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Wang X, Guo L, Zhang B, Wu J, Sun Y, Tao H, Sha J, Zhai J, Liu M. Haploinsufficiencies of FOXF1, FOXC2 and FOXL1 genes originated from deleted 16q24.1q24.2 fragment related with alveolar capillary dysplasia with misalignment of pulmonary veins and lymphedema-distichiasis syndrome: relationship to phenotype. Mol Cytogenet 2022; 15:48. [PMID: 36329475 PMCID: PMC9632103 DOI: 10.1186/s13039-022-00627-9] [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: 08/24/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
Objective We describe a fetus with a 2.12-Mb terminal deleted fragment in 16q associated with alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) and lymphedema-distichiasis syndrome (LDS) and intend to provide a comprehensive prenatal management strategy for the fetuses with ACDMPV and LDS through reviewing other similar published studies. Methods The fetus presented a series of diverse structural malformations including congenital cardiovascular, genitourinary and gastro-intestinal anomalies in ultrasound at 23 + 5 weeks of gestation (GA).
Amniocentesis was conducted for karyotype analysis and copy number variation sequencing (CNV-seq) after informed consent. Results The fetal karyotype was 46,XX, however the result of CNV-seq showed an approximately 2.12-Mb deletion in 16q24.1q24.2 (85220000-87340000) × 1 indicating pathogenicity. Conclusion Genomic testing should be recommend as a first line diagnostic tool for suspected ACDMPV and/or LDS or other genetic syndromes for the fetuses with structural abnormalities in clinical practice.
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Affiliation(s)
- Xuezhen Wang
- grid.252957.e0000 0001 1484 5512Graduate School of Bengbu Medical College, Donghai Avenue No. 2600, Bengbu, 233000 Anhui China ,grid.452207.60000 0004 1758 0558Department of Prenatal Diagnosis Medical Center, Xuzhou Central Hospital, No. 199 South Jiefang Road, Xuzhou, 221009 Jiangsu China
| | - Lili Guo
- grid.252957.e0000 0001 1484 5512Graduate School of Bengbu Medical College, Donghai Avenue No. 2600, Bengbu, 233000 Anhui China ,grid.452207.60000 0004 1758 0558Department of Prenatal Diagnosis Medical Center, Xuzhou Central Hospital, No. 199 South Jiefang Road, Xuzhou, 221009 Jiangsu China
| | - Bei Zhang
- grid.252957.e0000 0001 1484 5512Graduate School of Bengbu Medical College, Donghai Avenue No. 2600, Bengbu, 233000 Anhui China ,grid.452207.60000 0004 1758 0558Department of Prenatal Diagnosis Medical Center, Xuzhou Central Hospital, No. 199 South Jiefang Road, Xuzhou, 221009 Jiangsu China ,grid.417303.20000 0000 9927 0537Graduate School of Xuzhou Medical University, Jiangsu, 221000 Xuzhou China
| | - Jiebin Wu
- grid.252957.e0000 0001 1484 5512Graduate School of Bengbu Medical College, Donghai Avenue No. 2600, Bengbu, 233000 Anhui China ,grid.452207.60000 0004 1758 0558Department of Prenatal Diagnosis Medical Center, Xuzhou Central Hospital, No. 199 South Jiefang Road, Xuzhou, 221009 Jiangsu China ,grid.417303.20000 0000 9927 0537Graduate School of Xuzhou Medical University, Jiangsu, 221000 Xuzhou China
| | - Yu Sun
- grid.417303.20000 0000 9927 0537Graduate School of Xuzhou Medical University, Jiangsu, 221000 Xuzhou China ,Department of Obstetrics, Fengxian People’s Hospital, Feng Xian Renmin West Road No.51, Xuzhou, 221700 Jiangsu China
| | - Huimin Tao
- grid.452207.60000 0004 1758 0558Department of Prenatal Diagnosis Medical Center, Xuzhou Central Hospital, No. 199 South Jiefang Road, Xuzhou, 221009 Jiangsu China ,grid.417303.20000 0000 9927 0537Graduate School of Xuzhou Medical University, Jiangsu, 221000 Xuzhou China
| | - Jing Sha
- grid.452207.60000 0004 1758 0558Department of Prenatal Diagnosis Medical Center, Xuzhou Central Hospital, No. 199 South Jiefang Road, Xuzhou, 221009 Jiangsu China
| | - Jingfang Zhai
- grid.252957.e0000 0001 1484 5512Graduate School of Bengbu Medical College, Donghai Avenue No. 2600, Bengbu, 233000 Anhui China ,grid.452207.60000 0004 1758 0558Department of Prenatal Diagnosis Medical Center, Xuzhou Central Hospital, No. 199 South Jiefang Road, Xuzhou, 221009 Jiangsu China ,grid.417303.20000 0000 9927 0537Graduate School of Xuzhou Medical University, Jiangsu, 221000 Xuzhou China
| | - Min Liu
- grid.452207.60000 0004 1758 0558Department of Prenatal Diagnosis Medical Center, Xuzhou Central Hospital, No. 199 South Jiefang Road, Xuzhou, 221009 Jiangsu China ,grid.417303.20000 0000 9927 0537Graduate School of Xuzhou Medical University, Jiangsu, 221000 Xuzhou China
