1
|
Oussaada SM, Kilicarslan M, de Weijer BA, Gilijamse PW, Şekercan A, Virtue S, Janssen IMC, van de Laar A, Demirkiran A, van Wagensveld BA, Houdijk APJ, Jongejan A, Moerland PD, Verheij J, Geijtenbeek TB, Bloks VW, de Goffau MC, Romijn JA, Nieuwdorp M, Vidal-Puig A, Ter Horst KW, Serlie MJ. Tissue-specific inflammation and insulin sensitivity in subjects with obesity. Diabetes Res Clin Pract 2024; 211:111663. [PMID: 38616042 DOI: 10.1016/j.diabres.2024.111663] [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: 03/01/2024] [Revised: 04/01/2024] [Accepted: 04/05/2024] [Indexed: 04/16/2024]
Abstract
Obesity is associated with low-grade inflammation and insulin resistance (IR). The contribution of adipose tissue (AT) and hepatic inflammation to IR remains unclear. We conducted a study across three cohorts to investigate this relationship. The first cohort consists of six women with normal weight and twenty with obesity. In women with obesity, we found an upregulation of inflammatory markers in subcutaneous and visceral adipose tissue, isolated AT macrophages, and the liver, but no linear correlation with tissue-specific insulin sensitivity. In the second cohort, we studied 24 women with obesity in the upper vs lower insulin sensitivity quartile. We demonstrated that several omental and mesenteric AT inflammatory genes and T cell-related pathways are upregulated in IR, independent of BMI. The third cohort consists of 23 women and 18 men with obesity, studied before and one year after bariatric surgery. Weight loss following surgery was associated with downregulation of multiple immune pathways in subcutaneous AT and skeletal muscle, alongside notable metabolic improvements. Our results show that obesity is characterised by systemic and tissue-specific inflammation. Subjects with obesity and IR show a more pronounced inflammation phenotype, independent of BMI. Bariatric surgery-induced weight loss is associated with reduced inflammation and improved metabolic health.
Collapse
Affiliation(s)
- S M Oussaada
- Amsterdam UMC Location University of Amsterdam, Department of Endocrinology and Metabolism, Amsterdam Gastroenterology Endocrinology Metabolism, Meibergdreef 9, Amsterdam, the Netherlands
| | - M Kilicarslan
- Amsterdam UMC Location University of Amsterdam, Department of Endocrinology and Metabolism, Amsterdam Gastroenterology Endocrinology Metabolism, Meibergdreef 9, Amsterdam, the Netherlands
| | - B A de Weijer
- Amsterdam UMC Location University of Amsterdam, Department of Endocrinology and Metabolism, Amsterdam Gastroenterology Endocrinology Metabolism, Meibergdreef 9, Amsterdam, the Netherlands
| | - P W Gilijamse
- Amsterdam UMC Location University of Amsterdam, Department of Endocrinology and Metabolism, Amsterdam Gastroenterology Endocrinology Metabolism, Meibergdreef 9, Amsterdam, the Netherlands
| | - A Şekercan
- Amsterdam UMC Location University of Amsterdam, Department of Public Health, Meibergdreef 9, Amsterdam, the Netherlands; Amsterdam UMC Location University of Amsterdam, Department of Surgery, Meibergdreef 9, Amsterdam, the Netherlands
| | - S Virtue
- MRC Metabolic Diseases Unit, University of Cambridge Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - I M C Janssen
- Nederlandse Obesitas Kliniek, Departement of Science, Huis ter Heide, the Netherlands
| | - A van de Laar
- Spaarne Gasthuis, Department of Surgery, Haarlem, the Netherlands
| | - A Demirkiran
- Red Cross Hospital, Department of Gastrointestinal Surgery, Beverwijk, the Netherlands
| | - B A van Wagensveld
- NMC Royal Hospital, Department of Surgery, Abu Dhabi, United Arab Emirates
| | - A P J Houdijk
- Northwest Clinics, Department of Surgery, Alkmaar, the Netherlands
| | - A Jongejan
- Amsterdam UMC Location University of Amsterdam, Epidemiology and Data Science, Amsterdam, the Netherlands; Amsterdam Public Health, Methodology, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Inflammatory Diseases, Amsterdam, the Netherlands
| | - P D Moerland
- Amsterdam UMC Location University of Amsterdam, Epidemiology and Data Science, Amsterdam, the Netherlands; Amsterdam Public Health, Methodology, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Inflammatory Diseases, Amsterdam, the Netherlands
| | - J Verheij
- Amsterdam UMC Location University of Amsterdam, Department of Pathology, Amsterdam, the Netherlands
| | - T B Geijtenbeek
- Amsterdam UMC Location University of Amsterdam, Laboratory for Experimental Immunology, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Cancer Immunology, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Immunology, Amsterdam, the Netherlands
| | - V W Bloks
- University Medical Center Groningen, Department of Paediatrics, University of Groningen, Groningen, the Netherlands
| | - M C de Goffau
- Amsterdam UMC Location University of Amsterdam, Department of Experimental Vascular Medicine, Meibergdreef 9, Amsterdam, the Netherlands; Wellcome Trust Sanger Institute, Hinxton, UK; Amsterdam UMC, Tytgat Institute for Liver and Intestinal Research, Meibergdreef 9, Amsterdam, the Netherlands
| | - J A Romijn
- Amsterdam UMC Location University of Amsterdam, Department of Internal Medicine, Meibergdreef 9, Amsterdam, the Netherlands
| | - M Nieuwdorp
- Amsterdam UMC Location University of Amsterdam, Department of Vascular Medicine, Meibergdreef 9, Amsterdam, the Netherlands
| | - A Vidal-Puig
- MRC Metabolic Diseases Unit, University of Cambridge Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - K W Ter Horst
- Amsterdam UMC Location University of Amsterdam, Department of Endocrinology and Metabolism, Amsterdam Gastroenterology Endocrinology Metabolism, Meibergdreef 9, Amsterdam, the Netherlands
| | - M J Serlie
- Amsterdam UMC Location University of Amsterdam, Department of Endocrinology and Metabolism, Amsterdam Gastroenterology Endocrinology Metabolism, Meibergdreef 9, Amsterdam, the Netherlands; Section of Endocrinology, Yale School of Medicine, New Haven, USA.
| |
Collapse
|
2
|
de Vries LE, Jongejan A, Monteiro Fortes J, Balesar R, Rozemuller AJM, Moerland PD, Huitinga I, Swaab DF, Verhaagen J. Gene-expression profiling of individuals resilient to Alzheimer's disease reveals higher expression of genes related to metallothionein and mitochondrial processes and no changes in the unfolded protein response. Acta Neuropathol Commun 2024; 12:68. [PMID: 38664739 PMCID: PMC11046840 DOI: 10.1186/s40478-024-01760-9] [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] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 03/10/2024] [Indexed: 04/28/2024] Open
Abstract
Some individuals show a discrepancy between cognition and the amount of neuropathological changes characteristic for Alzheimer's disease (AD). This phenomenon has been referred to as 'resilience'. The molecular and cellular underpinnings of resilience remain poorly understood. To obtain an unbiased understanding of the molecular changes underlying resilience, we investigated global changes in gene expression in the superior frontal gyrus of a cohort of cognitively and pathologically well-defined AD patients, resilient individuals and age-matched controls (n = 11-12 per group). 897 genes were significantly altered between AD and control, 1121 between resilient and control and 6 between resilient and AD. Gene set enrichment analysis (GSEA) revealed that the expression of metallothionein (MT) and of genes related to mitochondrial processes was higher in the resilient donors. Weighted gene co-expression network analysis (WGCNA) identified gene modules related to the unfolded protein response, mitochondrial processes and synaptic signaling to be differentially associated with resilience or dementia. As changes in MT, mitochondria, heat shock proteins and the unfolded protein response (UPR) were the most pronounced changes in the GSEA and/or WGCNA, immunohistochemistry was used to further validate these processes. MT was significantly increased in astrocytes in resilient individuals. A higher proportion of the mitochondrial gene MT-CO1 was detected outside the cell body versus inside the cell body in the resilient compared to the control group and there were higher levels of heat shock protein 70 (HSP70) and X-box-binding protein 1 spliced (XBP1s), two proteins related to heat shock proteins and the UPR, in the AD donors. Finally, we show evidence for putative sex-specific alterations in resilience, including gene expression differences related to autophagy in females compared to males. Taken together, these results show possible mechanisms involving MTs, mitochondrial processes and the UPR by which individuals might maintain cognition despite the presence of AD pathology.
Collapse
Affiliation(s)
- Luuk E de Vries
- Department of Neuroregeneration, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Meibergdreef 47, 1105 BA, Amsterdam, The Netherlands.
| | - Aldo Jongejan
- Amsterdam UMC Location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Jennifer Monteiro Fortes
- Department of Neuropsychiatric Disorders, Netherlands Institute for Neuroscience, Institute of the Royal Netherlands Academy of Arts and Sciences, Meibergdreef 47, 1105 BA, Amsterdam, The Netherlands
| | - Rawien Balesar
- Department of Neuropsychiatric Disorders, Netherlands Institute for Neuroscience, Institute of the Royal Netherlands Academy of Arts and Sciences, Meibergdreef 47, 1105 BA, Amsterdam, The Netherlands
| | - Annemieke J M Rozemuller
- Department of Pathology, Amsterdam Neuroscience, Amsterdam UMC - Location VUmc, Amsterdam, The Netherlands
| | - Perry D Moerland
- Amsterdam UMC Location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Inge Huitinga
- Department of Neuroimmunology, Netherlands Institute for Neuroscience, Institute of the Royal Netherlands Academy of Arts and Sciences, Meibergdreef 47, 1105 BA, Amsterdam, The Netherlands
- Center for Neuroscience, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Dick F Swaab
- Department of Neuropsychiatric Disorders, Netherlands Institute for Neuroscience, Institute of the Royal Netherlands Academy of Arts and Sciences, Meibergdreef 47, 1105 BA, Amsterdam, The Netherlands
| | - Joost Verhaagen
- Department of Neuroregeneration, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Meibergdreef 47, 1105 BA, Amsterdam, The Netherlands.
- Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.
| |
Collapse
|
3
|
Janssens GE, Molenaars M, Herzog K, Grevendonk L, Remie CME, Vervaart MAT, Elfrink HL, Wever EJM, Schomakers BV, Denis SW, Waterham HR, Pras-Raves ML, van Weeghel M, van Kampen AHC, Tammaro A, Butter LM, van der Rijt S, Florquin S, Jongejan A, Moerland PD, Hoeks J, Schrauwen P, Vaz FM, Houtkooper RH. A conserved complex lipid signature marks human muscle aging and responds to short-term exercise. Nat Aging 2024:10.1038/s43587-024-00595-2. [PMID: 38609524 DOI: 10.1038/s43587-024-00595-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/22/2024] [Indexed: 04/14/2024]
Abstract
Studies in preclinical models suggest that complex lipids, such as phospholipids, play a role in the regulation of longevity. However, identification of universally conserved complex lipid changes that occur during aging, and how these respond to interventions, is lacking. Here, to comprehensively map how complex lipids change during aging, we profiled ten tissues in young versus aged mice using a lipidomics platform. Strikingly, from >1,200 unique lipids, we found a tissue-wide accumulation of bis(monoacylglycero)phosphate (BMP) during mouse aging. To investigate translational value, we assessed muscle tissue of young and older people, and found a similar marked BMP accumulation in the human aging lipidome. Furthermore, we found that a healthy-aging intervention consisting of moderate-to-vigorous exercise was able to lower BMP levels in postmenopausal female research participants. Our work implicates complex lipid biology as central to aging, identifying a conserved aging lipid signature of BMP accumulation that is modifiable upon a short-term healthy-aging intervention.
