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Ling Lundström M, Peterson C, Lampinen M, Hedin CRH, Keita ÅV, Kruse R, Magnusson MK, Lindqvist CM, Repsilber D, D'Amato M, Hjortswang H, Strid H, Rönnblom A, Söderholm JD, Öhman L, Venge P, Halfvarson J, Carlson M. Fecal Biomarkers of Neutrophil and Eosinophil Origin Reflect the Response to Biological Therapy and Corticosteroids in Patients With Inflammatory Bowel Disease. Clin Transl Gastroenterol 2023; 14:e00605. [PMID: 37256716 PMCID: PMC10462075 DOI: 10.14309/ctg.0000000000000605] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 05/15/2023] [Indexed: 06/02/2023] Open
Abstract
INTRODUCTION Fecal calprotectin (FC) is a noninvasive tool for examining response to biologics in inflammatory bowel disease (IBD), but its performance in relation to other novel fecal markers of various cellular origins is unknown. METHODS We performed a prospective multicenter cohort study and included patients with active IBD who provided a fecal sample at initiation of biological therapy. Levels of FC, myeloperoxidase (MPO), human neutrophil lipocalin (HNL), and eosinophil-derived neurotoxin (EDN) were analyzed and related to clinical remission status at 3 months. Changes in levels of markers at 3 months were calculated, and the impact of concomitant use of corticosteroids at baseline was estimated. RESULTS In patients achieving clinical remission (n = 27), a decrease in levels of FC ( P = 0.005), MPO ( P < 0.001), HNL ( P < 0.001), and EDN ( P < 0.001) was observed, whereas no significant decrease was seen in patients not achieving remission (n = 39). There was a significant difference in the change in the level of MPO ( P = 0.01) and HNL ( P = 0.02) between patients achieving clinical remission and those who did not, but changes in FC and EDN could not differentiate between these groups. Patients with concomitant systemic corticosteroids at inclusion had lower levels of HNL ( P = 0.01) and EDN ( P < 0.001) at baseline, compared with patients without corticosteroids. DISCUSSION Fecal MPO, HNL, and EDN are all promising biomarkers for assessing the treatment outcome of biologics in patients with IBD. Fecal levels of EDN and HNL are significantly affected by corticosteroids indicating a greater sensitivity to the effects of corticosteroids compared with levels of FC and MPO.
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Affiliation(s)
- Maria Ling Lundström
- Department of Medical Sciences, Gastroenterology Research Group, Uppsala University, Uppsala, Sweden;
| | - Christer Peterson
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, Uppsala, Sweden;
| | - Maria Lampinen
- Department of Medical Sciences, Gastroenterology Research Group, Uppsala University, Uppsala, Sweden;
| | - Charlotte R. H. Hedin
- Karolinska Institute, Department of Medicine Solna, Stockholm, Sweden;
- Karolinska University Hospital, Gastroenterology Unit, Department of Gastroenterology, Dermatovenereology and Rheumatology, Stockholm, Sweden;
| | - Åsa V. Keita
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden;
| | - Robert Kruse
- IRiSC–Inflammatory Response and Infection Susceptibility Centre and Department of Clinical Research Laboratory, Faculty of Medicine and Health, Örebro University, Örebro, Sweden;
| | - Maria K. Magnusson
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden;
| | | | - Dirk Repsilber
- School of Medical Sciences, Örebro University, Örebro, Sweden
| | - Mauro D'Amato
- Clinical Epidemiology Unit, Department of Medicine, Karolinska Institute, Solna, Sweden;
- Department of Medicine and Surgery, LUM University, Casamassima, Italy
- Gastrointestinal Genetics Lab, CIC BioGUNE–BRTA, Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Henrik Hjortswang
- Division of Gastroenterology and Hepatology, Department of Clinical and Experimental Science, Linköping University, Linköping, Sweden
| | - Hans Strid
- Department of Internal Medicine, Södra Älvsborgs Hospital, Borås, Sweden
| | - Anders Rönnblom
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Johan D. Söderholm
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden;
- Department of Surgery, Linköping University, Linköping, Sweden
| | - Lena Öhman
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden;
| | - Per Venge
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, Uppsala, Sweden;
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Marie Carlson
- Department of Medical Sciences, Gastroenterology Research Group, Uppsala University, Uppsala, Sweden;
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Koskela von Sydow A, Lindqvist CM, Asghar N, Johansson M, Sundqvist M, Mölling P, Stenmark B. Comparison of SARS-CoV-2 whole genome sequencing using tiled amplicon enrichment and bait hybridization. Sci Rep 2023; 13:6461. [PMID: 37081087 PMCID: PMC10116481 DOI: 10.1038/s41598-023-33168-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 04/07/2023] [Indexed: 04/22/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) pandemic has led to extensive virological monitoring by whole genome sequencing (WGS). Investigating the advantages and limitations of different protocols is key when conducting population-level WGS. SARS-CoV-2 positive samples with Ct values of 14-30 were run using three different protocols: the Twist Bioscience SARS‑CoV‑2 protocol with bait hybridization enrichment sequenced with Illumina, and two tiled amplicon enrichment protocols, ARTIC V3 and Midnight, sequenced with Illumina and Oxford Nanopore Technologies, respectively. Twist resulted in better coverage uniformity and coverage of the entire genome, but has several drawbacks: high human contamination, laborious workflow, high cost, and variation between batches. The ARTIC and Midnight protocol produced an even coverage across samples, and almost all reads were mapped to the SARS-CoV-2 reference. ARTIC and Midnight represent robust, cost-effective, and highly scalable methods that are appropriate in a clinical environment. Lineage designations were uniform across methods, representing the dominant lineages in Sweden during the period of collection. This study provides insights into methodological differences in SARS‑CoV‑2 sequencing and guidance in selecting suitable methods for various purposes.
