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Christina Wood-Bouwens
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Hanlee P Ji
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA. .,Stanford Genome Technology Center, Stanford University School of Medicine, Stanford, CA, USA.
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37
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Gonçalves O, Freitas R, Ferreira P, Araújo M, Zhang G, Mazan S, Cohn MJ, Castro LFC, Wilson JM. Molecular ontogeny of the stomach in the catshark Scyliorhinus canicula. Sci Rep 2019; 9:586. [PMID: 30679499 PMCID: PMC6346038 DOI: 10.1038/s41598-018-36413-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 11/21/2018] [Indexed: 01/27/2023] Open
Abstract
The origin of extracellular digestion in metazoans was accompanied by structural and physiological alterations of the gut. These adaptations culminated in the differentiation of a novel digestive structure in jawed vertebrates, the stomach. Specific endoderm/mesenchyme signalling is required for stomach differentiation, involving the growth and transcription factors: 1) Shh and Bmp4, required for stomach outgrowth; 2) Barx1, Sfrps and Sox2, required for gastric epithelium development and 3) Cdx1 and Cdx2, involved in intestinal versus gastric identity. Thus, modulation of endoderm/mesenchyme signalling emerges as a plausible mechanism linked to the origin of the stomach. In order to gain insight into the ancient mechanisms capable of generating this structure in jawed vertebrates, we characterised the development of the gut in the catshark Scyliorhinus canicula. As chondrichthyans, these animals retained plesiomorphic features of jawed vertebrates, including a well-differentiated stomach. We identified a clear molecular regionalization of their embryonic gut, characterised by the expression of barx1 and sox2 in the prospective stomach region and expression of cdx1 and cdx2 in the prospective intestine. Furthermore, we show that gastric gland development occurs close to hatching, accompanied by the onset of gastric proton pump activity. Our findings favour a scenario in which the developmental mechanisms involved in the origin of the stomach were present in the common ancestor of chondrichthyans and osteichthyans.
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Affiliation(s)
- Odete Gonçalves
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Univ. Porto, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), Univ. Porto, Porto, Portugal
| | - Renata Freitas
- I3S- Institute for Innovation and Health Research, Univ. Porto, Porto, Portugal. .,IBMC- Institute for Molecular and Cell Biology, Univ. Porto, Porto, Portugal.
| | - Patrícia Ferreira
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Univ. Porto, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), Univ. Porto, Porto, Portugal
| | - Mafalda Araújo
- I3S- Institute for Innovation and Health Research, Univ. Porto, Porto, Portugal.,IBMC- Institute for Molecular and Cell Biology, Univ. Porto, Porto, Portugal
| | - GuangJun Zhang
- Department of Comparative Pathobiology, Purdue Univ., Lafayette, USA.,Purdue Institute for Integrative Neuroscience, Purdue Univ., Lafayette, USA.,Purdue Univ. Center for Cancer, Purdue Univ., Lafayette, USA.,Purdue Institute for Inflammation, Immunology and Infectious Diseases, Purdue Univ., Lafayette, USA
| | - Sylvie Mazan
- CNRS, Sorbonne Universités, UPMC Univ. Paris, Observatoire Océanologique, Banyuls, France
| | - Martin J Cohn
- Howard Hughes Medical Institute, UF Genetics Institute, Univ. Florida, Florida, USA.,Department of Biology, UF Genetics Institute, Univ. Florida, Florida, USA.,Department of Molecular Genetics and Microbiology, UF Genetics Institute, Univ. Florida, Florida, USA
| | - L Filipe C Castro
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Univ. Porto, Porto, Portugal. .,Department of Biology, Faculty of Sciences, Univ. Porto, Porto, Portugal.
| | - Jonathan M Wilson
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Univ. Porto, Porto, Portugal. .,Department of Biology, Wilfrid Laurier Univ., Waterloo, Canada.