Collapse
Affiliation(s)
- Georges E Janssens
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands.
- Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam, the Netherlands.
| | - Marte Molenaars
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam, the Netherlands
| | - Katharina Herzog
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam, the Netherlands
| | - Lotte Grevendonk
- Department of Nutrition and Human Movement Sciences, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Centre, Maastricht, the Netherlands
- TI Food and Nutrition, Wageningen, the Netherlands
| | - Carlijn M E Remie
- Department of Nutrition and Human Movement Sciences, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Martin A T Vervaart
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Core Facility Metabolomics, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
| | - Hyung L Elfrink
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Core Facility Metabolomics, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
| | - Eric J M Wever
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Core Facility Metabolomics, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Epidemiology and Data Science, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
| | - Bauke V Schomakers
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Core Facility Metabolomics, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
| | - Simone W Denis
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam, the Netherlands
| | - Mia L Pras-Raves
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Core Facility Metabolomics, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Epidemiology and Data Science, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
| | - Michel van Weeghel
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Core Facility Metabolomics, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
| | - Antoine H C van Kampen
- Epidemiology and Data Science, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Methodology, Amsterdam, the Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, the Netherlands
| | - Alessandra Tammaro
- Pathology Department, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Infection and Immunity, Amsterdam, the Netherlands
| | - Loes M Butter
- Pathology Department, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Infection and Immunity, Amsterdam, the Netherlands
| | - Sanne van der Rijt
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam, the Netherlands
- Pathology Department, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
| | - Sandrine Florquin
- Pathology Department, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Infection and Immunity, Amsterdam, the Netherlands
| | - Aldo Jongejan
- Epidemiology and Data Science, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Methodology, Amsterdam, the Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, the Netherlands
| | - Perry D Moerland
- Epidemiology and Data Science, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Methodology, Amsterdam, the Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, the Netherlands
| | - Joris Hoeks
- Department of Nutrition and Human Movement Sciences, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Centre, Maastricht, the Netherlands
- TI Food and Nutrition, Wageningen, the Netherlands
| | - Patrick Schrauwen
- Department of Nutrition and Human Movement Sciences, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Centre, Maastricht, the Netherlands
- TI Food and Nutrition, Wageningen, the Netherlands
| | - Frédéric M Vaz
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands.
- Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam, the Netherlands.
- Core Facility Metabolomics, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands.
| | - Riekelt H Houtkooper
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands.
- Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam, the Netherlands.
- Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands.
| |
Collapse
|
4
|
van den Bosch AMR, van der Poel M, Fransen NL, Vincenten MCJ, Bobeldijk AM, Jongejan A, Engelenburg HJ, Moerland PD, Smolders J, Huitinga I, Hamann J. Profiling of microglia nodules in multiple sclerosis reveals propensity for lesion formation. Nat Commun 2024; 15:1667. [PMID: 38396116 PMCID: PMC10891081 DOI: 10.1038/s41467-024-46068-3] [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] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Microglia nodules (HLA-DR+ cell clusters) are associated with brain pathology. In this post-mortem study, we investigated whether they represent the first stage of multiple sclerosis (MS) lesion formation. We show that microglia nodules are associated with more severe MS pathology. Compared to microglia nodules in stroke, those in MS show enhanced expression of genes previously found upregulated in MS lesions. Furthermore, genes associated with lipid metabolism, presence of T and B cells, production of immunoglobulins and cytokines, activation of the complement cascade, and metabolic stress are upregulated in microglia nodules in MS. Compared to stroke, they more frequently phagocytose oxidized phospholipids and possess a more tubular mitochondrial network. Strikingly, in MS, some microglia nodules encapsulate partially demyelinated axons. Taken together, we propose that activation of microglia nodules in MS by cytokines and immunoglobulins, together with phagocytosis of oxidized phospholipids, may lead to a microglia phenotype prone to MS lesion formation.
Collapse
Affiliation(s)
- Aletta M R van den Bosch
- Neuroimmunology Research Group, Netherlands Institute for Neuroscience, Amsterdam, The Netherlands.
| | - Marlijn van der Poel
- Neuroimmunology Research Group, Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
| | - Nina L Fransen
- Neuroimmunology Research Group, Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
| | - Maria C J Vincenten
- Neuroimmunology Research Group, Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
| | - Anneleen M Bobeldijk
- Neuroimmunology Research Group, Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
| | - Aldo Jongejan
- Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Hendrik J Engelenburg
- Neuroimmunology Research Group, Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
| | - Perry D Moerland
- Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Joost Smolders
- Neuroimmunology Research Group, Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
- MS Center ErasMS, Department of Neurology and Immunology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Inge Huitinga
- Neuroimmunology Research Group, Netherlands Institute for Neuroscience, Amsterdam, The Netherlands.
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
| | - Jörg Hamann
- Neuroimmunology Research Group, Netherlands Institute for Neuroscience, Amsterdam, The Netherlands.
- Department of Experimental Immunology, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Center, Amsterdam, The Netherlands.
| |
Collapse
|
5
|
Buck TM, Quinn PMJ, Pellissier LP, Mulder AA, Jongejan A, Lu X, Boon N, Koot D, Almushattat H, Arendzen CH, Vos RM, Bradley EJ, Freund C, Mikkers HMM, Boon CJF, Moerland PD, Baas F, Koster AJ, Neefjes J, Berlin I, Jost CR, Wijnholds J. CRB1 is required for recycling by RAB11A+ vesicles in human retinal organoids. Stem Cell Reports 2023; 18:1793-1810. [PMID: 37541258 PMCID: PMC10545476 DOI: 10.1016/j.stemcr.2023.07.001] [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] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 08/06/2023] Open
Abstract
CRB1 gene mutations can cause early- or late-onset retinitis pigmentosa, Leber congenital amaurosis, or maculopathy. Recapitulating human CRB1 phenotypes in animal models has proven challenging, necessitating the development of alternatives. We generated human induced pluripotent stem cell (iPSC)-derived retinal organoids of patients with retinitis pigmentosa caused by biallelic CRB1 mutations and evaluated them against autologous gene-corrected hiPSCs and hiPSCs from healthy individuals. Patient organoids show decreased levels of CRB1 and NOTCH1 expression at the retinal outer limiting membrane. Proximity ligation assays show that human CRB1 and NOTCH1 can interact via their extracellular domains. CRB1 patient organoids feature increased levels of WDFY1+ vesicles, fewer RAB11A+ recycling endosomes, decreased VPS35 retromer complex components, and more degradative endolysosomal compartments relative to isogenic control organoids. Taken together, our data demonstrate that patient-derived retinal organoids enable modeling of retinal degeneration and highlight the importance of CRB1 in early endosome maturation receptor recycling in the retina.
Collapse
Affiliation(s)
- Thilo M Buck
- Department of Ophthalmology, Leiden University Medical Center (LUMC), Leiden 2333 ZA, the Netherlands
| | - Peter M J Quinn
- Department of Ophthalmology, Leiden University Medical Center (LUMC), Leiden 2333 ZA, the Netherlands
| | - Lucie P Pellissier
- Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam 1105 BA, the Netherlands
| | - Aat A Mulder
- Department of Cell & Chemical Biology, Leiden University Medical Center (LUMC), Leiden 2300 RC, the Netherlands
| | - Aldo Jongejan
- Bioinformatics Laboratory, Epidemiology & Data Science, Amsterdam University Medical Centers, Amsterdam 1105 AZ, the Netherlands
| | - Xuefei Lu
- Department of Ophthalmology, Leiden University Medical Center (LUMC), Leiden 2333 ZA, the Netherlands
| | - Nanda Boon
- Department of Ophthalmology, Leiden University Medical Center (LUMC), Leiden 2333 ZA, the Netherlands
| | - Daniëlle Koot
- Department of Ophthalmology, Leiden University Medical Center (LUMC), Leiden 2333 ZA, the Netherlands
| | - Hind Almushattat
- Department of Ophthalmology, Leiden University Medical Center (LUMC), Leiden 2333 ZA, the Netherlands
| | | | - Rogier M Vos
- Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam 1105 BA, the Netherlands
| | - Edward J Bradley
- Department of Genome Analysis, Amsterdam University Medical Centers, Amsterdam 1105 AZ, the Netherlands
| | - Christian Freund
- Leiden University Medical Center hiPSC Hotel, Leiden 2333 ZA, the Netherlands
| | - Harald M M Mikkers
- Department of Cell & Chemical Biology, Leiden University Medical Center (LUMC), Leiden 2300 RC, the Netherlands; Leiden University Medical Center hiPSC Hotel, Leiden 2333 ZA, the Netherlands
| | - Camiel J F Boon
- Department of Ophthalmology, Leiden University Medical Center (LUMC), Leiden 2333 ZA, the Netherlands; Department of Ophthalmology, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam 1000 AE, the Netherlands
| | - Perry D Moerland
- Bioinformatics Laboratory, Epidemiology & Data Science, Amsterdam University Medical Centers, Amsterdam 1105 AZ, the Netherlands
| | - Frank Baas
- Department of Genome Analysis, Amsterdam University Medical Centers, Amsterdam 1105 AZ, the Netherlands; Department of Clinical Genetics/LDGA, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Abraham J Koster
- Department of Cell & Chemical Biology, Leiden University Medical Center (LUMC), Leiden 2300 RC, the Netherlands
| | - Jacques Neefjes
- Department of Cell & Chemical Biology, Leiden University Medical Center (LUMC), Leiden 2300 RC, the Netherlands
| | - Ilana Berlin
- Department of Cell & Chemical Biology, Leiden University Medical Center (LUMC), Leiden 2300 RC, the Netherlands
| | - Carolina R Jost
- Department of Cell & Chemical Biology, Leiden University Medical Center (LUMC), Leiden 2300 RC, the Netherlands
| | - Jan Wijnholds
- Department of Ophthalmology, Leiden University Medical Center (LUMC), Leiden 2333 ZA, the Netherlands; Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam 1105 BA, the Netherlands.
| |
Collapse
|
6
|
Haselager MV, van Driel BF, Perelaer E, de Rooij D, Lashgari D, Loos R, Kater AP, Moerland PD, Eldering E. In Vitro 3D Spheroid Culture System Displays Sustained T Cell-dependent CLL Proliferation and Survival. Hemasphere 2023; 7:e938. [PMID: 37637994 PMCID: PMC10448932 DOI: 10.1097/hs9.0000000000000938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/26/2023] [Indexed: 08/29/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) cells are highly dependent on microenvironmental cells and signals. The lymph node (LN) is the critical site of in vivo CLL proliferation and development of resistance to both chemotherapy and targeted agents. We present a new model that incorporates key aspects of the CLL LN, which enables investigation of CLL cells in the context of a protective niche. We describe a three-dimensional (3D) in vitro culture system using ultra-low attachment plates to create spheroids of CLL cells derived from peripheral blood. Starting from CLL:T cell ratios as observed in LN samples, CLL activation was induced by either direct stimulation and/or indirectly via T cells. Compared with two-dimensional cultures, 3D cultures promoted CLL proliferation in a T cell-dependent manner, and enabled expansion for up to 7 weeks, including the formation of follicle-like structures after several weeks of culture. This model enables high-throughput drug screening, of which we describe response to Btk inhibition, venetoclax resistance, and T cell-mediated cytotoxicity as examples. In summary, we present the first LN-mimicking in vitro 3D culture for primary CLL, which enables readouts such as real-time drug screens, kinetic growth assays, and spatial localization. This is the first in vitro CLL system that allows testing of response and resistance to venetoclax and Bruton's tyrosine kinase inhibitors in the context of the tumor microenvironment, thereby opening up new possibilities for clinically useful applications.