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Elaidy NF, Harb OA, Mohamed AM, Hemeda R, Taha HF, Samir A, Elsayed AM, Osman G, Hendawy EIE. Prognostic Significances of NEDD-9 and FOXL-1 Expression in Intestinal Type Gastric Carcinoma: an Immunohistochemical Study. J Gastrointest Cancer 2021; 52:728-737. [PMID: 32794109 DOI: 10.1007/s12029-020-00471-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND Gastric cancer (GC) is mostly diagnosed at advanced stage, so prognosis is poor. Therefore, it is necessary to understand the molecular mechanism of GC development to design new targeted treatment to improve the prognosis of gastric cancer patients. AIM OF THE WORK To assess the prognostic value of NEDD-9 and FOXL-1 expression in intestinal type gastric cancer patients, as well as their relationship to clinicopathologic features of the disease and patients outcome. PATIENTS AND METHODS This is a retrospective study; we included 50 sections from formalin-fixed, paraffin-embedded tissue samples which included intestinal type GC and adjacent non-neoplastic gastric mucosa in the same block that were subjected to immunohistochemistry with anti-NEDD-9 and anti-FOXL-1 antibody. Patients were retrospectively followed up for about 5 years for assessment of tumor progression and survival in relation to marker expression. RESULTS High NEDD-9 and low FOXL-1 expression were found in intestinal type GC more than adjacent non-neoplastic mucosa (p < 0.001). NEDD-9 high expression and FOXL-1 low expression were associated with presence of helicobacter pylori gastritis (p = 0.010, 0.049), high grade (p = 0.007, 0.004), high stage (p < 0.001), presence of distant metastases (p = 0.029, 0.021), poor DFS (p = 0.003), and OS rates (< 0.001). CONCLUSION NEDD-9 overexpression and FOXL-1 deficiency in intestinal type GC can help in prediction of tumor prognosis and it can guide the selection of patients for future therapies in gastric carcinoma.
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Affiliation(s)
- Noha F Elaidy
- Department of Pathology, Faculty of Medicine, Zagazig University, Zagazig, 44519, Egypt
| | - Ola A Harb
- Department of Pathology, Faculty of Medicine, Zagazig University, Zagazig, 44519, Egypt.
| | - Abdel Motaleb Mohamed
- Department of Clinical Oncology& Nuclear Medicine, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Rehab Hemeda
- Department of Clinical Oncology& Nuclear Medicine, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Heba F Taha
- Department of Medical Oncology, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Amr Samir
- Department of Internal Medicine, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Ahmed M Elsayed
- Department of Tropical Medicine, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Gamal Osman
- Department of General Surgery, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Elsayed I El Hendawy
- Department of General Surgery, Faculty of Medicine, Zagazig University, Zagazig, Egypt
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3
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Pilarowski GO, Cazares T, Zhang L, Benjamin JS, Liu K, Jagannathan S, Mousa N, Kasten J, Barski A, Lindsley AW, Bjornsson HT. Abnormal Peyer patch development and B-cell gut homing drive IgA deficiency in Kabuki syndrome. J Allergy Clin Immunol 2020; 145:982-992. [DOI: 10.1016/j.jaci.2019.11.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/05/2019] [Accepted: 11/14/2019] [Indexed: 01/17/2023]
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Abstract
Tissues that undergo rapid cellular turnover, such as the mammalian haematopoietic system or the intestinal epithelium, are dependent on stem and progenitor cells that proliferate to provide differentiated cells to maintain organismal health. Stem and progenitor cells, in turn, are thought to rely on signals and growth factors provided by local niche cells to support their function and self-renewal. Several cell types have been hypothesized to provide the signals required for the proliferation and differentiation of the intestinal stem cells in intestinal crypts1-6. Here we identify subepithelial telocytes as an important source of Wnt proteins, without which intestinal stem cells cannot proliferate and support epithelial renewal. Telocytes are large but rare mesenchymal cells that are marked by expression of FOXL1 and form a subepithelial plexus that extends from the stomach to the colon. While supporting the entire epithelium, FOXL1+ telocytes compartmentalize the production of Wnt ligands and inhibitors to enable localized pathway activation. Conditional genetic ablation of porcupine (Porcn), which is required for functional maturation of all Wnt proteins, in mouse FOXL1+ telocytes causes rapid cessation of Wnt signalling to intestinal crypts, followed by loss of proliferation of stem and transit amplifying cells and impaired epithelial renewal. Thus, FOXL1+ telocytes are an important source of niche signals to intestinal stem cells.