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Affiliation(s)
- Anita Koskela von Sydow
- Department of Laboratory Medicine, Clinical Pathology and Genetics, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
- Clinical Genomics, Science for Life Laboratory, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
| | - Carl Mårten Lindqvist
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Clinical Genomics, Science for Life Laboratory, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Naveed Asghar
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Magnus Johansson
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Martin Sundqvist
- Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Paula Mölling
- Clinical Genomics, Science for Life Laboratory, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Bianca Stenmark
- Department of Laboratory Medicine, Clinical Pathology and Genetics, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Clinical Genomics, Science for Life Laboratory, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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3
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Moraes Holst L, Halfvarson J, Carlson M, Hedin C, Kruse R, Lindqvist CM, Bergemalm D, Almér S, Bresso F, Ling Lundström M, Repsilber D, D’Amato M, Keita Å, Hjortswang H, Söderholm J, Sundin J, Törnblom H, Simrén M, Strid H, Magnusson MK, Öhman L. Downregulated Mucosal Autophagy, Alpha Kinase-1 and IL-17 Signaling Pathways in Active and Quiescent Ulcerative Colitis. Clin Exp Gastroenterol 2022; 15:129-144. [PMID: 35928254 PMCID: PMC9343467 DOI: 10.2147/ceg.s368040] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 07/07/2022] [Indexed: 11/23/2022] Open
Abstract
Background Improved mucosal immune profiling in active and quiescent colonic inflammatory bowel disease (IBD) is needed to develop therapeutic options for treating and preventing flares. This study therefore aimed to provide a comprehensive mucosal characterization with emphasis on immunological host response of patients with active ulcerative colitis (UC active), UC during remission (UC remission) and active colonic Crohn’s disease (CD active). Methods Colonic biopsies from 47 study subjects were collected for gene expression and pathway analyses using the NanoString host-response panel, including 776 genes and 56 immune-related pathways. Results The majority of mucosal gene expression and signaling pathway scores were increased in active IBD (n=27) compared to healthy subjects (n=10). However, both active IBD and UC remission (n=10) demonstrated decreased gene expression and signaling pathway scores related to autophagy, alpha kinase-1 and IL-17 signaling pathways compared to healthy subjects. Further, UC remission was characterized by decreased scores of several signaling pathways linked to homeostasis along with increased mononuclear cell migration pathway score as compared to healthy subjects. No major differences in the colonic mucosal gene expression between CD active (n=7) and UC (n=20) active were observed. Conclusion This study indicates that autophagy, alpha kinase-1 and IL-17 signaling pathways are persistently downregulated in UC irrespective of disease activity. Further, UC patients in remission present a unique mucosal environment, potentially preventing patients from reaching and sustaining true homeostasis. These findings may enable better comprehension of the remitting and relapsing pattern of colonic IBD and guide future treatment and prevention of flares.