Collapse
Affiliation(s)
- Marco V. Haselager
- Department of Experimental Immunology, Amsterdam UMC Location University of Amsterdam, Meibergdreef, The Netherlands
- Lymphoma and Myeloma Center Amsterdam, LYMMCARE, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Cancer Immunology, Amsterdam, The Netherlands
| | - Bianca F. van Driel
- Department of Hematology, Amsterdam UMC Location University of Amsterdam, Meibergdreef, The Netherlands
| | - Eduard Perelaer
- Department of Experimental Immunology, Amsterdam UMC Location University of Amsterdam, Meibergdreef, The Netherlands
| | - Dennis de Rooij
- Department of Hematology, Amsterdam UMC Location University of Amsterdam, Meibergdreef, The Netherlands
| | - Danial Lashgari
- Amsterdam Institute for Infection and Immunity, Cancer Immunology, Amsterdam, The Netherlands
- Department of Epidemiology and Data Science, Amsterdam UMC Location University of Amsterdam, Meibergdreef, The Netherlands
| | - Remco Loos
- Center for Innovation and Translational Research Europe, Bristol Myers Squibb, Sevilla, Spain
| | - Arnon P. Kater
- Lymphoma and Myeloma Center Amsterdam, LYMMCARE, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Cancer Immunology, Amsterdam, The Netherlands
- Department of Hematology, Amsterdam UMC Location University of Amsterdam, Meibergdreef, The Netherlands
| | - Perry D. Moerland
- Department of Epidemiology and Data Science, Amsterdam UMC Location University of Amsterdam, Meibergdreef, The Netherlands
- Amsterdam Institute for Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology Amsterdam, The Netherlands
| | - Eric Eldering
- Department of Experimental Immunology, Amsterdam UMC Location University of Amsterdam, Meibergdreef, The Netherlands
- Lymphoma and Myeloma Center Amsterdam, LYMMCARE, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Cancer Immunology, Amsterdam, The Netherlands
| |
Collapse
|
7
|
Leeksma AC, Derks IAM, Garrick B, Jongejan A, Colombo M, Bloedjes T, Trowe T, Leisten JC, Howarth M, Malek M, Mortensen DS, Blease K, Groza MC, Narla RK, Loos R, Kersten M, Moerland PD, Guikema JEJ, Kater AP, Eldering E, Filvaroff EH. SMG1, a nonsense-mediated mRNA decay (NMD) regulator, as a candidate therapeutic target in multiple myeloma. Mol Oncol 2022; 17:284-297. [PMID: 36400430 PMCID: PMC9892823 DOI: 10.1002/1878-0261.13343] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/16/2022] [Accepted: 11/17/2022] [Indexed: 11/20/2022] Open
Abstract
Early data suggested that CC-115, a clinical molecule, already known to inhibit the mammalian target of rapamycin kinase (TORK) and DNA-dependent protein kinase (DNA-PK) may have additional targets beyond TORK and DNA-PK. Therefore, we aimed to identify such target(s) and investigate a potential therapeutic applicability. Functional profiling of 141 cancer cell lines revealed inhibition of kinase suppressor of morphogenesis in genitalia 1 (SMG1), a key regulator of the RNA degradation mechanism nonsense-mediated mRNA decay (NMD), as an additional target of CC-115. CC-115 treatment showed a dose-dependent increase of SMG1-mediated NMD transcripts. A subset of cell lines, including multiple myeloma (MM) cell lines sensitive to the endoplasmic reticulum stress-inducing compound thapsigargin, were highly susceptible to SMG1 inhibition. CC-115 caused the induction of UPR transcripts and cell death by mitochondrial apoptosis, requiring the presence of BAX/BAK and caspase activity. Superior antitumor activity of CC-115 over TORK inhibitors in primary human MM cells and three xenograft mouse models appeared to be via inhibition of SMG1. Our data support further development of SMG1 inhibitors as possible therapeutics in MM.
Collapse
Affiliation(s)
- Alexander C. Leeksma
- Department of Hematology, Amsterdam University Medical CentersUniversity of AmsterdamThe Netherlands,Department of Experimental ImmunologyAmsterdam University Medical CentersUniversity of AmsterdamThe Netherlands,Lymphoma and myeloma center Amsterdam (LYMMCARE), Cancer Center Amsterdam (CCA) and Amsterdam Infection and Immunity Institute (AIII)The Netherlands
| | - Ingrid A. M. Derks
- Department of Experimental ImmunologyAmsterdam University Medical CentersUniversity of AmsterdamThe Netherlands,Lymphoma and myeloma center Amsterdam (LYMMCARE), Cancer Center Amsterdam (CCA) and Amsterdam Infection and Immunity Institute (AIII)The Netherlands
| | - Brett Garrick
- Translational Research, Bristol Myers SquibbSan FranciscoCAUSA
| | - Aldo Jongejan
- Department of Clinical Epidemiology, Biostatistics and BioinformaticsAmsterdam University Medical Centers, University of AmsterdamThe Netherlands
| | - Martino Colombo
- Bristol Myers Squibb's Center for Innovation and Translational Research Europe (CITRE)SevilleSpain
| | - Timon Bloedjes
- Department of Pathology, Amsterdam University Medical Centers, Lymphoma and Myeloma Center Amsterdam (LYMMCARE)University of AmsterdamThe Netherlands
| | - Torsten Trowe
- Translational Research, Bristol Myers SquibbSan FranciscoCAUSA
| | | | | | - Mehnaz Malek
- Translational Research, Bristol Myers SquibbSan FranciscoCAUSA
| | | | - Kate Blease
- Discovery, Bristol Myers SquibbSan DiegoCAUSA
| | | | | | - Remco Loos
- Bristol Myers Squibb's Center for Innovation and Translational Research Europe (CITRE)SevilleSpain
| | - Marie‐José Kersten
- Department of Hematology, Amsterdam University Medical CentersUniversity of AmsterdamThe Netherlands
| | - Perry D. Moerland
- Department of Clinical Epidemiology, Biostatistics and BioinformaticsAmsterdam University Medical Centers, University of AmsterdamThe Netherlands
| | - Jeroen E. J. Guikema
- Department of Pathology, Amsterdam University Medical Centers, Lymphoma and Myeloma Center Amsterdam (LYMMCARE)University of AmsterdamThe Netherlands
| | - Arnon P. Kater
- Department of Hematology, Amsterdam University Medical CentersUniversity of AmsterdamThe Netherlands,Lymphoma and myeloma center Amsterdam (LYMMCARE), Cancer Center Amsterdam (CCA) and Amsterdam Infection and Immunity Institute (AIII)The Netherlands
| | - Eric Eldering
- Department of Experimental ImmunologyAmsterdam University Medical CentersUniversity of AmsterdamThe Netherlands,Lymphoma and myeloma center Amsterdam (LYMMCARE), Cancer Center Amsterdam (CCA) and Amsterdam Infection and Immunity Institute (AIII)The Netherlands
| | | |
Collapse
|
8
|
Claireaux M, Caniels TG, de Gast M, Han J, Guerra D, Kerster G, van Schaik BDC, Jongejan A, Schriek AI, Grobben M, Brouwer PJM, van der Straten K, Aldon Y, Capella-Pujol J, Snitselaar JL, Olijhoek W, Aartse A, Brinkkemper M, Bontjer I, Burger JA, Poniman M, Bijl TPL, Torres JL, Copps J, Martin IC, de Taeye SW, de Bree GJ, Ward AB, Sliepen K, van Kampen AHC, Moerland PD, Sanders RW, van Gils MJ. A public antibody class recognizes an S2 epitope exposed on open conformations of SARS-CoV-2 spike. Nat Commun 2022; 13:4539. [PMID: 35927266 PMCID: PMC9352689 DOI: 10.1038/s41467-022-32232-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 07/22/2022] [Indexed: 12/21/2022] Open
Abstract
Delineating the origins and properties of antibodies elicited by SARS-CoV-2 infection and vaccination is critical for understanding their benefits and potential shortcomings. Therefore, we investigate the SARS-CoV-2 spike (S)-reactive B cell repertoire in unexposed individuals by flow cytometry and single-cell sequencing. We show that ∼82% of SARS-CoV-2 S-reactive B cells harbor a naive phenotype, which represents an unusually high fraction of total human naive B cells (∼0.1%). Approximately 10% of these naive S-reactive B cells share an IGHV1-69/IGKV3-11 B cell receptor pairing, an enrichment of 18-fold compared to the complete naive repertoire. Following SARS-CoV-2 infection, we report an average 37-fold enrichment of IGHV1-69/IGKV3-11 B cell receptor pairing in the S-reactive memory B cells compared to the unselected memory repertoire. This class of B cells targets a previously undefined non-neutralizing epitope on the S2 subunit that becomes exposed on S proteins used in approved vaccines when they transition away from the native pre-fusion state because of instability. These findings can help guide the improvement of SARS-CoV-2 vaccines.
Collapse
Affiliation(s)
- Mathieu Claireaux
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Tom G Caniels
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Marlon de Gast
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Denise Guerra
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Gius Kerster
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Barbera D C van Schaik
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Public Health, Amsterdam, the Netherlands
| | - Aldo Jongejan
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Public Health, Amsterdam, the Netherlands
| | - Angela I Schriek
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Marloes Grobben
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Philip J M Brouwer
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Karlijn van der Straten
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
- Department of Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands
| | - Yoann Aldon
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Joan Capella-Pujol
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Jonne L Snitselaar
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Wouter Olijhoek
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Aafke Aartse
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Mitch Brinkkemper
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Ilja Bontjer
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Judith A Burger
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Meliawati Poniman
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Tom P L Bijl
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jeffrey Copps
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Isabel Cuella Martin
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Steven W de Taeye
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Godelieve J de Bree
- Department of Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Kwinten Sliepen
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Antoine H C van Kampen
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Public Health, Amsterdam, the Netherlands
| | - Perry D Moerland
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Public Health, Amsterdam, the Netherlands
| | - Rogier W Sanders
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands.