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38
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Li X, Zhang C, Gong T, Ni X, Li J, Zhan D, Liu M, Song L, Ding C, Xu J, Zhen B, Wang Y, Qin J. A time-resolved multi-omic atlas of the developing mouse stomach. Nat Commun 2018; 9:4910. [PMID: 30464175 PMCID: PMC6249217 DOI: 10.1038/s41467-018-07463-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 10/30/2018] [Indexed: 02/07/2023] Open
Abstract
The mammalian stomach is structurally highly diverse and its organ functionality critically depends on a normal embryonic development. Although there have been several studies on the morphological changes during stomach development, a system-wide analysis of the underlying molecular changes is lacking. Here, we present a comprehensive, temporal proteome and transcriptome atlas of the mouse stomach at multiple developmental stages. Quantitative analysis of 12,108 gene products allows identifying three distinct phases based on changes in proteins and RNAs and the gain of stomach functions on a longitudinal time scale. The transcriptome indicates functionally important isoforms relevant to development and identifies several functionally unannotated novel splicing junction transcripts that we validate at the peptide level. Importantly, many proteins differentially expressed in stomach development are also significantly overexpressed in diffuse-type gastric cancer. Overall, our study provides a resource to understand stomach development and its connection to gastric cancer tumorigenesis.
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Affiliation(s)
- Xianju Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China
| | - Chunchao Zhang
- Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Tongqing Gong
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China
| | - Xiaotian Ni
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China.,Department of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Jin'e Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China
| | - Dongdong Zhan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China.,Department of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Mingwei Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China
| | - Lei Song
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China
| | - Chen Ding
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Institutes of Biomedical Sciences, and School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Jianming Xu
- Department of Gastrointestinal Oncology, Affiliated Hospital Cancer Center, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Bei Zhen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China
| | - Yi Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China. .,Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Jun Qin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China. .,Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,State Key Laboratory of Genetic Engineering, Human Phenome Institute, Institutes of Biomedical Sciences, and School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200433, China.
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39
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Saberi S, Pournasr B, Farzaneh Z, Esmaeili M, Hosseini ME, Baharvand H, Mohammadi M. A simple and cost-efficient adherent culture platform for human gastric primary cells, as an in vitro model for Helicobacter pylori infection. Helicobacter 2018; 23:e12489. [PMID: 29774633 DOI: 10.1111/hel.12489] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND Most two- dimensional in vitro models for studying host- H. pylori interactions rely on tumor-derived cell lines, which harbor malignant alterations. The recent development of human gastric organoids has overcome this limitation and provides a highly sophisticated, yet costly, short-term model for H. pylori infection, with restricted use in low-budget centers. METHOD Tissue specimens from upper, middle, and lower stomachs of H. pylori-negative volunteers were collectively dispersed and cultured on mouse embryonic fibroblast (MEF) or collagen-coated plates. Gastric primary cells (GPCs) were evaluated by light microscopy, immunostaining, qRT-PCR and ELISA analysis of cellular secretions, before and after H. pylori infection. RESULTS The formation and long-term (up to 1 year) maintenance of GPCs was highly dependent on adherent inactivated MEF cells, cultured in enriched media. These cells were multipassageable and able to undergo stable freezer storage and subsequent revival. The cellular composition of GPCs included the combination of cytokeratin 18 (CK18) and E-cadherin (E-cad)-positive epithelial cells, MUC5AC-positive gastric cells, and leucine-rich repeat containing G protein-coupled receptor 5 (LGR5)-positive progenitor cells. These cells produced significant amounts of gastric pepsinogens I and II. GPCs also allowed for extended (up to 96 hours) H. pylori infection, during which they underwent morphological alterations (cellular vacuolation and elongation) and hyperproduction of gastric pepsinogens and inflammatory cytokines (IL-8 and TNF-α). CONCLUSION We, hereby, present a simple, consistent, and cost-efficient gastric cell culture system, which provides a suitable model for extended in vitro infection of H. pylori. This platform can be employed for a variety of gastric-related research.
