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Greuter T, Straumann A, Fernandez-Marrero Y, Germic N, Hosseini A, Chanwangpong A, Yousefi S, Simon D, Collins MH, Bussmann C, Chehade M, Dellon ES, Furuta GT, Gonsalves N, Hirano I, Moawad FJ, Biedermann L, Safroneeva E, Schoepfer AM, Simon HU. A Multicenter Long-Term Cohort Study of Eosinophilic Esophagitis Variants and Their Progression to Eosinophilic Esophagitis Over Time. Clin Transl Gastroenterol 2024; 15:e00664. [PMID: 38318864 PMCID: PMC11042771 DOI: 10.14309/ctg.0000000000000664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/06/2023] [Indexed: 02/07/2024] Open
Abstract
INTRODUCTION Eosinophilic esophagitis (EoE) variants have been recently characterized as conditions with symptoms of esophageal dysfunction resembling EoE, but absence of significant esophageal eosinophilia. Their disease course and severity have yet to be determined. METHODS Patients from 6 EoE centers with symptoms of esophageal dysfunction, but peak eosinophil counts of <15/hpf in esophageal biopsies and absence of gastroesophageal reflux disease with at least one follow-up visit were included. Clinical, (immuno)histological, and molecular features were determined and compared with EoE and healthy controls. RESULTS We included 54 patients with EoE variants (EoE-like esophagitis 53.7%; lymphocytic esophagitis 13.0%; and nonspecific esophagitis 33.3%). In 8 EoE-like esophagitis patients, EoE developed after a median of 14 months (interquartile range 3.6-37.6). Such progression increased over time (17.6% year 1, 32.0% year 3, and 62.2% year 6). Sequential RNA sequencing analyses revealed only 7 genes associated with this progression (with TSG6 and ALOX15 among the top 3 upregulated genes) with upregulation of a previously attenuated Th2 pathway. Immunostaining confirmed the involvement of eosinophil-associated proteins (TSG6 and ALOX15) and revealed a significantly increased number of GATA3-positive cells during progression, indicating a Th1/Th2 switch. Transition from one EoE variant (baseline) to another variant (during follow-up) was seen in 35.2% (median observation time of 17.3 months). DISCUSSION Transition of EoE variants to EoE suggests the presence of a disease spectrum. Few genes seem to be associated with the progression to EoE with upregulation of a previously attenuated Th2 signal. These genes, including GATA3 as a Th1/Th2 switch regulator, may represent potential therapeutic targets in early disease pathogenesis.
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Affiliation(s)
- Thomas Greuter
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland;
- Division of Gastroenterology and Hepatology, University Hospital Lausanne–Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland;
- GZO–Zurich Regional Health Center, Wetzikon, Switzerland;
| | - Alex Straumann
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland;
| | | | - Nina Germic
- Institute of Pharmacology, University of Bern, Bern, Switzerland;
| | - Aref Hosseini
- Institute of Pharmacology, University of Bern, Bern, Switzerland;
| | | | - Shida Yousefi
- Institute of Pharmacology, University of Bern, Bern, Switzerland;
| | - Dagmar Simon
- Department of Dermatology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland;
| | - Margaret H. Collins
- Division of Pathology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | | | - Mirna Chehade
- Mount Sinai Center for Eosinophilic Disorders, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Evan S. Dellon
- Division of Gastroenterology and Hepatology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Glenn T. Furuta
- Department of Pediatrics, Gastrointestinal Eosinophilic Diseases Program, University of Colorado School of Medicine, Digestive Health Institute, Children's Hospital Colorado, Aurora, Colorado, USA
| | - Nirmala Gonsalves
- Division of Gastroenterology and Hepatology, Northwestern University, Chicago, Illinois, USA
| | - Ikuo Hirano
- Division of Gastroenterology and Hepatology, Northwestern University, Chicago, Illinois, USA
| | - Fouad J. Moawad
- Division of Gastroenterology, Scripps Clinic, La Jolla Jolla, California, USA
| | - Luc Biedermann
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland;
| | - Ekaterina Safroneeva
- Insitute of Social and Preventive Medicine, University of Bern, Bern, Switzerland;
| | - Alain M. Schoepfer
- Division of Gastroenterology and Hepatology, University Hospital Lausanne–Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland;
| | - Hans-Uwe Simon
- Institute of Pharmacology, University of Bern, Bern, Switzerland;
- Institute of Biochemistry, Brandenburg Medical School, Neuruppin, Germany.