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands.
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA.
| | - Marit J van Gils
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands.
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands.
| |
Collapse
|
9
|
Leerink JM, Feijen EAM, Moerland PD, de Baat EC, Merkx R, van der Pal HJH, Tissing WJE, Louwerens M, van den Heuvel‐Eibrink MM, Versluys AB, Asselbergs FW, Sammani A, Teske AJ, van Dalen EC, van der Heiden‐van der Loo M, van Dulmen‐den Broeder E, de Vries ACH, Kapusta L, Loonen J, Pinto YM, Kremer LCM, Mavinkurve‐Groothuis AMC, Kok WEM. Candidate Plasma Biomarkers to Detect Anthracycline‐Related Cardiomyopathy in Childhood Cancer Survivors: A Case Control Study in the Dutch Childhood Cancer Survivor Study. J Am Heart Assoc 2022; 11:e025935. [PMID: 35861824 PMCID: PMC9707839 DOI: 10.1161/jaha.121.025935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background
Plasma biomarkers may aid in the detection of anthracycline‐related cardiomyopathy (ACMP). However, the currently available biomarkers have limited diagnostic value in long‐term childhood cancer survivors. This study sought to identify diagnostic plasma biomarkers for ACMP in childhood cancer survivors.
Methods and Results
We measured 275 plasma proteins in 28 ACMP cases with left ventricular ejection fraction <45%, 29 anthracycline‐treated controls with left ventricular ejection fraction ≥53% matched on sex, time after cancer, and anthracycline dose, and 29 patients with genetically determined dilated cardiomyopathy with left ventricular ejection fraction <45%. Multivariable linear regression was used to identify differentially expressed proteins. Elastic net model, including clinical characteristics, was used to assess discrimination of proteins diagnostic for ACMP. NT‐proBNP (N‐terminal pro‐B‐type natriuretic peptide) and the inflammatory markers CCL19 (C‐C motif chemokine ligands 19) and CCL20, PSPD (pulmonary surfactant protein‐D), and PTN (pleiotrophin) were significantly upregulated in ACMP compared with controls. An elastic net model selected 45 proteins, including NT‐proBNP, CCL19, CCL20 and PSPD, but not PTN, that discriminated ACMP cases from controls with an area under the receiver operating characteristic curve (AUC) of 0.78. This model was not superior to a model including NT‐proBNP and clinical characteristics (AUC=0.75;
P
=0.766). However, when excluding 8 ACMP cases with heart failure, the full model was superior to that including only NT‐proBNP and clinical characteristics (AUC=0.75 versus AUC=0.50;
P
=0.022). The same 45 proteins also showed good discrimination between dilated cardiomyopathy and controls (AUC=0.89), underscoring their association with cardiomyopathy.
Conclusions
We identified 3 specific inflammatory proteins as candidate plasma biomarkers for ACMP in long‐term childhood cancer survivors and demonstrated protein overlap with dilated cardiomyopathy.
Collapse
Affiliation(s)
- Jan M. Leerink
- Department of Cardiology, Amsterdam Cardiovascular Sciences Amsterdam University Medical Center, University of Amsterdam, Heart Center Amsterdam The Netherlands
- Princess Máxima Center for Pediatric Oncology Utrecht The Netherlands
| | | | - Perry D. Moerland
- Bioinformatics Laboratory, Department of Epidemiology and Data Science Amsterdam University Medical Center, University of Amsterdam Amsterdam The Netherlands
| | - Esmee C. de Baat
- Princess Máxima Center for Pediatric Oncology Utrecht The Netherlands
| | - Remy Merkx
- Department of Medical Imaging Radboud University Medical Center Nijmegen The Netherlands
| | | | - Wim J. E. Tissing
- Princess Máxima Center for Pediatric Oncology Utrecht The Netherlands
- Beatrix Children’s Hospital, Department of Pediatric Oncology University of Groningen, University Medical Center Groningen Groningen the Netherlands
| | - Marloes Louwerens
- Department of Internal Medicine Leiden University Medical Center Leiden The Netherlands
| | | | | | - Folkert W. Asselbergs
- Division of Heart and Lungs, Department of Cardiology University Medical Center Utrecht Utrecht The Netherlands
- Institute of Cardiovascular Science, Faculty of Population Health Sciences University College London London UK
- Health Data Research UK and Institute of Health Informatics University College London London UK
| | - Arjan Sammani
- Division of Heart and Lungs, Department of Cardiology University Medical Center Utrecht Utrecht The Netherlands
| | - Arco J. Teske
- Division of Heart and Lungs, Department of Cardiology University Medical Center Utrecht Utrecht The Netherlands
| | | | | | - Eline van Dulmen‐den Broeder
- Department of Pediatric Oncology Amsterdam University Medical Center, Vrije Universiteit Amsterdam The Netherlands
| | - Andrica C. H. de Vries
- Princess Máxima Center for Pediatric Oncology Utrecht The Netherlands
- Department of Pediatric Oncology Erasmus Medical Center Rotterdam The Netherlands
| | - Livia Kapusta
- Department of Pediatric Cardiology Amalia Children’s Hospital, Radboud University Medical Center Nijmegen The Netherlands
- Sackler School of Medicine, Department of Pediatrics, Pediatric Cardiology Unit Tel Aviv Sourasky Medical Center, Tel Aviv University Tel Aviv Israel
| | - Jacqueline Loonen
- Department of Hematology Radboud University Medical Center Nijmegen The Netherlands
| | - Yigal M. Pinto
- Department of Cardiology, Amsterdam Cardiovascular Sciences Amsterdam University Medical Center, University of Amsterdam, Heart Center Amsterdam The Netherlands
| | - Leontien C. M. Kremer
- Princess Máxima Center for Pediatric Oncology Utrecht The Netherlands
- University Medical Center Utrecht Wilhelmina Children’s Hospital Utrecht The Netherlands
- Amsterdam University Medical Center, University of Amsterdam Emma Children’s Hospital Amsterdam The Netherlands
| | | | - Wouter E. M. Kok
- Department of Cardiology, Amsterdam Cardiovascular Sciences Amsterdam University Medical Center, University of Amsterdam, Heart Center Amsterdam The Netherlands
| |
Collapse
|
10
|
Bosmans LA, van Tiel CM, Aarts SABM, Willemsen L, Baardman J, van Os BW, den Toom M, Beckers L, Ahern DJ, Levels JHM, Jongejan A, Moerland PD, Verberk SGS, van den Bossche J, de Winther MMPJ, Weber C, Atzler D, Monaco C, Gerdes N, Shami A, Lutgens E. Myeloid CD40 deficiency reduces atherosclerosis by impairing macrophages' transition into a pro-inflammatory state. Cardiovasc Res 2022; 119:1146-1160. [PMID: 35587037 DOI: 10.1093/cvr/cvac084] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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: 02/16/2022] [Revised: 04/20/2022] [Accepted: 05/04/2022] [Indexed: 11/13/2022] Open
Abstract
AIMS CD40 and its ligand, CD40L, play a critical role in driving atherosclerotic plaque development. Disrupted CD40-signaling reduces experimental atherosclerosis and induces a favourable stable plaque phenotype. We recently showed that small molecule-based inhibition of CD40-TNF Receptor Associated Factor-6 interactions attenuates atherosclerosis in hyperlipidaemic mice via macrophage-driven mechanisms. The present study aims to detail the function of myeloid CD40 in atherosclerosis using myeloid-specific CD40-deficient mice. METHOD AND RESULTS Cd40flox/flox and LysM-cre Cd40flox/flox mice on an Apoe-/- background were generated (CD40wt and CD40mac-/-, respectively). Atherosclerotic lesion size, as well as plaque macrophage content, were reduced in CD40mac-/- compared to CD40wt mice and their plaques displayed a reduction in necrotic core size. Transcriptomics analysis of the CD40mac-/- atherosclerotic aorta revealed downregulated pathways of immune pathways and inflammatory responses.Loss of CD40 in macrophages changed the representation of aortic macrophage subsets. Mass cytometry analysis revealed a higher content of a subset of alternative or resident-like CD206 + CD209b- macrophages in the atherosclerotic aorta of CD40mac-/- compared to CD40wt mice. RNA-sequencing of bone marrow-derived macrophages (BMDMs) of CD40mac-/- mice demonstrated upregulation of genes associated with alternatively activated macrophages (including Folr2, Thbs1, Sdc1 and Tns1). CONCLUSIONS We here show that absence of CD40 signalling in myeloid cells reduces atherosclerosis and limits systemic inflammation by preventing a shift in macrophage polarization towards pro-inflammatory states. Our study confirms the merit of macrophage-targeted inhibition of CD40 as a valuable therapeutic strategy to combat atherosclerosis.