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Affiliation(s)
- Samaneh Saberi
- HPGC Research Group, Department of Medical Biotechnology, Pasteur Institute of Iran, Tehran, Iran
| | - Behshad Pournasr
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Zahra Farzaneh
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Maryam Esmaeili
- HPGC Research Group, Department of Medical Biotechnology, Pasteur Institute of Iran, Tehran, Iran
| | - Mahmoud Eshagh Hosseini
- Gastroenterology Department, Amiralam Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.,Department of Developmental Biology, University of Science and Culture, Tehran, Iran
| | - Marjan Mohammadi
- HPGC Research Group, Department of Medical Biotechnology, Pasteur Institute of Iran, Tehran, Iran
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40
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Huang M, He H, Belenkaya T, Lin X. Multiple roles of epithelial heparan sulfate in stomach morphogenesis. J Cell Sci 2018; 131:jcs.210781. [PMID: 29700203 DOI: 10.1242/jcs.210781] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 04/19/2018] [Indexed: 12/12/2022] Open
Abstract
Heparan sulfate proteoglycans (HSPGs) have been shown to regulate various developmental processes. However, the function of heparan sulfate (HS) during the development of mammalian stomach has not been characterized yet. Here, we investigate the role of epithelial HS in embryonic stomach by examining mice deficient in the glycosyltransferase gene Ext1 We show that HS exhibits a specific and dynamic expression pattern in mouse embryonic stomach. Depletion of the epithelial HS leads to stomach hypoplasia, with phenotypic differences in the gastric mucosa between the forestomach and hindstomach. In the posterior stomach, HS depletion disrupts glandular stomach patterning and cytodifferentiation via attenuation of Fgf signaling activity. Inhibition of Fgf signaling in vitro recapitulates the patterning defect. Ligand and carbohydrate engagement assay (LACE) reveals a diminished assembly of Fgf10 and Fgfr2b in the mutant. In the anterior stomach, loss of epithelial HS leads to stratification and differentiation defects of the multilayered squamous epithelium, along with reduced Hh and Bmp signaling activity. Our data demonstrate that epithelial HS plays multiple roles in regulating mammalian stomach morphogenesis in a regional-specific manner.
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Affiliation(s)
- Meina Huang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China.,State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hua He
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tatyana Belenkaya
- Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Xinhua Lin
- State Key Laboratory of Genetic Engineering, Institute of Genetics, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China .,Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
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41
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Id2 Determines Intestinal Identity through Repression of the Foregut Transcription Factor Irx5. Mol Cell Biol 2018; 38:MCB.00250-17. [PMID: 29463648 PMCID: PMC5902590 DOI: 10.1128/mcb.00250-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 02/13/2018] [Indexed: 12/12/2022] Open
Abstract
The cellular components and function of the gastrointestinal epithelium exhibit distinct characteristics depending on the region, e.g., stomach or intestine. How these region-specific epithelial characteristics are generated during development remains poorly understood. Here, we report on the involvement of the helix-loop-helix inhibitor Id2 in establishing the specific characteristics of the intestinal epithelium. Id2−/− mice developed tumors in the small intestine. Histological analysis indicated that the intestinal tumors were derived from gastric metaplasia formed in the small intestine during development. Heterotopic Id2 expression in developing gastric epithelium induced a fate change to intestinal epithelium. Gene expression analysis revealed that foregut-enriched genes encoding Irx3 and Irx5 were highly induced in the midgut of Id2−/− embryos, and transgenic mice expressing Irx5 in the midgut endoderm developed tumors recapitulating the characteristics of Id2−/− mice. Altogether, our results demonstrate that Id2 plays a crucial role in the development of regional specificity in the gastrointestinal epithelium.