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Shoshkes-Carmel M, Wang YJ, Wangensteen KJ, Tóth B, Kondo A, Massasa EE, Itzkovitz S, Kaestner KH. Subepithelial telocytes are an important source of Wnts that supports intestinal crypts. Nature 2018; 557:242-246. [PMID: 29720649 PMCID: PMC5966331 DOI: 10.1038/s41586-018-0084-4] [Citation(s) in RCA: 349] [Impact Index Per Article: 58.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 02/27/2018] [Indexed: 12/03/2022]
Abstract
Tissues with rapid cellular turnover, such as the mammalian hematopoietic system or the intestinal epithelium, are dependent upon stem and progenitor cells, which through proliferation provide differentiated cells to maintain organismal health. Stem and progenitor cells, in turn, are thought to rely upon signals and growth factors provided by local niche cells to support their function and self-renewal. Several cell types have been proposed to provide the signals required for the proliferation and differentiation of the ISC in the crypt1–6. Here, we identify subepithelial telocytes as an important source of Wnt proteins, without which intestinal stem cells cannot proliferate and support epithelial renewal. Telocytes are large but rare mesenchymal cells that are marked by Foxl1 and PDGFRα expression and form a subepithelial plexus that extends from the stomach to the colon. While supporting the entire epithelium, Foxl1+ telocytes compartmentalize the production of Wnt ligands and inhibitors to enable localized pathway activation. Conditional gene ablation of Porcupine (Porcn), which is required for functional maturation of all Wnt proteins, in Foxl1+ telocytes causes rapid cessation of Wnt signaling to intestinal crypts, followed by loss of stem and transit amplifying cell proliferation and impaired epithelial renewal. Thus, Foxl1+ telocytes are an important source of niche signals to intestinal stem cells.
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Affiliation(s)
- Michal Shoshkes-Carmel
- Department of Genetics and Center for Molecular Studies in Digestive and Liver Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yue J Wang
- Department of Genetics and Center for Molecular Studies in Digestive and Liver Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kirk J Wangensteen
- Department of Genetics and Center for Molecular Studies in Digestive and Liver Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Beáta Tóth
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ayano Kondo
- Department of Genetics and Center for Molecular Studies in Digestive and Liver Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Efi E Massasa
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Klaus H Kaestner
- Department of Genetics and Center for Molecular Studies in Digestive and Liver Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Srinivasan L, Page G, Kirpalani H, Murray JC, Das A, Higgins RD, Carlo WA, Bell EF, Goldberg RN, Schibler K, Sood BG, Stevenson DK, Stoll BJ, Van Meurs KP, Johnson KJ, Levy J, McDonald SA, Zaterka-Baxter KM, Kennedy KA, Sánchez PJ, Duara S, Walsh MC, Shankaran S, Wynn JL, Cotten CM. Genome-wide association study of sepsis in extremely premature infants. Arch Dis Child Fetal Neonatal Ed 2017; 102:F439-F445. [PMID: 28283553 PMCID: PMC5563277 DOI: 10.1136/archdischild-2016-311545] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 02/02/2017] [Accepted: 02/13/2017] [Indexed: 12/16/2022]
Abstract
OBJECTIVE To identify genetic variants associated with sepsis (early-onset and late-onset) using a genome-wide association (GWA) analysis in a cohort of extremely premature infants. STUDY DESIGN Previously generated GWA data from the Neonatal Research Network's anonymised genomic database biorepository of extremely premature infants were used for this study. Sepsis was defined as culture-positive early-onset or late-onset sepsis or culture-proven meningitis. Genomic and whole-genome-amplified DNA was genotyped for 1.2 million single-nucleotide polymorphisms (SNPs); 91% of SNPs were successfully genotyped. We imputed 7.2 million additional SNPs. p Values and false discovery rates (FDRs) were calculated from multivariate logistic regression analysis adjusting for gender, gestational age and ancestry. Target statistical value was p<10-5. Secondary analyses assessed associations of SNPs with pathogen type. Pathway analyses were also run on primary and secondary end points. RESULTS Data from 757 extremely premature infants were included: 351 infants with sepsis and 406 infants without sepsis. No SNPs reached genome-wide significance levels (5×10-8); two SNPs in proximity to FOXC2 and FOXL1 genes achieved target levels of significance. In secondary analyses, SNPs for ELMO1, IRAK2 (Gram-positive sepsis), RALA, IMMP2L (Gram-negative sepsis) and PIEZO2 (fungal sepsis) met target significance levels. Pathways associated with sepsis and Gram-negative sepsis included gap junctions, fibroblast growth factor receptors, regulators of cell division and interleukin-1-associated receptor kinase 2 (p values<0.001 and FDR<20%). CONCLUSIONS No SNPs met genome-wide significance in this cohort of extremely low birthweight infants; however, areas of potential association and pathways meriting further study were identified.