Collapse
Affiliation(s)
- Laura A Bosmans
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences (ACS) & Amsterdam Infection and Immunity (AII), Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, The Netherlands
| | - Claudia M van Tiel
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences (ACS) & Amsterdam Infection and Immunity (AII), Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, The Netherlands
| | - Suzanne A B M Aarts
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences (ACS) & Amsterdam Infection and Immunity (AII), Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, The Netherlands
| | - Lisa Willemsen
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences (ACS) & Amsterdam Infection and Immunity (AII), Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, The Netherlands
| | - Jeroen Baardman
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences (ACS) & Amsterdam Infection and Immunity (AII), Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, The Netherlands
| | - Bram W van Os
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences (ACS) & Amsterdam Infection and Immunity (AII), Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, The Netherlands
| | - Myrthe den Toom
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences (ACS) & Amsterdam Infection and Immunity (AII), Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, The Netherlands
| | - Linda Beckers
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences (ACS) & Amsterdam Infection and Immunity (AII), Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, The Netherlands
| | - David J Ahern
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, UK
| | - Johannes H M Levels
- Department of Vascular Medicine, Amsterdam Cardiovascular Sciences (ACS), Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, The Netherlands
| | - Aldo Jongejan
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Perry D Moerland
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Sanne G S Verberk
- Department of Molecular Cell Biology and Immunology, Amsterdam Cardiovascular Sciences, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Jan van den Bossche
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences (ACS) & Amsterdam Infection and Immunity (AII), Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, The Netherlands.,Department of Molecular Cell Biology and Immunology, Amsterdam Cardiovascular Sciences, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Menno M P J de Winther
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences (ACS) & Amsterdam Infection and Immunity (AII), Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, The Netherlands
| | - Christian Weber
- Institute of Cardiovascular Prevention (IPEK), Ludwig Maximilian's University, Munich, Germany.,German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany.,Cardiovascular Research Institute Maastricht (CARIM), Department of Biochemistry, Maastricht University, Maastricht, the Netherlands.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Dorothee Atzler
- Institute of Cardiovascular Prevention (IPEK), Ludwig Maximilian's University, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.,Walter-Straub-Institute of Pharmacology and Toxicology, Ludwig-Maximilians Universität, München, Germany
| | - Claudia Monaco
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, UK
| | - Norbert Gerdes
- Division of Cardiology, Pulmonology and Vascular Medicine, Medical Faculty, University Hospital and Heinrich Heine University Düsseldorf, Germany
| | - Annelie Shami
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences (ACS) & Amsterdam Infection and Immunity (AII), Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, The Netherlands.,Dept. of Clinical Sciences Malmö, Lund University, Clinical Research Center, Malmö, Sweden
| | - Esther Lutgens
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences (ACS) & Amsterdam Infection and Immunity (AII), Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, The Netherlands.,Institute of Cardiovascular Prevention (IPEK), Ludwig Maximilian's University, Munich, Germany.,German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany.,Experimental Cardiovascular Immunology Laboratory, Dept of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| |
Collapse
|
11
|
Nuijens AC, Oei AL, van Oorschot B, Visser J, van Os RM, Moerland PD, Franken NAP, Rasch CRN, Stalpers LJA. Gamma-H2AX Foci Decay Ratio as a Stronger Predictive Factor of Late Radiation Toxicity Than Dose-Volume Parameters in a Prospective Cohort of Prostate Cancer Patients. Int J Radiat Oncol Biol Phys 2021; 112:212-221. [PMID: 34419566 DOI: 10.1016/j.ijrobp.2021.08.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/29/2021] [Accepted: 08/09/2021] [Indexed: 12/24/2022]
Abstract
PURPOSE Late radiation toxicity is a major dose-limiting factor in curative cancer radiation therapy. Previous studies identified several risk factors for late radiation toxicity, including both dose-volume factors and genetic predisposition. Herein, we investigated the contribution of genetic predisposition, particularly compared with dose-volume factors, to the risk of late radiation toxicity in patients treated with highly conformal radiation therapy. METHODS AND MATERIALS We included 179 patients with prostate cancer who underwent treatment with curative external beam radiation therapy between 2009 and 2013. Toxicity was graded according to the Common Terminology Criteria for Adverse Events version 4.0. Transcriptional responsiveness of homologous recombination repair genes and γ-H2AX foci decay ratios (FDRs) were determined in ex vivo irradiated lymphocytes in a previous analysis. Dose-volume parameters were retrieved by delineating the organs at risk (OARs) on CT planning images. Associations between risk factors and grade ≥2 urinary and bowel late radiation toxicities were assessed using univariable and multivariable logistic regression analyses. The analyses were performed using the highest toxicity grade recorded during the follow-up per patient. RESULTS The median follow-up period was 31 months. One hundred and one patients (56%) developed grade ≥2 late radiation toxicity. Cumulative rates for urinary and bowel grade ≥2 late toxicities were 46% and 17%, respectively. In the multivariable analysis, factors significantly associated with grade ≥2 late toxicity were transurethral resection of the prostate (P = .013), γ-H2AX FDR <3.41 (P = .008), and rectum V70 >11.52% (P = .017). CONCLUSIONS Our results suggest that impaired DNA double-strand break repair in lymphocytes, as quantified by γ-H2AX FDR, is the most critical determining factor of late radiation toxicity. The limited influence of dose-volume parameters could be due to the use of increasingly conformal techniques, leading to improved dose-volume parameters of the organs at risk.
Collapse
Affiliation(s)
- Anna C Nuijens
- Department of Radiation Oncology, Amsterdam UMC, University of Amsterdam, Meibergdreef, Amsterdam, the Netherlands; Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC, University of Amsterdam, Cancer Center Amsterdam, Meibergdreef, Amsterdam, the Netherlands
| | - Arlene L Oei
- Department of Radiation Oncology, Amsterdam UMC, University of Amsterdam, Meibergdreef, Amsterdam, the Netherlands; Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC, University of Amsterdam, Cancer Center Amsterdam, Meibergdreef, Amsterdam, the Netherlands
| | - Bregje van Oorschot
- Department of Radiation Oncology, Amsterdam UMC, University of Amsterdam, Meibergdreef, Amsterdam, the Netherlands; Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC, University of Amsterdam, Cancer Center Amsterdam, Meibergdreef, Amsterdam, the Netherlands
| | - Jorrit Visser
- Department of Radiation Oncology, Amsterdam UMC, University of Amsterdam, Meibergdreef, Amsterdam, the Netherlands
| | - Rob M van Os
- Department of Radiation Oncology, Amsterdam UMC, University of Amsterdam, Meibergdreef, Amsterdam, the Netherlands
| | - Perry D Moerland
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam UMC, University of Amsterdam, Meibergdreef, Amsterdam, the Netherlands
| | - Nicolaas A P Franken
- Department of Radiation Oncology, Amsterdam UMC, University of Amsterdam, Meibergdreef, Amsterdam, the Netherlands; Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC, University of Amsterdam, Cancer Center Amsterdam, Meibergdreef, Amsterdam, the Netherlands
| | - Coen R N Rasch
- Department of Radiation Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Lukas J A Stalpers
- Department of Radiation Oncology, Amsterdam UMC, University of Amsterdam, Meibergdreef, Amsterdam, the Netherlands.
| |
Collapse
|
12
|
Milićević N, Ait-Hmyed Hakkari O, Bagchi U, Sandu C, Jongejan A, Moerland PD, Ten Brink JB, Hicks D, Bergen AA, Felder-Schmittbuhl MP. Core circadian clock genes Per1 and Per2 regulate the rhythm in photoreceptor outer segment phagocytosis. FASEB J 2021; 35:e21722. [PMID: 34160105 DOI: 10.1096/fj.202100293rr] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/13/2021] [Accepted: 05/24/2021] [Indexed: 02/07/2023]
Abstract
Retinal photoreceptors undergo daily renewal of their distal outer segments, a process indispensable for maintaining retinal health. Photoreceptor outer segment (POS) phagocytosis occurs as a daily peak, roughly about 1 hour after light onset. However, the underlying cellular and molecular mechanisms which initiate this process are still unknown. Here we show that, under constant darkness, mice deficient for core circadian clock genes (Per1 and Per2) lack a daily peak in POS phagocytosis. By qPCR analysis, we found that core clock genes were rhythmic over 24 hours in both WT and Per1, Per2 double mutant whole retinas. More precise transcriptomics analysis of laser capture microdissected WT photoreceptors revealed no differentially expressed genes between time points preceding and during the peak of POS phagocytosis. In contrast, we found that microdissected WT retinal pigment epithelium (RPE) had a number of genes that were differentially expressed at the peak phagocytic time point compared to adjacent ones. We also found a number of differentially expressed genes in Per1, Per2 double mutant RPE compared to WT ones at the peak phagocytic time point. Finally, based on STRING analysis, we found a group of interacting genes that potentially drive POS phagocytosis in the RPE. This potential pathway consists of genes such as: Pacsin1, Syp, Camk2b, and Camk2d among others. Our findings indicate that Per1 and Per2 are necessary clock components for driving POS phagocytosis and suggest that this process is transcriptionally driven by the RPE.
Collapse
Affiliation(s)
- Nemanja Milićević
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.,Centre National de la Recherche Scientifique, Institut des Neurosciences Cellulaires et Intégratives, Université de Strasbourg, Strasbourg, France
| | - Ouafa Ait-Hmyed Hakkari
- Centre National de la Recherche Scientifique, Institut des Neurosciences Cellulaires et Intégratives, Université de Strasbourg, Strasbourg, France
| | - Udita Bagchi
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.,Centre National de la Recherche Scientifique, Institut des Neurosciences Cellulaires et Intégratives, Université de Strasbourg, Strasbourg, France
| | - Cristina Sandu
- Centre National de la Recherche Scientifique, Institut des Neurosciences Cellulaires et Intégratives, Université de Strasbourg, Strasbourg, France
| | - Aldo Jongejan
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, Amsterdam, the Netherlands
| | - Perry D Moerland
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, Amsterdam, the Netherlands
| | - Jacoline B Ten Brink
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - David Hicks
- Centre National de la Recherche Scientifique, Institut des Neurosciences Cellulaires et Intégratives, Université de Strasbourg, Strasbourg, France
| | - Arthur A Bergen
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.,Department of Ophthalmology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.,Netherlands Institute for Neuroscience (NIN-KNAW), Amsterdam, the Netherlands
| | - Marie-Paule Felder-Schmittbuhl
- Centre National de la Recherche Scientifique, Institut des Neurosciences Cellulaires et Intégratives, Université de Strasbourg, Strasbourg, France
| |
Collapse
|
13
|
Borgoni S, Sofyalı E, Soleimani M, Wilhelm H, Müller-Decker K, Will R, Noronha A, Beumers L, Verschure PJ, Yarden Y, Magnani L, van Kampen AH, Moerland PD, Wiemann S. Time-Resolved Profiling Reveals ATF3 as a Novel Mediator of Endocrine Resistance in Breast Cancer. Cancers (Basel) 2020; 12:E2918. [PMID: 33050633 PMCID: PMC7650760 DOI: 10.3390/cancers12102918] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/29/2020] [Accepted: 10/07/2020] [Indexed: 01/05/2023] Open
Abstract
Breast cancer is one of the leading causes of death for women worldwide. Patients whose tumors express Estrogen Receptor α account for around 70% of cases and are mostly treated with targeted endocrine therapy. However, depending on the degree of severity of the disease at diagnosis, 10 to 40% of these tumors eventually relapse due to resistance development. Even though recent novel approaches as the combination with CDK4/6 inhibitors increased the overall survival of relapsing patients, this remains relatively short and there is a urgent need to find alternative targetable pathways. In this study we profiled the early phases of the resistance development process to uncover drivers of this phenomenon. Time-resolved analysis revealed that ATF3, a member of the ATF/CREB family of transcription factors, acts as a novel regulator of the response to therapy via rewiring of central signaling processes towards the adaptation to endocrine treatment. ATF3 was found to be essential in controlling crucial processes such as proliferation, cell cycle, and apoptosis during the early response to treatment through the regulation of MAPK/AKT signaling pathways. Its essential role was confirmed in vivo in a mouse model, and elevated expression of ATF3 was verified in patient datasets, adding clinical relevance to our findings. This study proposes ATF3 as a novel mediator of endocrine resistance development in breast cancer and elucidates its role in the regulation of downstream pathways activities.
Collapse
Affiliation(s)
- Simone Borgoni
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; (E.S.); (H.W.); (L.B.)
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany
| | - Emre Sofyalı
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; (E.S.); (H.W.); (L.B.)
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany
| | - Maryam Soleimani
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.S.); (A.H.C.v.K.); (P.D.M.)