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Affiliation(s)
- Luiza Moraes Holst
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Marie Carlson
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Charlotte Hedin
- Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
| | - Robert Kruse
- Department of Clinical Research Laboratory, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Carl Mårten Lindqvist
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Daniel Bergemalm
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Sven Almér
- Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
| | - Francesca Bresso
- Karolinska University Hospital, Gastroenterology Unit, Department of Gastroenterology, Dermatovenereology and Rheumatology, Stockholm, Sweden
| | | | - Dirk Repsilber
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Mauro D’Amato
- Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- Gastrointestinal Genetics Lab, CIC bioGUNE - BRTA, Derio, Spain
| | - Åsa Keita
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Henrik Hjortswang
- Department of Clinical and Experimental Science, Linköping University, Linköping, Sweden
| | - Johan Söderholm
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Johanna Sundin
- Department of Internal Medicine & Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, Gothenburg, Sweden
| | - Hans Törnblom
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Simrén
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Center for Functional Gastrointestinal and Motility Disorders, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hans Strid
- Department of Internal Medicine, Södra Älvsborg Hospital, Borås, Sweden
| | - Maria K Magnusson
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lena Öhman
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Correspondence: Lena Öhman, Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden, Tel +46703616499, Email
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Juzenas S, Hübenthal M, Lindqvist CM, Kruse R, Steiert TA, Degenhardt F, Schulte D, Nikolaus S, Zeissig S, Bergemalm D, Almer S, Hjortswang H, Bresso F, Strüning N, Kupcinskas J, Keller A, Lieb W, Rosenstiel P, Schreiber S, D’Amato M, Halfvarson J, Hemmrich-Stanisak G, Franke A. Detailed Transcriptional Landscape of Peripheral Blood Points to Increased Neutrophil Activation in Treatment-Naïve Inflammatory Bowel Disease. J Crohns Colitis 2022; 16:1097-1109. [PMID: 35022690 PMCID: PMC9351981 DOI: 10.1093/ecco-jcc/jjac003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/13/2021] [Accepted: 01/08/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND AND AIMS Inflammatory bowel disease [IBD] is a chronic relapsing disorder of the gastrointestinal tract, which generally manifests as Crohn's disease [CD] or ulcerative colitis [UC]. These subtypes are heterogeneous in terms of disease location and histological features, while sharing common clinical presentation, genetic associations and, thus, common immune regulatory pathways. METHODS Using miRNA and mRNA coupled transcriptome profiling and systems biology approaches, we report a comprehensive analysis of blood transcriptomes from treatment-naïve [n = 110] and treatment-exposed [n = 177] IBD patients as well as symptomatic [n = 65] and healthy controls [n = 95]. RESULTS Broadly, the peripheral blood transcriptomes of CD and UC patients were similar. However, there was an extensive gene deregulation in the blood of IBD patients, while only a slight deregulation in symptomatic controls, when compared with healthy controls. The deregulated mRNAs and miRNAs are mainly involved in the innate immunity and are especially enriched in neutrophil activation-related pathways. Oxidative phosphorylation and neutrophil activation-related modules were found to be differentially co-expressed among treatment-naïve IBD as compared to healthy controls. In the deregulated neutrophil activation-related co-expression module, IL1B was identified as the central gene. Levels of co-expression among IL1B and chemosensing receptor [CXCR1/2 and FPR1/2] genes were reduced in the blood of IBD patients when compared with healthy controls. CONCLUSIONS Immune dysregulation seen in peripheral blood transcriptomes of treatment-naïve IBD patients is mainly driven by neutrophil activation.
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Affiliation(s)
- Simonas Juzenas
- Corresponding author: Simonas Juzenas, PhD, Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University of Kiel (CAU), Rosalind-Franklin-Str. 12, D-24105 Kiel, Germany.
| | - Matthias Hübenthal
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany,Department of Dermatology, Quincke Research Center, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Carl Mårten Lindqvist
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany,School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Robert Kruse
- Department of Clinical Research Laboratory, Faculty of Medicine and Health, Örebro University, Örebro, Sweden,iRiSC – Inflammatory Response and Infection Susceptibility Centre, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Tim Alexander Steiert
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Dominik Schulte
- Division of Endocrinology, Diabetes and Clinical Nutrition, Department of Medicine I, University Hospital of Schleswig-Holstein, Kiel, Germany,Institute of Diabetes and Clinical Metabolic Research, Kiel University, Kiel, Germany
| | - Susanna Nikolaus
- Department of Internal Medicine I, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Sebastian Zeissig
- Medical Department 1, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden, Germany,Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Daniel Bergemalm
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Sven Almer
- Department of Medicine, Karolinska Institutet, Solna, and Division of Gastroenterology, Karolinska University Hospital, Stockholm, Sweden
| | - Henrik Hjortswang
- Department of Gastroenterology and Hepatology, Linköping University, Linköping, and Department of Health, Medicine, and Caring Sciences, Linköping University, Linköping, Sweden
| | - Francesca Bresso
- Department of Medicine, Karolinska Institutet, Solna, and Division of Gastroenterology, Karolinska University Hospital, Stockholm, Sweden
| | | | - Nina Strüning
- Department of Internal Medicine I, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Juozas Kupcinskas
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Wolfgang Lieb
- Institute of Epidemiology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany,Department of Internal Medicine I, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Mauro D’Amato
- Unit of Clinical Epidemiology, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden,Gastrointestinal Genetics Lab, CIC bioGUNE – BRTA, Derio, Spain,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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Meira de-Faria F, Casado-Bedmar M, Mårten Lindqvist C, Jones MP, Walter SA, Keita ÅV. Altered interaction between enteric glial cells and mast cells in the colon of women with irritable bowel syndrome. Neurogastroenterol Motil 2021; 33:e14130. [PMID: 33797165 DOI: 10.1111/nmo.14130] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 02/22/2021] [Accepted: 03/09/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND Enteric glial cells (EGC) and mast cells (MC) are intimately associated with gastrointestinal physiological functions. We aimed to investigate EGC-MC interaction in irritable bowel syndrome (IBS), a gut-brain disorder linked to increased intestinal permeability, and MC. METHODS Parallel approaches were used to quantify EGC markers in colonic biopsies from healthy controls (HC) and patients with IBS. Data were correlated with MC, vasoactive intestinal polypeptide (VIP) and VIP receptors (VPAC1/VPAC2) expressions, and bacterial translocation through biopsies mounted in Ussing chambers. In addition, we investigated the effects of EGC mediators on colonic permeability and the pharmacological-induced responses of EGC and MC cell lines. KEY RESULTS Immunofluorescence of IBS colonic mucosa, as well as Western blotting and ELISA of IBS biopsy lysates, revealed increased glial fibrillary intermediate filament (GFAP) expression, indicating EGC activation. Mucosal GFAP correlated with increased MC and VPAC1+ MC numbers and decreased VIP+ MC, which seemed to control bacterial translocation in HC. In the contrary, EGC activation in IBS correlated with less MC and VPAC1+ MC numbers, and more VIP+ MC. In vitro, MC and EGC cell lines showed intracellular calcium responses to each other's mediators. Furthermore, EGC mediators prevented VIP-induced MC degranulation, while MC mediators induced a reactive EGC phenotype. In Ussing chambers, EGC mediators decreased paracellular passage through healthy colonic biopsies. CONCLUSIONS & INFERENCES Findings suggest the involvement of EGC and MC in the control of barrier function in the human colon and indicate a potential EGC-MC interaction that seems altered in IBS, with detrimental consequences to colonic permeability. Altogether, results suggest that imbalanced EGC-MC communication contributes to the pathophysiology of IBS.