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42
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Yan C, Ji Y, Huang T, Yu F, Gao Y, Gu Y, Qi Q, Du J, Dai J, Ma H, Jin G. An esophageal adenocarcinoma susceptibility locus at 9q22 also confers risk to esophageal squamous cell carcinoma by regulating the function of BARX1. Cancer Lett 2018; 421:103-111. [PMID: 29454095 DOI: 10.1016/j.canlet.2018.02.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 02/04/2018] [Accepted: 02/11/2018] [Indexed: 02/02/2023]
Abstract
Genome wide association studies (GWAS) have identified a series of genetic variants associated with the risk of esophageal adenocarcinoma (EAC)/Barrett's esophagus (BE), which was different from those loci for esophageal squamous cell carcinoma (ESCC). It is important to evaluate whether these susceptibility loci for EAC/BE are also implicated in ESCC development. In the current study, we analyzed genetic variants at 3p13, 9q22, 16q24 and 19p13 in a case-control study including 2139 ESCC patients and 2463 cancer-free controls in a Chinese population, and further characterized the biological relevance of genetic variants by functional assays. We found that the G allele of rs11789015 at 9q22, as compared with the A allele, was significantly associated with a decreased risk of ESCC with a per-allele odds ratio of 0.77 (95%CI, 0.65-0.90; P = 1.38 × 10-3), whereas the other three loci were not associated with ESCC risk. We further found that rs11789015-G allele correlated with decreased mRNA and protein levels of BARX1. Dual-luciferase reporter gene assay revealed that the A > G change at rs11789015 significantly decreased the promoter activity of BARX1. Both the mRNA and protein levels of BARX1 were significantly higher in ESCC tumor tissues compared with the corresponding normal tissues. Moreover, the deletion of BARX1 substantially reduced ESCC cells growth, migration and invasion. In conclusion, these results suggest that genetic variants at 9q22 are associated with the risk of both EAC/BE and ESCC, possibly by regulating the function of BARX1.
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Affiliation(s)
- Caiwang Yan
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Yong Ji
- Department of Cardiothoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Tongtong Huang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Fei Yu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yong Gao
- Department of Medical Oncology, The Affiliated Huaian First People's Hospital of Nanjing Medical University, Huai'an, China
| | - Yayun Gu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qi Qi
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jiangbo Du
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Juncheng Dai
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hongxia Ma
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Guangfu Jin
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China.
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43
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Noguchi TAK, Kurisaki A. Formation of Stomach Tissue by Organoid Culture Using Mouse Embryonic Stem Cells. Methods Mol Biol 2018; 1597:217-228. [PMID: 28361321 DOI: 10.1007/978-1-4939-6949-4_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
In this chapter, we describe a method for the induction of stomach organoids from mouse embryonic stem (ES) cells. We used an embryoid body-based differentiation method to induce gastric primordial epithelium covered with mesenchyme and further differentiate it in Matrigel by 3D culture. The differentiated organoid contains both corpus- and antrum-specific mature gastric tissue cells. This protocol may be useful for a variety of studies in developmental biology and disease modeling of the stomach.
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Affiliation(s)
- Taka-Aki K Noguchi
- Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Ten-noudai, Tsukuba, Ibaraki, Japan.
| | - Akira Kurisaki
- Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Ten-noudai, Tsukuba, Ibaraki, Japan.
- Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.
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44
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Eicher AK, Berns HM, Wells JM. Translating Developmental Principles to Generate Human Gastric Organoids. Cell Mol Gastroenterol Hepatol 2018; 5:353-363. [PMID: 29552623 PMCID: PMC5852324 DOI: 10.1016/j.jcmgh.2017.12.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/22/2017] [Indexed: 12/24/2022]
Abstract
Gastric diseases, including peptic ulcer disease and gastric cancer, are highly prevalent in human beings. Despite this, the cellular biology of the stomach remains poorly understood relative to other gastrointestinal organs such as the liver, intestine, and colon. In particular, little is known about the molecular basis of stomach development and the differentiation of gastric lineages. Although animal models are useful for studying gastric development, function, and disease, there are major structural and physiological differences in human stomachs that render these models insufficient. To look at gastric development, function, and disease in a human context, a model system of the human stomach is imperative. This review details how this was achieved through the directed differentiation of human pluripotent stem cells in a 3-dimensional environment into human gastric organoids (HGOs). Similar to previous work that has generated human intestine, colon, and lung tissue in vitro, HGOs were generated in vitro through a step-wise differentiation designed to mimic the temporal-spatial signaling dynamics that control stomach development in vivo. HGOs can be used for a variety of purposes, including genetic modeling, drug screening, and potentially even in future patient transplantation. Moreover, HGOs are well suited to study the development and interactions of nonepithelial cell types, such as endothelial, neuronal, and mesenchymal, which remain almost completely unstudied. This review discusses the basics of stomach morphology, function, and developmental pathways involved in generating HGOs. We also highlight important gaps in our understanding of how epithelial and mesenchymal interactions are essential for the development and overall function of the human stomach.