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Heike Wilhelm
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; (E.S.); (H.W.); (L.B.)
| | - Karin Müller-Decker
- Tumor Models Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany;
| | - Rainer Will
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany;
| | - Ashish Noronha
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel; (A.N.); (Y.Y.)
| | - Lukas Beumers
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; (E.S.); (H.W.); (L.B.)
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany
| | - Pernette J. Verschure
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands;
| | - Yosef Yarden
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel; (A.N.); (Y.Y.)
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, W12 0NN London, UK;
| | - Antoine H.C. van Kampen
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.S.); (A.H.C.v.K.); (P.D.M.)
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Perry D. Moerland
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.S.); (A.H.C.v.K.); (P.D.M.)
| | - Stefan Wiemann
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; (E.S.); (H.W.); (L.B.)
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany
| |
Collapse
|
14
|
Soleimani Dodaran M, Borgoni S, Sofyalı E, Verschure PJ, Wiemann S, Moerland PD, van Kampen AHC. Candidate methylation sites associated with endocrine therapy resistance in ER+/HER2- breast cancer. BMC Cancer 2020; 20:676. [PMID: 32684154 PMCID: PMC7368985 DOI: 10.1186/s12885-020-07100-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/23/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Estrogen receptor (ER) positive breast cancer is often effectively treated with drugs that inhibit ER signaling, i.e., tamoxifen (TAM) and aromatase inhibitors (AIs). However, 30% of ER+ breast cancer patients develop resistance to therapy leading to tumour recurrence. Changes in the methylation profile have been implicated as one of the mechanisms through which therapy resistance develops. Therefore, we aimed to identify methylation loci associated with endocrine therapy resistance. METHODS We used genome-wide DNA methylation profiles of primary ER+/HER2- tumours from The Cancer Genome Atlas in combination with curated data on survival and treatment to predict development of endocrine resistance. Association of individual DNA methylation markers with survival was assessed using Cox proportional hazards models in a cohort of ER+/HER2- tumours (N = 552) and two sub-cohorts corresponding to the endocrine treatment (AI or TAM) that patients received (N = 210 and N = 172, respectively). We also identified multivariable methylation signatures associated with survival using Cox proportional hazards models with elastic net regularization. Individual markers and multivariable signatures were compared with DNA methylation profiles generated in a time course experiment using the T47D ER+ breast cancer cell line treated with tamoxifen or deprived from estrogen. RESULTS We identified 134, 5 and 1 CpGs for which DNA methylation is significantly associated with survival in the ER+/HER2-, TAM and AI cohorts respectively. Multi-locus signatures consisted of 203, 36 and 178 CpGs and showed a large overlap with the corresponding single-locus signatures. The methylation signatures were associated with survival independently of tumour stage, age, AI treatment, and luminal status. The single-locus signature for the TAM cohort was conserved among the loci that were differentially methylated in endocrine-resistant T47D cells. Similarly, multi-locus signatures for the ER+/HER2- and AI cohorts were conserved in endocrine-resistant T47D cells. Also at the gene set level, several sets related to endocrine therapy and resistance were enriched in both survival and T47D signatures. CONCLUSIONS We identified individual and multivariable DNA methylation markers associated with therapy resistance independently of luminal status. Our results suggest that these markers identified from primary tumours prior to endocrine treatment are associated with development of endocrine resistance.
Collapse
MESH Headings
- Antineoplastic Agents, Hormonal/pharmacology
- Antineoplastic Agents, Hormonal/therapeutic use
- Aromatase Inhibitors/pharmacology
- Aromatase Inhibitors/therapeutic use
- Biomarkers, Tumor/genetics
- Breast Neoplasms/drug therapy
- Breast Neoplasms/genetics
- Breast Neoplasms/mortality
- Breast Neoplasms/pathology
- Carcinoma, Ductal, Breast/drug therapy
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/mortality
- Carcinoma, Ductal, Breast/pathology
- Cohort Studies
- CpG Islands/genetics
- DNA Methylation
- Drug Resistance, Neoplasm/genetics
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Humans
- Receptor, ErbB-2/metabolism
- Receptors, Estrogen/metabolism
- Survival Analysis
- Tamoxifen/pharmacology
- Tamoxifen/therapeutic use
Collapse
Affiliation(s)
- Maryam Soleimani Dodaran
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Amsterdam Public Health research institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, AZ, 1105, The Netherlands
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
| | - Simone Borgoni
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
- Faculty of Biosciences, University Heidelberg, 69120, Heidelberg, Germany
| | - Emre Sofyalı
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
- Faculty of Biosciences, University Heidelberg, 69120, Heidelberg, Germany
| | - Pernette J Verschure
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
| | - Stefan Wiemann
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
- Faculty of Biosciences, University Heidelberg, 69120, Heidelberg, Germany
| | - Perry D Moerland
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Amsterdam Public Health research institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, AZ, 1105, The Netherlands.
| | - Antoine H C van Kampen
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Amsterdam Public Health research institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, AZ, 1105, The Netherlands.
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands.
| |
Collapse
|
15
|
Richmond PA, van der Kloet F, Vaz FM, Lin D, Uzozie A, Graham E, Kobor M, Mostafavi S, Moerland PD, Lange PF, van Kampen AHC, Wasserman WW, Engelen M, Kemp S, van Karnebeek CDM. Multi-Omic Approach to Identify Phenotypic Modifiers Underlying Cerebral Demyelination in X-Linked Adrenoleukodystrophy. Front Cell Dev Biol 2020; 8:520. [PMID: 32671069 PMCID: PMC7330173 DOI: 10.3389/fcell.2020.00520] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 03/13/2020] [Accepted: 06/02/2020] [Indexed: 12/12/2022] Open
Abstract
X-linked adrenoleukodystrophy (ALD) is a peroxisomal metabolic disorder with a highly complex clinical presentation. ALD is caused by mutations in the ABCD1 gene, and is characterized by the accumulation of very long-chain fatty acids in plasma and tissues. Disease-causing mutations are 'loss of function' mutations, with no prognostic value with respect to the clinical outcome of an individual. All male patients with ALD develop spinal cord disease and a peripheral neuropathy in adulthood, although age of onset is highly variable. However, the lifetime prevalence to develop progressive white matter lesions, termed cerebral ALD (CALD), is only about 60%. Early identification of transition to CALD is critical since it can be halted by allogeneic hematopoietic stem cell therapy only in an early stage. The primary goal of this study is to identify molecular markers which may be prognostic of cerebral demyelination from a simple blood sample, with the hope that blood-based assays can replace the current protocols for diagnosis. We collected six well-characterized brother pairs affected by ALD and discordant for the presence of CALD and performed multi-omic profiling of blood samples including genome, epigenome, transcriptome, metabolome/lipidome, and proteome profiling. In our analysis we identify discordant genomic alleles present across all families as well as differentially abundant molecular features across the omics technologies. The analysis was focused on univariate modeling to discriminate the two phenotypic groups, but was unable to identify statistically significant candidate molecular markers. Our study highlights the issues caused by a large amount of inter-individual variation, and supports the emerging hypothesis that cerebral demyelination is a complex mix of environmental factors and/or heterogeneous genomic alleles. We confirm previous observations about the role of immune response, specifically auto-immunity and the potential role of PFN1 protein overabundance in CALD in a subset of the families. We envision our methodology as well as dataset has utility to the field for reproducing previous or enabling future modifier investigations.
Collapse
Affiliation(s)
- Phillip A. Richmond
- Center for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Frans van der Kloet
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Department of Pediatrics, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Frederic M. Vaz
- Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Department of Clinical Chemistry, Amsterdam Gastroenterology & Metabolism, Amsterdam, Netherlands
| | - David Lin
- Center for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Anuli Uzozie
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Michael Cuccione Childhood Cancer Research Program, BC Children’s Hospital, Vancouver, BC, Canada
| | - Emma Graham
- Center for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Michael Kobor
- Center for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Sara Mostafavi
- Center for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Perry D. Moerland
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Philipp F. Lange
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Michael Cuccione Childhood Cancer Research Program, BC Children’s Hospital, Vancouver, BC, Canada
| | - Antoine H. C. van Kampen
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Wyeth W. Wasserman
- Center for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Marc Engelen
- Department of Pediatric Neurology, Amsterdam Neuroscience, Amsterdam Leukodystrophy Center, Emma Children’s Hospital, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Department of Neurology, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Stephan Kemp
- Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Department of Clinical Chemistry, Amsterdam Gastroenterology & Metabolism, Amsterdam, Netherlands
- Department of Pediatric Neurology, Amsterdam Neuroscience, Amsterdam Leukodystrophy Center, Emma Children’s Hospital, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Clara D. M. van Karnebeek
- Center for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
- Department of Pediatrics, Emma Children’s Hospital, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Department of Pediatrics, Amalia Children’s Hospital, Radboud University Medical Center, Nijmegen, Netherlands
| |
Collapse
|
16
|
Adam AAA, Jongejan A, Moerland PD, van der Mark VA, Oude Elferink RP, Chamuleau RAFM, Hoekstra R. Genome-wide expression profiling reveals increased stability and mitochondrial energy metabolism of the human liver cell line HepaRG-CAR. Cytotechnology 2020; 72:377-395. [PMID: 32130581 PMCID: PMC7225227 DOI: 10.1007/s10616-020-00384-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/24/2020] [Indexed: 02/06/2023] Open
Abstract
Human liver cell line HepaRG is a well-known source of human hepatocyte-like cells which, however, displays limited biotransformation and a tendency to transform after 20 passages. The new HepaRG-CAR cell line overexpressing constitutive androstane receptor (CAR, NR1I3), a regulator of detoxification and energy metabolism outperforms the parental HepaRG cell line in various liver functions. To further characterize this cell line and assess its stability we compared HepaRG-CAR with HepaRG cells at different passages for their expression profile, ammonia and lactate metabolism, bile acid and reactive oxygen species (ROS) production. Transcriptomic profiling of HepaRG-CAR vs. HepaRG early-passage revealed downregulation of hypoxia, glycolysis and proliferation and upregulation of oxidative phosphorylation genesets. In addition CAR overexpression downregulated the mTORC1 signaling pathway, which, as mediator of proliferation and metabolic reprogramming, may play an important role in the establishment of the HepaRG-CAR phenotype. The ammonia and lactate metabolism and bile acid production of HepaRG-CAR cells was stable for 10 additional passages compared to HepaRG cells. Interestingly, bile acid production was 4.5-fold higher in HepaRG-CAR vs. HepaRG cells, whereas lactate and ROS production were 2.7- and 2.0-fold lower, respectively. Principal component analysis showed clustering of HepaRG-CAR (early- and late-passage) and HepaRG early-passage and not with HepaRG late-passage indicating that passaging exerted larger effect on the transcriptional profile of HepaRG than HepaRG-CAR cells. In conclusion, overexpression of CAR in HepaRG cells improves their bile acid production, mitochondrial energy metabolism, and stability, with the latter possibly due to reduced ROS production, resulting in an optimized source of human hepatocytes.