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Affiliation(s)
- Lakshmi Srinivasan
- Department of Pediatrics, The Children’s Hospital of Philadelphia and The University of Pennsylvania, Philadelphia, PA
| | - Grier Page
- Social, Statistical and Environmental Sciences Unit, RTI International, Research Triangle Park, NC
| | - Haresh Kirpalani
- Department of Pediatrics, The Children’s Hospital of Philadelphia and The University of Pennsylvania, Philadelphia, PA
| | | | - Abhik Das
- Social, Statistical and Environmental Sciences Unit, RTI International, Rockville, MD
| | - Rosemary D. Higgins
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Waldemar A. Carlo
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL
| | - Edward F. Bell
- University of Iowa, Department of Pediatrics, Iowa City, IA
| | | | - Kurt Schibler
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH
| | - Beena G. Sood
- Department of Pediatrics, Wayne State University, Detroit, MI
| | - David K. Stevenson
- Department of Pediatrics, Division of Neonatal and Developmental Medicine, Stanford University School of Medicine and Lucile Packard Children’s Hospital, Palo Alto, CA
| | - Barbara J. Stoll
- Emory University School of Medicine, Department of Pediatrics, Children’s Healthcare of Atlanta, Atlanta, GA
| | - Krisa P. Van Meurs
- Department of Pediatrics, Division of Neonatal and Developmental Medicine, Stanford University School of Medicine and Lucile Packard Children’s Hospital, Palo Alto, CA
| | | | - Joshua Levy
- Social, Statistical and Environmental Sciences Unit, RTI International, Research Triangle Park, NC
| | - Scott A. McDonald
- Social, Statistical and Environmental Sciences Unit, RTI International, Research Triangle Park, NC
| | | | - Kathleen A. Kennedy
- Department of Pediatrics, University of Texas Medical School at Houston, Houston, TX
| | - Pablo J. Sánchez
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Shahnaz Duara
- University of Miami Miller School of Medicine, Miami, FL
| | - Michele C. Walsh
- Department of Pediatrics, Rainbow Babies & Children’s Hospital, Case Western Reserve University, Cleveland, OH
| | | | - James L. Wynn
- Department of Pediatrics, University of Florida, Gainesville, FL
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7
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Low level of FOXL1 indicates a worse prognosis for gastric cancer patients. Tumour Biol 2016; 37:11331-7. [DOI: 10.1007/s13277-016-4890-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 01/19/2016] [Indexed: 12/26/2022] Open
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Yu S, Shao L, Kilbride H, Zwick DL. Haploinsufficiencies of FOXF1 and FOXC2 genes associated with lethal alveolar capillary dysplasia and congenital heart disease. Am J Med Genet A 2010; 152A:1257-62. [PMID: 20425831 DOI: 10.1002/ajmg.a.33378] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Neonatal deaths account for about 67% of all deaths during the first year of life in the USA. Genetic defects are important factors contributing to neonatal deaths and congenital anomalies. Here we report on the identification of a 1.37 Mb de novo deletion of chromosome 16q24.1-q24.2 by microarray-based comparative genomic hybridization (aCGH) technique in a newborn boy with lethal severe alveolar capillary dysplasia and multiple congenital anomalies who died of irreversible pulmonary hypertension, respiratory failure and cor pulmonale at three days of age. The phenotypic findings and causal genes (FOXF1 and FOXC2) involved in producing this unusual syndrome are detailed. Our findings independently confirm the results in a previous publication describing multiple patients with similar clinical and genetic observations, and highlight the importance of scanning human genomes at high resolution for identifications of micro-imbalances as pathogenic causes in neonates with unexplained congenital anomalies. (c) 2010 Wiley-Liss, Inc.
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Affiliation(s)
- Shihui Yu
- Children's Mercy Hospitals and Clinics and University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
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Moose HE, Kelly LE, Nekkalapudi S, El-Hodiri HM. Ocular forkhead transcription factors: seeing eye to eye. THE INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY 2009; 53:29-36. [PMID: 19123124 DOI: 10.1387/ijdb.072505hm] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Forkhead transcription factors comprise a large family of proteins with diverse functions during development. Recently, there has been accumulating evidence that several members of this family of proteins play an important role in the development of the vertebrate retina. Here, we summarize the cumulative data which demonstrates the integral role that forkhead factors play in cell cycle control of retinal precursors, as well as in cell fate determination, during retinal development. The expression patterns for 14 retinal expressed forkhead transcription factors are presented with an emphasis on comparing the expression profiles across species. The functional data regarding forkhead gene products expressed within the retina are discussed. As presented, these data suggest that forkhead gene products contribute to the complex regulation of proliferation and differentiation of retinal precursors during vertebrate eye development.
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Affiliation(s)
- Holly E Moose
- Integrated Biomedical Sciences Graduate Program, College of Medicine, The Ohio State University, Columbus, OH 43205, USA
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10
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Genomic and genic deletions of the FOX gene cluster on 16q24.1 and inactivating mutations of FOXF1 cause alveolar capillary dysplasia and other malformations. Am J Hum Genet 2009; 84:780-91. [PMID: 19500772 PMCID: PMC2694971 DOI: 10.1016/j.ajhg.2009.05.005] [Citation(s) in RCA: 308] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2009] [Revised: 05/14/2009] [Accepted: 05/18/2009] [Indexed: 11/30/2022] Open
Abstract
Alveolar capillary dysplasia with misalignment of pulmonary veins (ACD/MPV) is a rare, neonatally lethal developmental disorder of the lung with defining histologic abnormalities typically associated with multiple congenital anomalies (MCA). Using array CGH analysis, we have identified six overlapping microdeletions encompassing the FOX transcription factor gene cluster in chromosome 16q24.1q24.2 in patients with ACD/MPV and MCA. Subsequently, we have identified four different heterozygous mutations (frameshift, nonsense, and no-stop) in the candidate FOXF1 gene in unrelated patients with sporadic ACD/MPV and MCA. Custom-designed, high-resolution microarray analysis of additional ACD/MPV samples revealed one microdeletion harboring FOXF1 and two distinct microdeletions upstream of FOXF1, implicating a position effect. DNA sequence analysis revealed that in six of nine deletions, both breakpoints occurred in the portions of Alu elements showing eight to 43 base pairs of perfect microhomology, suggesting replication error Microhomology-Mediated Break-Induced Replication (MMBIR)/Fork Stalling and Template Switching (FoSTeS) as a mechanism of their formation. In contrast to the association of point mutations in FOXF1 with bowel malrotation, microdeletions of FOXF1 were associated with hypoplastic left heart syndrome and gastrointestinal atresias, probably due to haploinsufficiency for the neighboring FOXC2 and FOXL1 genes. These differences reveal the phenotypic consequences of gene alterations in cis.