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Affiliation(s)
- Felipe Meira de-Faria
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Maite Casado-Bedmar
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Carl Mårten Lindqvist
- Department of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | | | - Susanna A Walter
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.,Department of Gastroenterology, Linköping University, Linköping, Sweden
| | - Åsa V Keita
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
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Casado-Bedmar M, de-Faria FM, Biskou O, Lindqvist CM, Ranasinghe PD, Bednarska O, Peterson C, Walter SA, Carlson M, Keita ÅV. Elevated F-EDN correlates with mucosal eosinophil degranulation in patients with IBS-A possible association with microbiota? J Leukoc Biol 2021; 111:655-665. [PMID: 34151454 DOI: 10.1002/jlb.4a0521-228r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Eosinophils have been linked to functional dyspepsia; however, less is known about their role in irritable bowel syndrome (IBS). This study tested the hypothesis of alterations in levels of fecal eosinophil-derived neurotoxin (F-EDN) and eosinophil density and degranulation within the colonic mucosa of IBS patients compared with healthy controls (HC). Colonic biopsies were collected from 37 IBS patients and 20 HC and analyzed for eosinophil numbers and local degranulation of eosinophil cationic protein (ECP) by histologic procedures. Fecal samples were collected for F-EDN and microbiota analysis. Differentiated 15HL-60 cells were used in vitro to investigate the direct effect of live bacteria on eosinophil activation measured by a colorimetric assay with o-phenylenediamine (OPD) substrate. We observed a higher number of eosinophils and increased extracellular ECP in the mucosa of IBS patients compared with HC. Moreover, F-EDN levels in IBS samples were elevated compared with HC and positively correlated to extracellular ECP. Metagenomic analysis showed significant correlations between bacterial composition and eosinophil measurements in both HC and IBS patients. In vitro experiments revealed an increased degranulation of 15HL-60 after stimulation with Salmonella typhimurium, Salmonella enterica, and Yersinia enterocolitica. To conclude, we could demonstrate alterations related to eosinophils in IBS, and, for the first time, a positive correlation between F-EDN levels and degranulated eosinophils in the colonic mucosa of IBS patients. Together our results suggest that eosinophils play a role in the pathophysiology of IBS and the mechanisms might be linked to an altered microbiota.
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Affiliation(s)
- Maite Casado-Bedmar
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Felipe Meira de-Faria
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Olga Biskou
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | | | - Purnika Damindi Ranasinghe
- Institute of Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Olga Bednarska
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.,Department of Gastroenterology, Linköping, Sweden
| | - Christer Peterson
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, Uppsala, Sweden and Diagnostics Development, Uppsala, Sweden
| | - Susanna A Walter
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.,Department of Gastroenterology, Linköping, Sweden
| | - Marie Carlson
- Department of Medical Sciences, Gastroenterology Research Group, Uppsala University, Uppsala, Sweden
| | - Åsa V Keita
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
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Holster S, Repsilber D, Geng D, Hyötyläinen T, Salonen A, Lindqvist CM, Rajan SK, de Vos WM, Brummer RJ, König J. Correlations between microbiota and metabolites after faecal microbiota transfer in irritable bowel syndrome. Benef Microbes 2020; 12:17-30. [PMID: 33350360 DOI: 10.3920/bm2020.0010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Faecal microbiota transfer (FMT) consists of the infusion of donor faecal material into the intestine of a patient with the aim to restore a disturbed gut microbiota. In this study, it was investigated whether FMT has an effect on faecal microbial composition, its functional capacity, faecal metabolite profiles and their interactions in 16 irritable bowel syndrome (IBS) patients. Faecal samples from eight different time points before and until six months after allogenic FMT (faecal material from a healthy donor) as well as autologous FMT (own faecal material) were analysed by 16S RNA gene amplicon sequencing and gas chromatography coupled to mass spectrometry (GS-MS). The results showed that the allogenic FMT resulted in alterations in the microbial composition that were detectable up to six months, whereas after autologous FMT this was not the case. Similar results were found for the functional profiles, which were predicted from the phylogenetic sequencing data. While both allogenic FMT as well as autologous FMT did not have an effect on the faecal metabolites measured in this study, correlations between the microbial composition and the metabolites showed that the microbe-metabolite interactions seemed to be disrupted after allogenic FMT compared to autologous FMT. This shows that FMT can lead to altered interactions between the gut microbiota and its metabolites in IBS patients. Further research should investigate if and how this affects efficacy of FMT treatments.