Collapse
Affiliation(s)
- Aziza A. A. Adam
- Tytgat Institute for Liver and Intestinal Research, AG&M, Amsterdam UMC, University of Amsterdam, Meibergdreef 69-71, 1105 BK Amsterdam, The Netherlands
| | - Aldo Jongejan
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Perry D. Moerland
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Vincent A. van der Mark
- Tytgat Institute for Liver and Intestinal Research, AG&M, Amsterdam UMC, University of Amsterdam, Meibergdreef 69-71, 1105 BK Amsterdam, The Netherlands
- Surgical Laboratory, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Ronald P. Oude Elferink
- Tytgat Institute for Liver and Intestinal Research, AG&M, Amsterdam UMC, University of Amsterdam, Meibergdreef 69-71, 1105 BK Amsterdam, The Netherlands
| | - Robert A. F. M. Chamuleau
- Tytgat Institute for Liver and Intestinal Research, AG&M, Amsterdam UMC, University of Amsterdam, Meibergdreef 69-71, 1105 BK Amsterdam, The Netherlands
| | - Ruurdtje Hoekstra
- Tytgat Institute for Liver and Intestinal Research, AG&M, Amsterdam UMC, University of Amsterdam, Meibergdreef 69-71, 1105 BK Amsterdam, The Netherlands
- Surgical Laboratory, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| |
Collapse
|
17
|
Molenaars M, Janssens GE, Williams EG, Jongejan A, Lan J, Rabot S, Joly F, Moerland PD, Schomakers BV, Lezzerini M, Liu YJ, McCormick MA, Kennedy BK, van Weeghel M, van Kampen AHC, Aebersold R, MacInnes AW, Houtkooper RH. A Conserved Mito-Cytosolic Translational Balance Links Two Longevity Pathways. Cell Metab 2020; 31:549-563.e7. [PMID: 32084377 PMCID: PMC7214782 DOI: 10.1016/j.cmet.2020.01.011] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [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: 12/18/2018] [Revised: 08/22/2019] [Accepted: 01/22/2020] [Indexed: 12/13/2022]
Abstract
Slowing down translation in either the cytosol or the mitochondria is a conserved longevity mechanism. Here, we found a non-interventional natural correlation of mitochondrial and cytosolic ribosomal proteins (RPs) in mouse population genetics, suggesting a translational balance. Inhibiting mitochondrial translation in C. elegans through mrps-5 RNAi repressed cytosolic translation. Transcriptomics integrated with proteomics revealed that this inhibition specifically reduced translational efficiency of mRNAs required in growth pathways while increasing stress response mRNAs. The repression of cytosolic translation and extension of lifespan from mrps-5 RNAi were dependent on atf-5/ATF4 and independent from metabolic phenotypes. We found the translational balance to be conserved in mammalian cells upon inhibiting mitochondrial translation pharmacologically with doxycycline. Lastly, extending this in vivo, doxycycline repressed cytosolic translation in the livers of germ-free mice. These data demonstrate that inhibiting mitochondrial translation initiates an atf-5/ATF4-dependent cascade leading to coordinated repression of cytosolic translation, which could be targeted to promote longevity.
Collapse
Affiliation(s)
- Marte Molenaars
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology and Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
| | - Georges E Janssens
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology and Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
| | - Evan G Williams
- Institute of Molecular Systems Biology, ETH Zurich, Zürich, Switzerland
| | - Aldo Jongejan
- Bioinformatics Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Jiayi Lan
- Institute of Molecular Systems Biology, ETH Zurich, Zürich, Switzerland
| | - Sylvie Rabot
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Fatima Joly
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Perry D Moerland
- Bioinformatics Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Bauke V Schomakers
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology and Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands; Core Facility Metabolomics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Marco Lezzerini
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology and Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
| | - Yasmine J Liu
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology and Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
| | - Mark A McCormick
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, USA; Autophagy, Inflammation, and Metabolism Center of Biological Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Brian K Kennedy
- Buck Institute for Research on Aging, Novato, CA, USA; Departments of Biochemistry and Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Michel van Weeghel
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology and Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands; Core Facility Metabolomics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Antoine H C van Kampen
- Bioinformatics Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zurich, Zürich, Switzerland; Faculty of Science, University of Zürich, Switzerland
| | - Alyson W MacInnes
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology and Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
| | - Riekelt H Houtkooper
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology and Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands.
| |
Collapse
|
18
|
Hermkens DMA, Stam OCG, de Wit NM, Fontijn RD, Jongejan A, Moerland PD, Mackaaij C, Waas ISE, Daemen MJAP, de Vries HE. Profiling the unique protective properties of intracranial arterial endothelial cells. Acta Neuropathol Commun 2019; 7:151. [PMID: 31610812 PMCID: PMC6792251 DOI: 10.1186/s40478-019-0805-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 09/07/2019] [Indexed: 02/07/2023] Open
Abstract
Cardiovascular disorders, like atherosclerosis and hypertension, are increasingly known to be associated with vascular cognitive impairment (VCI). In particular, intracranial atherosclerosis is one of the main causes of VCI, although plaque development occurs later in time and is structurally different compared to atherosclerosis in extracranial arteries. Recent data suggest that endothelial cells (ECs) that line the intracranial arteries may exert anti-atherosclerotic effects due to yet unidentified pathways. To gain insights into underlying mechanisms, we isolated post-mortem endothelial cells from both the intracranial basilar artery (BA) and the extracranial common carotid artery (CCA) from the same individual (total of 15 individuals) with laser capture microdissection. RNA sequencing revealed a distinct molecular signature of the two endothelial cell populations of which the most prominent ones were validated by means of qPCR. Our data reveal for the first time that intracranial artery ECs exert an immune quiescent phenotype. Secondly, genes known to be involved in the response of ECs to damage (inflammation, differentiation, adhesion, proliferation, permeability and oxidative stress) are differentially expressed in intracranial ECs compared to extracranial ECs. Finally, Desmoplakin (DSP) and Hop Homeobox (HOPX), two genes expressed at a higher level in intracranial ECs, and Sodium Voltage-Gated Channel Beta Subunit 3 (SCN3B), a gene expressed at a lower level in intracranial ECs compared to extracranial ECs, were shown to be responsive to shear stress and/or hypoxia. With our data we present a set of intracranial-specific endothelial genes that may contribute to its protective phenotype, thereby supporting proper perfusion and consequently may preserve cognitive function. Deciphering the molecular regulation of the vascular bed in the brain may lead to the identification of novel potential intervention strategies to halt vascular associated disorders, such as atherosclerosis and vascular cognitive dysfunction.
Collapse
|
19
|
Seijkens TTP, van Tiel CM, Kusters PJH, Atzler D, Soehnlein O, Zarzycka B, Aarts SABM, Lameijer M, Gijbels MJ, Beckers L, den Toom M, Slütter B, Kuiper J, Duchene J, Aslani M, Megens RTA, van 't Veer C, Kooij G, Schrijver R, Hoeksema MA, Boon L, Fay F, Tang J, Baxter S, Jongejan A, Moerland PD, Vriend G, Bleijlevens B, Fisher EA, Duivenvoorden R, Gerdes N, de Winther MPJ, Nicolaes GA, Mulder WJM, Weber C, Lutgens E. Targeting CD40-Induced TRAF6 Signaling in Macrophages Reduces Atherosclerosis. J Am Coll Cardiol 2019; 71:527-542. [PMID: 29406859 PMCID: PMC5800892 DOI: 10.1016/j.jacc.2017.11.055] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 11/02/2017] [Accepted: 11/16/2017] [Indexed: 02/05/2023]
Abstract
Background Disrupting the costimulatory CD40-CD40L dyad reduces atherosclerosis, but can result in immune suppression. The authors recently identified small molecule inhibitors that block the interaction between CD40 and tumor necrosis factor receptor-associated factor (TRAF) 6 (TRAF-STOPs), while leaving CD40-TRAF2/3/5 interactions intact, thereby preserving CD40-mediated immunity. Objectives This study evaluates the potential of TRAF-STOP treatment in atherosclerosis. Methods The effects of TRAF-STOPs on atherosclerosis were investigated in apolipoprotein E deficient (Apoe−/−) mice. Recombinant high-density lipoprotein (rHDL) nanoparticles were used to target TRAF-STOPs to macrophages. Results TRAF-STOP treatment of young Apoe−/− mice reduced atherosclerosis by reducing CD40 and integrin expression in classical monocytes, thereby hampering monocyte recruitment. When Apoe−/− mice with established atherosclerosis were treated with TRAF-STOPs, plaque progression was halted, and plaques contained an increase in collagen, developed small necrotic cores, and contained only a few immune cells. TRAF-STOP treatment did not impair “classical” immune pathways of CD40, including T-cell proliferation and costimulation, Ig isotype switching, or germinal center formation, but reduced CD40 and β2-integrin expression in inflammatory monocytes. In vitro testing and transcriptional profiling showed that TRAF-STOPs are effective in reducing macrophage migration and activation, which could be attributed to reduced phosphorylation of signaling intermediates of the canonical NF-κB pathway. To target TRAF-STOPs specifically to macrophages, TRAF-STOP 6877002 was incorporated into rHDL nanoparticles. Six weeks of rHDL-6877002 treatment attenuated the initiation of atherosclerosis in Apoe−/− mice. Conclusions TRAF-STOPs can overcome the current limitations of long-term CD40 inhibition in atherosclerosis and have the potential to become a future therapeutic for atherosclerosis.