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11
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Gohlke JM, Thomas R, Zhang Y, Rosenstein MC, Davis AP, Murphy C, Becker KG, Mattingly CJ, Portier CJ. Genetic and environmental pathways to complex diseases. BMC SYSTEMS BIOLOGY 2009; 3:46. [PMID: 19416532 PMCID: PMC2680807 DOI: 10.1186/1752-0509-3-46] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Accepted: 05/05/2009] [Indexed: 12/23/2022]
Abstract
BACKGROUND Pathogenesis of complex diseases involves the integration of genetic and environmental factors over time, making it particularly difficult to tease apart relationships between phenotype, genotype, and environmental factors using traditional experimental approaches. RESULTS Using gene-centered databases, we have developed a network of complex diseases and environmental factors through the identification of key molecular pathways associated with both genetic and environmental contributions. Comparison with known chemical disease relationships and analysis of transcriptional regulation from gene expression datasets for several environmental factors and phenotypes clustered in a metabolic syndrome and neuropsychiatric subnetwork supports our network hypotheses. This analysis identifies natural and synthetic retinoids, antipsychotic medications, Omega 3 fatty acids, and pyrethroid pesticides as potential environmental modulators of metabolic syndrome phenotypes through PPAR and adipocytokine signaling and organophosphate pesticides as potential environmental modulators of neuropsychiatric phenotypes. CONCLUSION Identification of key regulatory pathways that integrate genetic and environmental modulators define disease associated targets that will allow for efficient screening of large numbers of environmental factors, screening that could set priorities for further research and guide public health decisions.
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Affiliation(s)
- Julia M Gohlke
- Environmental Systems Biology Group, Laboratory of Molecular Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Reuben Thomas
- Environmental Systems Biology Group, Laboratory of Molecular Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Yonqing Zhang
- Gene Expression and Genomics Unit, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Michael C Rosenstein
- Department of Bioinformatics, Mount Desert Island Biological Laboratory, Old Bar Harbor Road, Salisbury Cove, ME 04672, USA
| | - Allan P Davis
- Department of Bioinformatics, Mount Desert Island Biological Laboratory, Old Bar Harbor Road, Salisbury Cove, ME 04672, USA
| | - Cynthia Murphy
- Department of Bioinformatics, Mount Desert Island Biological Laboratory, Old Bar Harbor Road, Salisbury Cove, ME 04672, USA
| | - Kevin G Becker
- Gene Expression and Genomics Unit, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Carolyn J Mattingly
- Department of Bioinformatics, Mount Desert Island Biological Laboratory, Old Bar Harbor Road, Salisbury Cove, ME 04672, USA
| | - Christopher J Portier
- Environmental Systems Biology Group, Laboratory of Molecular Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
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12
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Madison BB, McKenna LB, Dolson D, Epstein DJ, Kaestner KH. FoxF1 and FoxL1 link hedgehog signaling and the control of epithelial proliferation in the developing stomach and intestine. J Biol Chem 2008; 284:5936-44. [PMID: 19049965 DOI: 10.1074/jbc.m808103200] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The hedgehog (Hh) signaling pathway is a key component of cross-talk during vertebrate gut development, involving endodermally secreted Sonic (Shh) and Indian hedgehog (Ihh) proteins that directly signal to adjacent mesoderm. Here we show that the closely linked mesenchymal forkhead transcription factors Foxf1 and Foxl1 are part of this signaling cascade. Analysis of conserved non-coding sequences surrounding Foxf1 and Foxl1 identified seven Gli binding sites, with two sites near Foxl1 being identical among mammalian, bird, fish, and amphibian species. In vitro experiments indicate that Gli2 binds to these Gli sites, several of which are critical for Gli2-mediated activation of a luciferase reporter in 293 cells. In addition, we demonstrate occupancy of one of these elements by Gli proteins in the intestine in vivo using chromatin immunoprecipitation. Furthermore, expression of both Foxf1 and Foxl1 is reduced in the Gli2/Gli3 mutant gut. These results provide compelling evidence that Foxf1 and Foxl1 are mediators of the Hh (endoderm) to mesoderm signaling pathway.