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Key Words
- 3-D, 3-dimensional
- BMP, bone morphogenetic protein
- Directed Differentiation
- ECL, enterochromaffin-like
- ENCC, enteric neural crest cell
- ENS, enteric nervous system
- Endoderm
- GI, gastrointestinal
- Gastric Development
- HDGC, hereditary diffuse gastric cancer
- HGO, human gastric organoid
- Organoids
- PSC, pluripotent stem cell
- Pluripotent Stem Cells
- Shh, Sonic hedgehog
- e, embryonic day
- hPSC, human pluripotent stem cell
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Affiliation(s)
- Alexandra K. Eicher
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - H. Matthew Berns
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - James M. Wells
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio,Division of Endocrinology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio,Center for Stem Cell and Organoid Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio,Correspondence Address correspondence to: James M. Wells, PhD, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, Ohio 45229. fax: (513) 636-4317.Cincinnati Children's Hospital Medical Center3333 Burnet AvenueCincinnatiOhio 45229
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45
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Patterning the gastrointestinal epithelium to confer regional-specific functions. Dev Biol 2018; 435:97-108. [PMID: 29339095 DOI: 10.1016/j.ydbio.2018.01.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 01/01/2018] [Accepted: 01/10/2018] [Indexed: 12/12/2022]
Abstract
The gastrointestinal (GI) tract, in simplest terms, can be described as an epithelial-lined muscular tube extending along the cephalocaudal axis from the oral cavity to the anus. Although the general architecture of the GI tract organs is conserved from end to end, the presence of different epithelial tissue structures and unique epithelial cell types within each organ enables each to perform the distinct digestive functions required for efficient nutrient assimilation. Spatiotemporal regulation of signaling pathways and downstream transcription factors controls GI epithelial morphogenesis during development to confer essential regional-specific epithelial structures and functions. Here, we discuss the fundamental functions of each GI tract organ and summarize the diversity of epithelial structures present along the cephalocaudal axis of the GI tract. Next, we discuss findings, primarily from genetic mouse models, that have defined the roles of key transcription factors during epithelial morphogenesis, including p63, SOX2, SOX15, GATA4, GATA6, HNF4A, and HNF4G. Additionally, we examine how the Hedgehog, WNT, and BMP signaling pathways contribute to defining unique epithelial features along the cephalocaudal axis of the GI tract. Lastly, we examine the molecular mechanisms controlling regionalized cytodifferentiation of organ-specific epithelial cell types within the GI tract, concentrating on the stomach and small intestine. The delineation of GI epithelial patterning mechanisms in mice has provided fundamental knowledge to guide the development and refinement of three-dimensional GI organotypic culture models such as those derived from directed differentiation of human pluripotent stem cells and those derived directly from human tissue samples. Continued examination of these pathways will undoubtedly provide vital insights into the mechanisms of GI development and disease and may afford new avenues for innovative tissue engineering and personalized medicine approaches to treating GI diseases.
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Matsu-Ura T, Moore SR, Hong CI. WNT Takes Two to Tango: Molecular Links between the Circadian Clock and the Cell Cycle in Adult Stem Cells. J Biol Rhythms 2017; 33:5-14. [PMID: 29277155 DOI: 10.1177/0748730417745913] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Like two dancers, the circadian clock and cell cycle are biological oscillators engaged in bidirectional communication, resulting in circadian clock-gated cell division cycles in species ranging from cyanobacteria to mammals. The identified mechanisms for this phenomenon have expanded beyond intracellular molecular coupling components to include intercellular connections. However, detailed molecular mechanisms, dynamics, and physiological functions of the circadian clock and cell cycle as coupled oscillators remain largely unknown. In this review, we discuss current understanding of this connection in light of recent findings that have uncovered intercellular coupling between the circadian clock in Paneth cells and the cell cycle in intestinal stem cells via WNT signaling. This extends the impact of circadian rhythms regulating the timing of cell divisions beyond the intracellular domain of homogenous cell populations into dynamic, multicellular systems. In-depth understanding of the molecular links and dynamics of these two oscillators will identify potential targets and temporal regimens for effective chronotherapy.