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Affiliation(s)
- S Holster
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
| | - D Repsilber
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
| | - D Geng
- Man-Technology-Environmental Research Centre, Faculty of Business, Science and Engineering, School of Science and Technology, Örebro University, Örebro, Sweden
| | - T Hyötyläinen
- Man-Technology-Environmental Research Centre, Faculty of Business, Science and Engineering, School of Science and Technology, Örebro University, Örebro, Sweden
| | - A Salonen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - C M Lindqvist
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
| | - S K Rajan
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
| | - W M de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Laboratory of Microbiology, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - R J Brummer
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
| | - J König
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
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Fart F, Rajan SK, Wall R, Rangel I, Ganda-Mall JP, Tingö L, Brummer RJ, Repsilber D, Schoultz I, Lindqvist CM. Differences in Gut Microbiome Composition between Senior Orienteering Athletes and Community-Dwelling Older Adults. Nutrients 2020; 12:nu12092610. [PMID: 32867153 PMCID: PMC7551621 DOI: 10.3390/nu12092610] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 07/18/2020] [Revised: 08/14/2020] [Accepted: 08/18/2020] [Indexed: 02/06/2023] Open
Abstract
Background: Gastrointestinal (GI) health is an important aspect of general health. Gastrointestinal symptoms are of specific importance for the elderly, an increasing group globally. Hence, promoting the elderly’s health and especially gastrointestinal health is important. Gut microbiota can influence gastrointestinal health by modulation of the immune system and the gut–brain axis. Diverse gut microbiota have been shown to be beneficial; however, for the elderly, the gut microbiota is often less diverse. Nutrition and physical activity, in particular, are two components that have been suggested to influence composition or diversity. Materials and Methods: In this study, we compared gut microbiota between two groups of elderly individuals: community-dwelling older adults and physically active senior orienteering athletes, where the latter group has less gastrointestinal symptoms and a reported better well-being. With this approach, we explored if certain gut microbiota were related to healthy ageing. The participant data and faecal samples were collected from these two groups and the microbiota was whole-genome sequenced and taxonomically classified with MetaPhlAn. Results: The physically active senior orienteers had a more homogeneous microbiota within the group and a higher abundance of Faecalibacterium prausnitzii compared to the community-dwelling older adults. Faecalibacterium prausnitzii has previously shown to have beneficial properties. Senior orienteers also had a lower abundance of Parasutterella excrementihominis and Bilophila unclassified, which have been associated with impaired GI health. We could not observe any difference between the groups in terms of Shannon diversity index. Interestingly, a subgroup of community-dwelling older adults showed an atypical microbiota profile as well as the parameters for gastrointestinal symptoms and well-being closer to senior orienteers. Conclusions: Our results suggest specific composition characteristics of healthy microbiota in the elderly, and show that certain components of nutrition as well as psychological distress are not as tightly connected with composition or diversity variation in faecal microbiota samples.
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Affiliation(s)
- Frida Fart
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 702 81 Örebro, Sweden; (F.F.); (S.K.R.); (R.W.); (I.R.); (J.P.G.-M.); (L.T.); (R.J.B.); (D.R.); (I.S.)
| | - Sukithar Kochappi Rajan
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 702 81 Örebro, Sweden; (F.F.); (S.K.R.); (R.W.); (I.R.); (J.P.G.-M.); (L.T.); (R.J.B.); (D.R.); (I.S.)
| | - Rebecca Wall
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 702 81 Örebro, Sweden; (F.F.); (S.K.R.); (R.W.); (I.R.); (J.P.G.-M.); (L.T.); (R.J.B.); (D.R.); (I.S.)
| | - Ignacio Rangel
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 702 81 Örebro, Sweden; (F.F.); (S.K.R.); (R.W.); (I.R.); (J.P.G.-M.); (L.T.); (R.J.B.); (D.R.); (I.S.)
| | - John Peter Ganda-Mall
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 702 81 Örebro, Sweden; (F.F.); (S.K.R.); (R.W.); (I.R.); (J.P.G.-M.); (L.T.); (R.J.B.); (D.R.); (I.S.)