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Affiliation(s)
- Blair B Madison
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
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13
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Chen BS, Yang SK, Lan CY, Chuang YJ. A systems biology approach to construct the gene regulatory network of systemic inflammation via microarray and databases mining. BMC Med Genomics 2008; 1:46. [PMID: 18823570 PMCID: PMC2567339 DOI: 10.1186/1755-8794-1-46] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Accepted: 09/30/2008] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Inflammation is a hallmark of many human diseases. Elucidating the mechanisms underlying systemic inflammation has long been an important topic in basic and clinical research. When primary pathogenetic events remains unclear due to its immense complexity, construction and analysis of the gene regulatory network of inflammation at times becomes the best way to understand the detrimental effects of disease. However, it is difficult to recognize and evaluate relevant biological processes from the huge quantities of experimental data. It is hence appealing to find an algorithm which can generate a gene regulatory network of systemic inflammation from high-throughput genomic studies of human diseases. Such network will be essential for us to extract valuable information from the complex and chaotic network under diseased conditions. RESULTS In this study, we construct a gene regulatory network of inflammation using data extracted from the Ensembl and JASPAR databases. We also integrate and apply a number of systematic algorithms like cross correlation threshold, maximum likelihood estimation method and Akaike Information Criterion (AIC) on time-lapsed microarray data to refine the genome-wide transcriptional regulatory network in response to bacterial endotoxins in the context of dynamic activated genes, which are regulated by transcription factors (TFs) such as NF-kappaB. This systematic approach is used to investigate the stochastic interaction represented by the dynamic leukocyte gene expression profiles of human subject exposed to an inflammatory stimulus (bacterial endotoxin). Based on the kinetic parameters of the dynamic gene regulatory network, we identify important properties (such as susceptibility to infection) of the immune system, which may be useful for translational research. Finally, robustness of the inflammatory gene network is also inferred by analyzing the hubs and "weak ties" structures of the gene network. CONCLUSION In this study, Data mining and dynamic network analyses were integrated to examine the gene regulatory network in the inflammatory response system. Compared with previous methodologies reported in the literatures, the proposed gene network perturbation method has shown a great improvement in analyzing the systemic inflammation.
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Affiliation(s)
- Bor-Sen Chen
- Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Shih-Kuang Yang
- Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Chung-Yu Lan
- Department of Life Science, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Yung-Jen Chuang
- Department of Life Science, National Tsing Hua University, Hsinchu, 300, Taiwan
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14
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Saban MR, O'Donnell MA, Hurst RE, Wu XR, Simpson C, Dozmorov I, Davis C, Saban R. Molecular networks discriminating mouse bladder responses to intravesical bacillus Calmette-Guerin (BCG), LPS, and TNF-alpha. BMC Immunol 2008; 9:4. [PMID: 18267009 PMCID: PMC2262873 DOI: 10.1186/1471-2172-9-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2007] [Accepted: 02/11/2008] [Indexed: 12/26/2022] Open
Abstract
Background Despite being a mainstay for treating superficial bladder carcinoma and a promising agent for interstitial cystitis, the precise mechanism of Bacillus Calmette-Guerin (BCG) remains poorly understood. It is particularly unclear whether BCG is capable of altering gene expression in the bladder target organ beyond its well-recognized pro-inflammatory effects and how this relates to its therapeutic efficacy. The objective of this study was to determine differentially expressed genes in the mouse bladder following chronic intravesical BCG therapy and to compare the results to non-specific pro inflammatory stimuli (LPS and TNF-α). For this purpose, C57BL/6 female mice received four weekly instillations of BCG, LPS, or TNF-α. Seven days after the last instillation, the urothelium along with the submucosa was removed from detrusor muscle and the RNA was extracted from both layers for cDNA array experiments. Microarray results were normalized by a robust regression analysis and only genes with an expression above a conditional threshold of 0.001 (3SD above background) were selected for analysis. Next, genes presenting a 3-fold ratio in regard to the control group were entered in Ingenuity Pathway Analysis (IPA) for a comparative analysis in order to determine genes specifically regulated by BCG, TNF-α, and LPS. In addition, the transcriptome was precipitated with an antibody against RNA polymerase II and real-time polymerase chain reaction assay (Q-PCR) was used to confirm some of the BCG-specific transcripts. Results Molecular networks of treatment-specific genes generated several hypotheses regarding the mode of action of BCG. BCG-specific genes involved small GTPases and BCG-specific networks overlapped with the following canonical signaling pathways: axonal guidance, B cell receptor, aryl hydrocarbon receptor, IL-6, PPAR, Wnt/β-catenin, and cAMP. In addition, a specific detrusor network expressed a high degree of overlap with the development of the lymphatic system. Interestingly, TNF-α-specific networks overlapped with the following canonical signaling pathways: PPAR, death receptor, and apoptosis. Finally, LPS-specific networks overlapped with the LPS/IL-1 mediated inhibition of RXR. Because NF-kappaB occupied a central position in several networks, we further determined whether this transcription factor was part of the responses to BCG. Electrophoretic mobility shift assays confirmed the participation of NF-kappaB in the mouse bladder responses to BCG. In addition, BCG treatment of a human urothelial cancer cell line (J82) also increased the binding activity of NF-kappaB, as determined by precipitation of the chromatin by a NF-kappaB-p65 antibody and Q-PCR of genes bearing a NF-kappaB consensus sequence. Next, we tested the hypothesis of whether small GTPases such as LRG-47 are involved in the uptake of BCG by the bladder urothelium. Conclusion As expected, BCG treatment induces the transcription of genes belonging to common pro-inflammatory networks. However, BCG also induces unique genes belonging to molecular networks involved in axonal guidance and lymphatic system development within the bladder target organ. In addition, NF-kappaB seems to play a predominant role in the bladder responses to BCG therapy. Finally, in intact urothelium, BCG-GFP internalizes in LRG-47-positive vesicles. These results provide a molecular framework for the further study of the involvement of immune and nervous systems in the bladder responses to BCG therapy.