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Affiliation(s)
- Toru Matsu-Ura
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Sean R Moore
- Division of Pediatric Gastroenterology, Hepatology & Nutrition, Department of Pediatrics, University of Virginia School of Medicine, UVA Child Health Research Center, Virginia
| | - Christian I Hong
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, Ohio.,Department of Pediatrics, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Ohio
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Ramanathan A, Srijaya TC, Sukumaran P, Zain RB, Abu Kasim NH. Homeobox genes and tooth development: Understanding the biological pathways and applications in regenerative dental science. Arch Oral Biol 2017; 85:23-39. [PMID: 29031235 DOI: 10.1016/j.archoralbio.2017.09.033] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 09/27/2017] [Accepted: 09/30/2017] [Indexed: 12/31/2022]
Abstract
OBJECTIVES Homeobox genes are a group of conserved class of transcription factors that function as key regulators during the embryonic developmental processes. They act as master regulator for developmental genes, which involves coordinated actions of various auto and cross-regulatory mechanisms. In this review, we summarize the expression pattern of homeobox genes in relation to the tooth development and various signaling pathways or molecules contributing to the specific actions of these genes in the regulation of odontogenesis. MATERIALS AND METHODS An electronic search was undertaken using combination of keywords e.g. Homeobox genes, tooth development, dental diseases, stem cells, induced pluripotent stem cells, gene control region was used as search terms in PubMed and Web of Science and relevant full text articles and abstract were retrieved that were written in English. A manual hand search in text books were also carried out. Articles related to homeobox genes in dentistry and tissue engineering and regenerative medicine of odontogenesis were selected. RESULTS The possible perspective of stem cells technology in odontogenesis and subsequent analysis of gene correction pertaining to dental disorders through the possibility of induced pluripotent stem cells technology is also inferred. CONCLUSIONS We demonstrate the promising role of tissue engineering and regenerative medicine on odontogenesis, which can generate a new ray of hope in the field of dental science.
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Affiliation(s)
- Anand Ramanathan
- Oral Cancer Research and Coordinating Center, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia; Department of Oral & Maxillofacial Clinical Science, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia.
| | | | - Prema Sukumaran
- Department of Restorative Dentistry, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia.
| | - Rosnah Binti Zain
- Oral Cancer Research and Coordinating Center, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia; Department of Oral & Maxillofacial Clinical Science, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia; Faculty of Dentistry, MAHSA University, Jenjarom, Selangor, Malaysia.
| | - Noor Hayaty Abu Kasim
- Department of Restorative Dentistry, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia.
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48
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Trecartin A, Grikscheit T. Tissue Engineering Functional Gastrointestinal Regions: The Importance of Stem and Progenitor Cells. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a025700. [PMID: 28320829 DOI: 10.1101/cshperspect.a025700] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The intestine shows extraordinary regenerative potential that might be harnessed to alleviate numerous morbid and lethal human diseases. The intestinal stem cells regenerate the epithelium every 5 days throughout an individual's lifetime. Understanding stem-cell signaling affords power to influence the niche environment for growing intestine. The manifold approaches to tissue engineering may be organized by variations of three basic components required for the transplantation and growth of stem/progenitor cells: (1) cell delivery materials or scaffolds; (2) donor cells including adult stem cells, induced pluripotent stem cells, and in vitro expansion of isolated or cocultured epithelial, smooth muscle, myofibroblasts, or nerve cells; and (3) environmental modulators or biopharmaceuticals. Tissue engineering has been applied to the regeneration of every major region of the gastrointestinal tract from esophagus to colon, with scientists around the world aiming to carry these techniques into human therapy.