- Laboratory of Translational Mucosal Immunology, Digestive Diseases Research Unit, Vall d’Hebron Institut de Recerca, Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain
| | - Lina Tingö
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 702 81 Örebro, Sweden; (F.F.); (S.K.R.); (R.W.); (I.R.); (J.P.G.-M.); (L.T.); (R.J.B.); (D.R.); (I.S.)
| | - Robert J. Brummer
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 702 81 Örebro, Sweden; (F.F.); (S.K.R.); (R.W.); (I.R.); (J.P.G.-M.); (L.T.); (R.J.B.); (D.R.); (I.S.)
| | - Dirk Repsilber
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 702 81 Örebro, Sweden; (F.F.); (S.K.R.); (R.W.); (I.R.); (J.P.G.-M.); (L.T.); (R.J.B.); (D.R.); (I.S.)
| | - Ida Schoultz
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 702 81 Örebro, Sweden; (F.F.); (S.K.R.); (R.W.); (I.R.); (J.P.G.-M.); (L.T.); (R.J.B.); (D.R.); (I.S.)
| | - Carl Mårten Lindqvist
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 702 81 Örebro, Sweden; (F.F.); (S.K.R.); (R.W.); (I.R.); (J.P.G.-M.); (L.T.); (R.J.B.); (D.R.); (I.S.)
- Correspondence:
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9
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Keita ÅV, Lindqvist CM, Öst Å, Magana CDL, Schoultz I, Halfvarson J. Gut Barrier Dysfunction-A Primary Defect in Twins with Crohn's Disease Predominantly Caused by Genetic Predisposition. J Crohns Colitis 2018; 12:1200-1209. [PMID: 29659773 PMCID: PMC6225972 DOI: 10.1093/ecco-jcc/jjy045] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS The aetiology of Crohn's disease is poorly understood. By investigating twin pairs discordant for Crohn's disease, we aimed to assess whether the dysregulated barrier represents a cause or a consequence of inflammation and to evaluate the impact of genetic predisposition on barrier function. METHODS Ileal biopsies from 15 twin pairs discordant for Crohn's disease [monozygotic n = 9, dizygotic n = 6] and 10 external controls were mounted in Ussing chambers to assess paracellular permeability to 51Chromium [Cr]-EDTA and trancellular passage to non-pathogenic E. coli K-12. Experiments were performed with and without provocation with acetylsalicylic acid. Immunofluorescence and ELISA were used to quantify the expression level of tight junction proteins. RESULTS Healthy co-twins and affected twins displayed increased 51Cr-EDTA permeability at 120 min, both with acetylsalicylic acid [p < 0.001] and without [p < 0.001] when compared with controls. A significant increase in 51Cr-EDTA flux was already seen at 20 min in healthy monozygotic co-twins compared with controls [p≤0.05] when stratified by zygosity, but not in healthy dizygotic co-twins. No difference in E. coli passage was observed between groups. Immunofluorescence of the tight junction proteins claudin-5 and tricellulin showed lower levels in healthy co-twins [p < 0.05] and affected twins [p < 0.05] compared with external controls, while ELISA only showed lower tricellulin in Crohn's disease twins [p < 0.05]. CONCLUSION Our results suggest that barrier dysfunction is a primary defect in Crohn's disease, since changes were predominantly seen in healthy monozygotic co-twins. Passage of E. coli seems to be a consequence of inflammation, rather than representing a primary defect.
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Affiliation(s)
- Åsa V Keita
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden,Corresponding author: Åsa V. Keita, PhD, Department of Clinical and Experimental Medicine, Division of Surgery, Orthopedics & Oncology, Medical Faculty, Linköping University, 581 85 Linköping, Sweden. Tel: 46-101-038-919;
| | - Carl Mårten Lindqvist
- Department of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Åke Öst
- Department of Pathology and Cytology, Aleris Medilab, Täby, Sweden
| | - Carlos D L Magana
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Ida Schoultz
- Department of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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10
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Ganda Mall JP, Löfvendahl L, Lindqvist CM, Brummer RJ, Keita ÅV, Schoultz I. Differential effects of dietary fibres on colonic barrier function in elderly individuals with gastrointestinal symptoms. Sci Rep 2018; 8:13404. [PMID: 30194322 PMCID: PMC6128877 DOI: 10.1038/s41598-018-31492-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 08/17/2018] [Indexed: 02/08/2023] Open
Abstract
Gastrointestinal problems are common in elderly and often associated with psychological distress and increased levels of corticotrophin-releasing hormone, a hormone known to cause mast cell (MC) degranulation and perturbed intestinal barrier function. We investigated if dietary fibres (non-digestible polysaccharides [NPS]) could attenuate MC-induced colonic hyperpermeability in elderly with gastrointestinal (GI) symptoms. Colonic biopsies from elderly with diarrhoea and/or constipation (n = 18) and healthy controls (n = 19) were mounted in Ussing chambers and pre-stimulated with a yeast-derived beta (β)-glucan (0.5 mg/ml) or wheat-derived arabinoxylan (0.1 mg/ml) before the addition of the MC-degranulator Compound (C) 48/80 (10 ng/ml). Permeability markers were compared pre and post exposure to C48/80 in both groups and revealed higher baseline permeability in elderly with GI symptoms. β-glucan significantly attenuated C48/80-induced hyperpermeability in elderly with GI symptoms but not in healthy controls. Arabinoxylan reduced MC-induced paracellular and transcellular hyperpermeability across the colonic mucosa of healthy controls, but did only attenuate transcellular permeability in elderly with GI symptoms. Our novel findings indicate that NPS affect the intestinal barrier differently depending on the presence of GI symptoms and could be important in the treatment of moderate constipation and/or diarrhoea in elderly.