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Rajkumar AP, Qvist P, Lazarus R, Lescai F, Ju J, Nyegaard M, Mors O, Børglum AD, Li Q, Christensen JH. Experimental validation of methods for differential gene expression analysis and sample pooling in RNA-seq. BMC Genomics 2015; 16:548. [PMID: 26208977 PMCID: PMC4515013 DOI: 10.1186/s12864-015-1767-y] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 07/10/2015] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Massively parallel cDNA sequencing (RNA-seq) experiments are gradually superseding microarrays in quantitative gene expression profiling. However, many biologists are uncertain about the choice of differentially expressed gene (DEG) analysis methods and the validity of cost-saving sample pooling strategies for their RNA-seq experiments. Hence, we performed experimental validation of DEGs identified by Cuffdiff2, edgeR, DESeq2 and Two-stage Poisson Model (TSPM) in a RNA-seq experiment involving mice amygdalae micro-punches, using high-throughput qPCR on independent biological replicate samples. Moreover, we sequenced RNA-pools and compared their results with sequencing corresponding individual RNA samples. RESULTS False-positivity rate of Cuffdiff2 and false-negativity rates of DESeq2 and TSPM were high. Among the four investigated DEG analysis methods, sensitivity and specificity of edgeR was relatively high. We documented the pooling bias and that the DEGs identified in pooled samples suffered low positive predictive values. CONCLUSIONS Our results highlighted the need for combined use of more sensitive DEG analysis methods and high-throughput validation of identified DEGs in future RNA-seq experiments. They indicated limited utility of sample pooling strategies for RNA-seq in similar setups and supported increasing the number of biological replicate samples.
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Affiliation(s)
- Anto P Rajkumar
- Department of Biomedicine, Aarhus University, 6, Bartholins Allé, Aarhus C, Aarhus, 8000, Denmark.
- Mental Health of Older Adults and Dementia Clinical Academic Group, South London and Maudsley NHS foundation trust, London, UK.
- Wolfson Centre for Age Related Diseases, Institute of Psychiatry, Psychology, & Neuroscience, King's College, London, UK.
- The Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, 8000, Denmark.
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, 8000, Denmark.
| | - Per Qvist
- Department of Biomedicine, Aarhus University, 6, Bartholins Allé, Aarhus C, Aarhus, 8000, Denmark.
- The Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, 8000, Denmark.
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, 8000, Denmark.
| | - Ross Lazarus
- Computational Biology, Baker IDI heart and diabetes institute, Victoria, 8008, Australia.
| | - Francesco Lescai
- Department of Biomedicine, Aarhus University, 6, Bartholins Allé, Aarhus C, Aarhus, 8000, Denmark.
- The Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, 8000, Denmark.
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, 8000, Denmark.
| | - Jia Ju
- Beijing Genomics Institute, Shenzhen, 518083, China.
| | - Mette Nyegaard
- Department of Biomedicine, Aarhus University, 6, Bartholins Allé, Aarhus C, Aarhus, 8000, Denmark.
- The Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, 8000, Denmark.
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, 8000, Denmark.
| | - Ole Mors
- The Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, 8000, Denmark.
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, 8000, Denmark.
- Research Department P, Aarhus University Hospital, Risskov, Denmark.
| | - Anders D Børglum
- Department of Biomedicine, Aarhus University, 6, Bartholins Allé, Aarhus C, Aarhus, 8000, Denmark.
- The Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, 8000, Denmark.
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, 8000, Denmark.
- Research Department P, Aarhus University Hospital, Risskov, Denmark.
- Translational Neuropsychiatry Unit, Aarhus University, Aarhus, 8240, Denmark.
| | - Qibin Li
- Beijing Genomics Institute, Shenzhen, 518083, China.
| | - Jane H Christensen
- Department of Biomedicine, Aarhus University, 6, Bartholins Allé, Aarhus C, Aarhus, 8000, Denmark.
- The Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, 8000, Denmark.
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, 8000, Denmark.
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