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Affiliation(s)
- Andrew Trecartin
- Department of Pediatric Surgery, Children's Hospital Los Angeles, Los Angeles, California 90027
| | - Tracy Grikscheit
- Department of Pediatric Surgery, Children's Hospital Los Angeles, Los Angeles, California 90027
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Abstract
Metaplasia is the replacement of one differentiated somatic cell type with another differentiated somatic cell type in the same tissue. Typically, metaplasia is triggered by environmental stimuli, which may act in concert with the deleterious effects of microorganisms and inflammation. The cell of origin for intestinal metaplasia in the oesophagus and stomach and for pancreatic acinar-ductal metaplasia has been posited through genetic mouse models and lineage tracing but has not been identified in other types of metaplasia, such as squamous metaplasia. A hallmark of metaplasia is a change in cellular identity, and this process can be regulated by transcription factors that initiate and/or maintain cellular identity, perhaps in concert with epigenetic reprogramming. Universally, metaplasia is a precursor to low-grade dysplasia, which can culminate in high-grade dysplasia and carcinoma. Improved clinical screening for and surveillance of metaplasia might lead to better prevention or early detection of dysplasia and cancer.
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Affiliation(s)
- Veronique Giroux
- University of Pennsylvania Perelman School of Medicine, 951 BRB, 421 Curie Boulevard, Philadelphia, Pennsylvania 19104, USA
| | - Anil K Rustgi
- University of Pennsylvania Perelman School of Medicine, 951 BRB, 421 Curie Boulevard, Philadelphia, Pennsylvania 19104, USA
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50
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Flanagan DJ, Vincan E, Phesse TJ. Winding back Wnt signalling: potential therapeutic targets for treating gastric cancers. Br J Pharmacol 2017; 174:4666-4683. [PMID: 28568899 DOI: 10.1111/bph.13890] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 05/17/2017] [Accepted: 05/22/2017] [Indexed: 12/21/2022] Open
Abstract
Gastric cancer persists as a frequent and deadly disease that claims over 700 000 lives annually. Gastric cancer is a multifactorial disease that is genetically, cytologically and architecturally more heterogeneous than other gastrointestinal cancers, making it therapeutically challenging. As such, and largely attributed to late-stage diagnosis, gastric cancer patients show only partial response to standard chemo and targeted molecular therapies, highlighting an urgent need to develop new targeted therapies for this disease. Wnt signalling has a well-documented history in the genesis of many cancers and is, therefore, an attractive therapeutic target. As such, drug discovery has focused on developing inhibitors that target multiple nodes of the Wnt signalling cascade, some of which have progressed to clinical trials. The collective efforts of patient genomic profiling has uncovered genetic lesions to multiple components of the Wnt pathway in gastric cancer patients, which strongly suggest that Wnt-targeted therapies could offer therapeutic benefits for gastric cancer patients. These data have been supported by studies in mouse models of gastric cancer, which identify Wnt signalling as a driver of gastric tumourigenesis. Here, we review the current literature regarding Wnt signalling in gastric cancer and highlight the suitability of each class of Wnt inhibitor as a potential treatment for gastric cancer patients, in relation to the type of Wnt deregulation observed. LINKED ARTICLES This article is part of a themed section on WNT Signalling: Mechanisms and Therapeutic Opportunities. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.24/issuetoc.
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Affiliation(s)
- Dustin J Flanagan
- Molecular Oncology Laboratory, University of Melbourne, Melbourne, VIC, Australia.,Victorian Infectious Diseases Reference Laboratory, Doherty Institute of Infection and Immunity, Melbourne, VIC, Australia
| | - Elizabeth Vincan
- Molecular Oncology Laboratory, University of Melbourne, Melbourne, VIC, Australia.,Victorian Infectious Diseases Reference Laboratory, Doherty Institute of Infection and Immunity, Melbourne, VIC, Australia.,School of Biomedical Sciences, Curtin University, Perth, WA, Australia
| | - Toby J Phesse
- Molecular Oncology Laboratory, University of Melbourne, Melbourne, VIC, Australia.,Victorian Infectious Diseases Reference Laboratory, Doherty Institute of Infection and Immunity, Melbourne, VIC, Australia.,Cell Signalling and Cancer Laboratory, European Cancer Stem Cell Research Institute, Cardiff University, Cardiff, UK
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