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Affiliation(s)
- J P Ganda Mall
- Nutrition-Gut-Brain Interactions Research Centre, School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.,Nutrition and physical activity research centre, School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - L Löfvendahl
- Nutrition-Gut-Brain Interactions Research Centre, School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - C M Lindqvist
- Nutrition-Gut-Brain Interactions Research Centre, School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - R J Brummer
- Nutrition-Gut-Brain Interactions Research Centre, School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Å V Keita
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - I Schoultz
- Nutrition-Gut-Brain Interactions Research Centre, School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden. .,Nutrition and physical activity research centre, School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
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11
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Ganda Mall JP, Östlund-Lagerström L, Lindqvist CM, Algilani S, Rasoal D, Repsilber D, Brummer RJ, Keita ÅV, Schoultz I. Are self-reported gastrointestinal symptoms among older adults associated with increased intestinal permeability and psychological distress? BMC Geriatr 2018; 18:75. [PMID: 29554871 PMCID: PMC5859527 DOI: 10.1186/s12877-018-0767-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 03/12/2018] [Indexed: 12/13/2022] Open
Abstract
Background Despite the substantial number of older adults suffering from gastrointestinal (GI) symptoms little is known regarding the character of these complaints and whether they are associated with an altered intestinal barrier function and psychological distress. Our aim was to explore the relationship between self-reported gut health, intestinal permeability and psychological distress among older adults. Methods Three study populations were included: 1) older adults with GI symptoms (n = 24), 2) a group of older adults representing the general elderly population in Sweden (n = 22) and 3) senior orienteering athletes as a potential model of healthy ageing (n = 27). Questionnaire data on gut-health, psychological distress and level of physical activity were collected. Intestinal permeability was measured by quantifying zonulin in plasma. The level of systemic and local inflammation was monitored by measuring C-reactive protein (CRP), hydrogen peroxide in plasma and calprotectin in stool samples. The relationship between biomarkers and questionnaire data in the different study populations was illustrated using a Principal Component Analysis (PCA). Results Older adults with GI symptoms displayed significantly higher levels of both zonulin and psychological distress than both general older adults and senior orienteering athletes. The PCA analysis revealed a separation between senior orienteering athletes and older adults with GI symptoms and showed an association between GI symptoms, psychological distress and zonulin. Conclusions Older adults with GI symptoms express increased plasma levels of zonulin, which might reflect an augmented intestinal permeability. In addition, this group suffer from higher psychological distress compared to general older adults and senior orienteering athletes. This relationship was further confirmed by a PCA plot, which illustrated an association between GI symptoms, psychological distress and intestinal permeability.
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Affiliation(s)
- John-Peter Ganda Mall
- Nutrition Gut Brain Interactions Research Centre, Department of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.,Nutrition and Physical Activity Research Centre, Department of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Lina Östlund-Lagerström
- Nutrition Gut Brain Interactions Research Centre, Department of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.,Nutrition and Physical Activity Research Centre, Department of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Carl Mårten Lindqvist
- Nutrition Gut Brain Interactions Research Centre, Department of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Samal Algilani
- Nutrition and Physical Activity Research Centre, Department of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Dara Rasoal
- Nutrition and Physical Activity Research Centre, Department of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Dirk Repsilber
- Nutrition Gut Brain Interactions Research Centre, Department of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Robert J Brummer
- Nutrition Gut Brain Interactions Research Centre, Department of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Åsa V Keita
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Ida Schoultz
- Nutrition and Physical Activity Research Centre, Department of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
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12
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Marincevic-Zuniga Y, Dahlberg J, Nilsson S, Raine A, Nystedt S, Lindqvist CM, Berglund EC, Abrahamsson J, Cavelier L, Forestier E, Heyman M, Lönnerholm G, Nordlund J, Syvänen AC. Transcriptome sequencing in pediatric acute lymphoblastic leukemia identifies fusion genes associated with distinct DNA methylation profiles. J Hematol Oncol 2017; 10:148. [PMID: 28806978 PMCID: PMC5557398 DOI: 10.1186/s13045-017-0515-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/03/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Structural chromosomal rearrangements that lead to expressed fusion genes are a hallmark of acute lymphoblastic leukemia (ALL). In this study, we performed transcriptome sequencing of 134 primary ALL patient samples to comprehensively detect fusion transcripts. METHODS We combined fusion gene detection with genome-wide DNA methylation analysis, gene expression profiling, and targeted sequencing to determine molecular signatures of emerging ALL subtypes. RESULTS We identified 64 unique fusion events distributed among 80 individual patients, of which over 50% have not previously been reported in ALL. Although the majority of the fusion genes were found only in a single patient, we identified several recurrent fusion gene families defined by promiscuous fusion gene partners, such as ETV6, RUNX1, PAX5, and ZNF384, or recurrent fusion genes, such as DUX4-IGH. Our data show that patients harboring these fusion genes displayed characteristic genome-wide DNA methylation and gene expression signatures in addition to distinct patterns in single nucleotide variants and recurrent copy number alterations. CONCLUSION Our study delineates the fusion gene landscape in pediatric ALL, including both known and novel fusion genes, and highlights fusion gene families with shared molecular etiologies, which may provide additional information for prognosis and therapeutic options in the future.