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Affiliation(s)
- Marcia R Saban
- College of Medicine, Department of Physiology, Oklahoma University Health Sciences Center (OUHSC), Oklahoma City, OK 73104, USA.
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15
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Nakada C, Satoh S, Tabata Y, Arai KI, Watanabe S. Transcriptional repressor foxl1 regulates central nervous system development by suppressing shh expression in zebra fish. Mol Cell Biol 2006; 26:7246-57. [PMID: 16980626 PMCID: PMC1592895 DOI: 10.1128/mcb.00429-06] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
We identified zebra fish forkhead transcription factor l1 (zfoxl1) as a gene strongly expressed in neural tissues such as midbrain, hindbrain, and the otic vesicle at the early embryonic stage. Loss of the function of zfoxl1 effected by morpholino antisense oligonucleotide resulted in defects in midbrain and eye development, and in that of formation of the pectoral fins. Interestingly, ectopic expression of shh in the midbrain and elevated pax2a expression in the optic stalk were observed in foxl1 MO-injected embryos. In contrast, expression of pax6a, which is negatively regulated by shh, was suppressed in the thalamus and pretectum regions, supporting the idea of augmentation of the shh signaling pathway by suppression of foxl1. Expression of zfoxl1-EnR (repressing) rather than zfoxl1-VP16 (activating) resulted in a phenotype similar to that induced by foxl1-mRNA, suggesting that foxl1 may act as a transcriptional repressor of shh in zebra fish embryos. Supporting this notion, foxl1 suppressed isolated 2.7-kb shh promoter activity in PC12 cells, and the minimal region of foxl1 required for its transcriptional repressor activity showed strong homology with the groucho binding motif, which is found in genes encoding various homeodomain proteins. In view of all of our data taken together, we propose zfoxl1 to be a novel regulator of neural development that acts by suppressing shh expression.
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MESH Headings
- Amino Acid Sequence
- Animals
- Biomarkers
- Brain/cytology
- Brain/embryology
- Brain/metabolism
- Cells, Cultured
- Embryo, Nonmammalian/cytology
- Embryo, Nonmammalian/embryology
- Fibroblasts/metabolism
- Forkhead Transcription Factors/chemistry
- Forkhead Transcription Factors/isolation & purification
- Forkhead Transcription Factors/metabolism
- Gastrula/metabolism
- Gene Expression Regulation, Developmental
- Hedgehog Proteins
- Mice
- Molecular Sequence Data
- NIH 3T3 Cells
- Oligonucleotides, Antisense/metabolism
- PC12 Cells
- Promoter Regions, Genetic/genetics
- Protein Binding
- Protein Structure, Tertiary
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Rats
- Repressor Proteins/chemistry
- Repressor Proteins/isolation & purification
- Repressor Proteins/metabolism
- Trans-Activators/genetics
- Trans-Activators/metabolism
- Transcription, Genetic
- Zebrafish/embryology
- Zebrafish/metabolism
- Zebrafish Proteins/chemistry
- Zebrafish Proteins/isolation & purification
- Zebrafish Proteins/metabolism
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Affiliation(s)
- Chisako Nakada
- Department of Molecular and Developmental Biology, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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16
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Abstract
During evolution, the development of secondary lymphoid organs has evolved as a strategy to promote adaptive immune responses at sites of antigen sequestration. Mesenteric lymph nodes (LNs) and Peyer's patches (PPs) are localized in proximity to mucosal surfaces, and their development is coordinated by a series of temporally and spatially regulated molecular events involving the collaboration between hematopoietic, mesenchymal, and, for PPs, epithelial cells. Transcriptional control of cellular differentiation, production of cytokines as well as adhesion molecules are mandatory for organogenesis, recruitment of mature leukocytes, and lymphoid tissue organization. Similar to fetal and neonatal organogenesis, lymphoid tissue neoformation can occur in adult individuals at sites of chronic stimulation via cytokines and TNF-family member molecules. These molecules represent new therapeutic targets to manipulate the microenvironment during autoimmune diseases.
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Affiliation(s)
- D Finke
- Center for Biomedicine, Developmental Immunology, Department of Clinical and Biological Sciences (DKBW), University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland.