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Affiliation(s)
- Yanara Marincevic-Zuniga
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johan Dahlberg
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sara Nilsson
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Amanda Raine
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sara Nystedt
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Carl Mårten Lindqvist
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Eva C Berglund
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jonas Abrahamsson
- Department of Pediatrics, Institution for Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lucia Cavelier
- Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
| | - Erik Forestier
- Department of Medical Biosciences, University of Umeå, Umeå, Sweden
| | - Mats Heyman
- Karolinska Institutet, Childhood Cancer Research Unit, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Gudmar Lönnerholm
- Department of Women's and Children's Health, Pediatric Oncology, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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13
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Lindqvist CM, Nordlund J, Ekman D, Johansson A, Moghadam BT, Raine A, Övernäs E, Dahlberg J, Wahlberg P, Henriksson N, Abrahamsson J, Frost BM, Grandér D, Heyman M, Larsson R, Palle J, Söderhäll S, Forestier E, Lönnerholm G, Syvänen AC, Berglund EC. The mutational landscape in pediatric acute lymphoblastic leukemia deciphered by whole genome sequencing. Hum Mutat 2015; 36:118-28. [PMID: 25355294 PMCID: PMC4309499 DOI: 10.1002/humu.22719] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 10/22/2014] [Indexed: 12/15/2022]
Abstract
Genomic characterization of pediatric acute lymphoblastic leukemia (ALL) has identified distinct patterns of genes and pathways altered in patients with well-defined genetic aberrations. To extend the spectrum of known somatic variants in ALL, we performed whole genome and transcriptome sequencing of three B-cell precursor patients, of which one carried the t(12;21)ETV6-RUNX1 translocation and two lacked a known primary genetic aberration, and one T-ALL patient. We found that each patient had a unique genome, with a combination of well-known and previously undetected genomic aberrations. By targeted sequencing in 168 patients, we identified KMT2D and KIF1B as novel putative driver genes. We also identified a putative regulatory non-coding variant that coincided with overexpression of the growth factor MDK. Our results contribute to an increased understanding of the biological mechanisms that lead to ALL and suggest that regulatory variants may be more important for cancer development than recognized to date. The heterogeneity of the genetic aberrations in ALL renders whole genome sequencing particularly well suited for analysis of somatic variants in both research and diagnostic applications.
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Affiliation(s)
- Carl Mårten Lindqvist
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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14
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Berglund EC, Lindqvist CM, Hayat S, Övernäs E, Henriksson N, Nordlund J, Wahlberg P, Forestier E, Lönnerholm G, Syvänen AC. Accurate detection of subclonal single nucleotide variants in whole genome amplified and pooled cancer samples using HaloPlex target enrichment. BMC Genomics 2013; 14:856. [PMID: 24314227 PMCID: PMC4046713 DOI: 10.1186/1471-2164-14-856] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 11/25/2013] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Target enrichment and resequencing is a widely used approach for identification of cancer genes and genetic variants associated with diseases. Although cost effective compared to whole genome sequencing, analysis of many samples constitutes a significant cost, which could be reduced by pooling samples before capture. Another limitation to the number of cancer samples that can be analyzed is often the amount of available tumor DNA. We evaluated the performance of whole genome amplified DNA and the power to detect subclonal somatic single nucleotide variants in non-indexed pools of cancer samples using the HaloPlex technology for target enrichment and next generation sequencing. RESULTS We captured a set of 1528 putative somatic single nucleotide variants and germline SNPs, which were identified by whole genome sequencing, with the HaloPlex technology and sequenced to a depth of 792-1752. We found that the allele fractions of the analyzed variants are well preserved during whole genome amplification and that capture specificity or variant calling is not affected. We detected a large majority of the known single nucleotide variants present uniquely in one sample with allele fractions as low as 0.1 in non-indexed pools of up to ten samples. We also identified and experimentally validated six novel variants in the samples included in the pools. CONCLUSION Our work demonstrates that whole genome amplified DNA can be used for target enrichment equally well as genomic DNA and that accurate variant detection is possible in non-indexed pools of cancer samples. These findings show that analysis of a large number of samples is feasible at low cost, even when only small amounts of DNA is available, and thereby significantly increases the chances of indentifying recurrent mutations in cancer samples.
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Affiliation(s)
- Eva C Berglund
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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