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17
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Takano-Maruyama M, Hase K, Fukamachi H, Kato Y, Koseki H, Ohno H. Foxl1-deficient mice exhibit aberrant epithelial cell positioning resulting from dysregulated EphB/EphrinB expression in the small intestine. Am J Physiol Gastrointest Liver Physiol 2006; 291:G163-70. [PMID: 16469829 DOI: 10.1152/ajpgi.00019.2006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The winged helix transcription factor Foxl1, expressed in the gut mesenchyme, regulates epithelial cell proliferation and differentiation through the Wnt/beta-catenin pathway. To better understand the role of Foxl1 in epithelial morphogenesis, we examined the tissue structure and positioning of epithelial cells in the small intestine of Foxl1-deficient mice. The small intestine of Foxl1-deficient mice manifested aberrant crypt structure, including widely distributed Paneth cells, which coincided with the ectopic and increased expression of EphB2 and EphB3, which are key regulators of epithelial cell positioning. Furthermore, real-time quantitative PCR indicated that a subset of Wnt family genes was highly expressed in the gut mesenchyme of Foxl1-deficient mice compared with that of wild-type mice. Such an increase in Wnt expression was remarkable in the mesenchyme, where the aberrant Paneth cell positioning was observed by in situ hybridization. Foxl1 plays an important role in the maintenance of crypt architecture and epithelial cell positioning through the mesenchymal-epithelial interaction in the small intestine. This interaction is essential for the normal regulation of the Wnt/beta-catenin pathway and the subsequent EphB/EphrinB expression.
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Affiliation(s)
- Masumi Takano-Maruyama
- Laboratory for Epithelial Immunobiology, Research Center for Allergy and Immunology, RIKEN, 1-7-22 Suehiro, Tsurumi-ku, Yokohama 230-0045, Japan
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18
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Sato T, Endoh M, Yoshida H, Yasuo S, Katsuno T, Saito Y, Isono KI, Koseki H. Mammalian Polycomb complexes are required for Peyer's patch development by regulating lymphoid cell proliferation. Gene 2006; 379:166-74. [PMID: 16815646 DOI: 10.1016/j.gene.2006.05.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2006] [Revised: 05/10/2006] [Accepted: 05/11/2006] [Indexed: 10/24/2022]
Abstract
The vertebrate Polycomb Group (PcG) genes encode proteins that form large multimeric and chromatin-associated complexes implicated in the stable repression of developmentally essential genes. Rnf110 and Phc2 are shown to be components of mammalian PcG multimeric complexes in HeLa cells. Here we report defects in Peyer's patch (PP) development in Rnf110 mutant mice, which is synergically exaggerated by Phc2 mutation. PP development involves a series of inductive interactions and subsequent differentiation and proliferation between lymphoid and mesenchymal cells in late gestational stage. Rnf110 and Phc2 mutations impair development of PP anlagen by affecting proliferation of lymphoid lineage cells populated in PP anlagen in gene-dosage dependent manner. We suggest that PcG complexes may act to mediate certain inductive signals maybe through IL-7Ralpha to allow sufficient proliferation of lymphoid inducer cells during PP organogenesis.
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Affiliation(s)
- Toru Sato
- Department of Clinical Cell Biology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chiba, Japan
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19
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Abstract
Lymphotoxins (LT) provide essential communication links between lymphocytes and the surrounding stromal and parenchymal cells and together with the two related cytokines, tumor necrosis factor (TNF) and LIGHT (LT-related inducible ligand that competes for glycoprotein D binding to herpesvirus entry mediator on T cells), form an integrated signaling network necessary for efficient innate and adaptive immune responses. Recent studies have identified signaling pathways that regulate several genes, including chemokines and interferons, which participate in the development and function of microenvironments in lymphoid tissue and host defense. Disruption of the LT/TNF/LIGHT network alleviates inflammation in certain autoimmune disease models, but decreases resistance to selected pathogens. Pharmacological disruption of this network in human autoimmune diseases such as rheumatoid arthritis alleviates inflammation in a significant number of patients, but not in other diseases, a finding that challenges our molecular paradigms of autoimmunity and perhaps will reveal novel roles for this network in pathogenesis.
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Affiliation(s)
- Carl F Ware
- Division of Molecular Immunology, La Jolla Institute for Allergy and Immunology, San Diego, California 92121, USA.
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20
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Kato Y, Fukamachi H, Takano-Maruyama M, Aoe T, Murahashi Y, Horie S, Suzuki Y, Saito Y, Koseki H, Ohno H. Reduction of SNAP25 in acid secretion defect of Foxl1-/- gastric parietal cells. Biochem Biophys Res Commun 2004; 320:766-72. [PMID: 15240114 DOI: 10.1016/j.bbrc.2004.05.209] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2004] [Indexed: 10/26/2022]
Abstract
Foxl1 is a winged helix transcription factor expressed in the mesenchyme of the gastrointestinal tract. In the absence of Foxl1, parietal cells fail to secrete gastric acid in response to various secretagogue stimuli including cAMP. A marked decrease in H+,K(+)-ATPase expression was observed even though a substantial number of parietal cells still existed in Foxl1-deficient mice. Ultrastructural analysis suggested that the gastric acid secretion defect in Foxl1-deficient mice is mainly due to impairment in the fusion of cytoplasmic tubulovesicular structures to the apical canalicular plasma membrane. Among the molecules involved in the membrane fusion event, only SNAP25 showed a significant decrease in mRNA expression, which likely caused the impairment in acid secretion from parietal cells in Foxl1-deficient mice, with the reduction in H+,K(+)-ATPase expression contributing to additional effect.
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Affiliation(s)
- Yasutaka Kato
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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