Collapse
Affiliation(s)
- Tom T P Seijkens
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands; Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University, Munich, Germany
| | - Claudia M van Tiel
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Pascal J H Kusters
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Dorothee Atzler
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands; Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University, Munich, Germany; Walther-Straub-Institut for Pharmacology and Toxicology, Ludwig-Maximilians-University, Munich, Germany; German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany
| | - Oliver Soehnlein
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University, Munich, Germany; German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany
| | - Barbara Zarzycka
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, the Netherlands
| | - Suzanne A B M Aarts
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Marnix Lameijer
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Marion J Gijbels
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands; Department of Pathology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, the Netherlands; Department of Molecular Genetics, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, the Netherlands
| | - Linda Beckers
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Myrthe den Toom
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Bram Slütter
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Johan Kuiper
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Johan Duchene
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University, Munich, Germany
| | - Maria Aslani
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University, Munich, Germany
| | - Remco T A Megens
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University, Munich, Germany; Department of Biomedical Engineering, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, the Netherlands
| | - Cornelis van 't Veer
- Center for Experimental and Molecular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Gijs Kooij
- Department of Molecular Cell Biology and Immunology, Neuroscience Campus Amsterdam, VU Medical Center, Amsterdam, the Netherlands
| | - Roy Schrijver
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany
| | - Marten A Hoeksema
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands
| | | | - Francois Fay
- Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jun Tang
- Bioceros BV, Utrecht, the Netherlands; Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Samantha Baxter
- Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Aldo Jongejan
- Department of Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Perry D Moerland
- Department of Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Gert Vriend
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Boris Bleijlevens
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Edward A Fisher
- Division of Cardiology, Department of Medicine, Marc and Ruti Bell Program in Vascular Biology, New York University School of Medicine, New York, New York
| | - Raphael Duivenvoorden
- Department of Vascular Medicine, Academic Medical Center, Amsterdam, the Netherlands
| | - Norbert Gerdes
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University, Munich, Germany; Division of Cardiology, Pulmonology, and Vascular Medicine, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Menno P J de Winther
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands; Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University, Munich, Germany
| | - Gerry A Nicolaes
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, the Netherlands
| | - Willem J M Mulder
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands; Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Christian Weber
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University, Munich, Germany; German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany; Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, the Netherlands
| | - Esther Lutgens
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands; Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University, Munich, Germany.
| |
Collapse
|
20
|
Stenvers DJ, Jongejan A, Atiqi S, Vreijling JP, Limonard EJ, Endert E, Baas F, Moerland PD, Fliers E, Kalsbeek A, Bisschop PH. Diurnal rhythms in the white adipose tissue transcriptome are disturbed in obese individuals with type 2 diabetes compared with lean control individuals. Diabetologia 2019; 62:704-716. [PMID: 30737520 DOI: 10.1007/s00125-019-4813-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [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: 10/17/2018] [Accepted: 12/18/2018] [Indexed: 12/23/2022]
Abstract
AIMS/HYPOTHESIS Animal studies have indicated that disturbed diurnal rhythms of clock gene expression in adipose tissue can induce obesity and type 2 diabetes. The importance of the circadian timing system for energy metabolism is well established, but little is known about the diurnal regulation of (clock) gene expression in obese individuals with type 2 diabetes. In this study we aimed to identify key disturbances in the diurnal rhythms of the white adipose tissue transcriptome in obese individuals with type 2 diabetes. METHODS In a case-control design, we included six obese individuals with type 2 diabetes and six healthy, lean control individuals. All participants were provided with three identical meals per day for 3 days at zeitgeber time (ZT, with ZT 0:00 representing the time of lights on) 0:30, 6:00 and 11:30. Four sequential subcutaneous abdominal adipose tissue samples were obtained, on day 2 at ZT 15:30, and on day 3 at ZT 0:15, ZT 5:45 and ZT 11:15. Gene expression was measured using RNA sequencing. RESULTS The core clock genes showed reduced amplitude oscillations in the individuals with type 2 diabetes compared with the healthy control individuals. Moreover, in individuals with type 2 diabetes, only 1.8% (303 genes) of 16,818 expressed genes showed significant diurnal rhythmicity, compared with 8.4% (1421 genes) in healthy control individuals. Enrichment analysis revealed a loss of rhythm in individuals with type 2 diabetes of canonical metabolic pathways involved in the regulation of lipolysis. Enrichment analysis of genes with an altered mesor in individuals with type 2 diabetes showed decreased activity of the translation initiating pathway 'EIF2 signaling'. Individuals with type 2 diabetes showed a reduced diurnal rhythm in postprandial glucose concentrations. CONCLUSIONS/INTERPRETATION Diurnal clock and metabolic gene expression rhythms are decreased in subcutaneous adipose tissue of obese individuals with type 2 diabetes compared with lean control participants. Future investigation is needed to explore potential treatment targets as identified by our study, including clock enhancement and induction of EIF2 signalling. DATA AVAILABILITY The raw sequencing data and supplementary files for rhythmic expression analysis and Ingenuity Pathway Analysis have been deposited in NCBI Gene Expression Omnibus (GEO series accession number GSE104674).
Collapse
Affiliation(s)
- Dirk Jan Stenvers
- Department of Endocrinology and Metabolism, Amsterdam UMC, location AMC, University of Amsterdam, room F5-162, P.O. Box 22660, 1100 DD, Amsterdam, the Netherlands.
| | - Aldo Jongejan
- Bioinformatics Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Sadaf Atiqi
- Department of Endocrinology and Metabolism, Amsterdam UMC, location AMC, University of Amsterdam, room F5-162, P.O. Box 22660, 1100 DD, Amsterdam, the Netherlands
| | - Jeroen P Vreijling
- Neurogenetics Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Eelkje J Limonard
- Department of Endocrinology and Metabolism, Amsterdam UMC, location AMC, University of Amsterdam, room F5-162, P.O. Box 22660, 1100 DD, Amsterdam, the Netherlands
| | - Erik Endert
- Department of Clinical Chemistry, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Frank Baas
- Neurogenetics Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Perry D Moerland
- Bioinformatics Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Eric Fliers
- Department of Endocrinology and Metabolism, Amsterdam UMC, location AMC, University of Amsterdam, room F5-162, P.O. Box 22660, 1100 DD, Amsterdam, the Netherlands
| | - Andries Kalsbeek
- Department of Endocrinology and Metabolism, Amsterdam UMC, location AMC, University of Amsterdam, room F5-162, P.O. Box 22660, 1100 DD, Amsterdam, the Netherlands
- Hypothalamic Integration Mechanisms, Netherlands Institute for Neuroscience (NIN), Amsterdam, the Netherlands
| | - Peter H Bisschop
- Department of Endocrinology and Metabolism, Amsterdam UMC, location AMC, University of Amsterdam, room F5-162, P.O. Box 22660, 1100 DD, Amsterdam, the Netherlands
| |
Collapse
|
21
|
De Vries LCS, Duarte JM, De Krijger M, Welting O, Van Hamersveld PHP, Van Leeuwen-Hilbers FWM, Moerland PD, Jongejan A, D'Haens GR, De Jonge WJ, Wildenberg ME. A JAK1 Selective Kinase Inhibitor and Tofacitinib Affect Macrophage Activation and Function. Inflamm Bowel Dis 2019; 25:647-660. [PMID: 30668755 DOI: 10.1093/ibd/izy364] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [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: 03/23/2018] [Revised: 07/07/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Janus kinases (JAKs) mediate cytokine signaling involved in inflammatory bowel disease. The pan-JAK inhibitor tofacitinib has shown efficacy in the treatment of ulcerative colitis. However, concerns regarding adverse events due to their wide spectrum inhibition fueled efforts to develop selective JAK inhibitors. Given the crucial role of myeloid cells in intestinal immune homeostasis, we evaluated the effect of pan-JAK and selective JAK inhibitors on pro- and anti-inflammatory macrophage polarization and function (M1/M2) and in experimental colitis. METHODS Murine bone marrow-derived macrophages or human monocytes were treated using JAK1 and JAK3 selective inhibitors (JAK1i;JAK3i) and tofacitinib and were evaluated by transcriptional, functional, and metabolic analyses. In vivo, oral administration of JAK1i and tofacitinib (10 or 30 mg/kg) was tested in both acute and acute rescue dextran sodium sulfate (DSS) colitis. RESULTS Both tofacitinib and JAK1i but not JAK3i effectively inhibited STAT1 phosphorylation and interferon gamma-induced transcripts in M1 polarized macrophages. Strikingly, transcriptional profiling suggested a switch from M1 to M2 type macrophages, which was supported by increased protein expression of M2-associated markers. In addition, both inhibitors enhanced oxidative phosphorylation rates. In vivo, JAK1i and tofacitinib did not protect mice from acute DSS-induced colitis but ameliorated recovery from weight loss and disease activity during acute rescue DSS-induced colitis at the highest dose. CONCLUSION JAK1i and tofacitinib but not JAK3i induce phenotypical and functional characteristics of anti-inflammatory macrophages, suggesting JAK1 as the main effector pathway for tofacitinib in these cells. In vivo, JAK1i and tofacitinib modestly affect acute rescue DSS-induced colitis.
Collapse
Affiliation(s)
- L C S De Vries
- Tytgat Institute for Liver and Intestinal Research, AMC, Amsterdam, the Netherlands.,Department of Gastroenterology and Hepatology, AMC, Amsterdam, the Netherlands
| | - J M Duarte
- Tytgat Institute for Liver and Intestinal Research, AMC, Amsterdam, the Netherlands
| | - M De Krijger
- Tytgat Institute for Liver and Intestinal Research, AMC, Amsterdam, the Netherlands.,Department of Gastroenterology and Hepatology, AMC, Amsterdam, the Netherlands
| | - O Welting
- Tytgat Institute for Liver and Intestinal Research, AMC, Amsterdam, the Netherlands
| | - P H P Van Hamersveld
- Tytgat Institute for Liver and Intestinal Research, AMC, Amsterdam, the Netherlands
| | | | - P D Moerland
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, AMC, Amsterdam, the Netherlands
| | - A Jongejan
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, AMC, Amsterdam, the Netherlands
| | - G R D'Haens
- Department of Gastroenterology and Hepatology, AMC, Amsterdam, the Netherlands
| | - W J De Jonge
- Tytgat Institute for Liver and Intestinal Research, AMC, Amsterdam, the Netherlands
| | - M E Wildenberg
- Tytgat Institute for Liver and Intestinal Research, AMC, Amsterdam, the Netherlands.,Department of Gastroenterology and Hepatology, AMC, Amsterdam, the Netherlands
| |
Collapse
|
22
|
Reiniers MJ, de Haan L, Weijer R, Wiggers JK, Jongejan A, Moerland PD, Alles LK, van Kampen AHC, van Gulik TM, Heger M, van Golen RF. Effect of preoperative biliary drainage on cholestasis-associated inflammatory and fibrotic gene signatures in perihilar cholangiocarcinoma. Br J Surg 2018; 106:55-58. [PMID: 30395349 DOI: 10.1002/bjs.11022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 09/12/2018] [Accepted: 09/18/2018] [Indexed: 11/07/2022]
Abstract
Preoperative biliary drainage (PBD) is used routinely in the evaluation of patients with potentially resectable perihilar cholangiocarcinoma to relieve cholestasis and improve the liver's resilience to surgery. Little preclinical or translatational data are, however, currently available to guide the use of PBD in this patient group. The effect of PBD on hepatic gene expression profiles was therefore studied by microarray analysis. Drainage affects inflammatory and fibrotic gene signatures.
Collapse
Affiliation(s)
- M J Reiniers
- Department of Experimental Surgery, University of Amsterdam, Amsterdam, The Netherlands
| | - L de Haan
- Department of Experimental Surgery, University of Amsterdam, Amsterdam, The Netherlands
| | - R Weijer
- Department of Experimental Surgery, University of Amsterdam, Amsterdam, The Netherlands
| | - J K Wiggers
- Department of Experimental Surgery, University of Amsterdam, Amsterdam, The Netherlands
| | - A Jongejan
- Bioinformatics Laboratory, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - P D Moerland
- Bioinformatics Laboratory, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - L K Alles
- Department of Experimental Surgery, University of Amsterdam, Amsterdam, The Netherlands
| | - A H C van Kampen
- Bioinformatics Laboratory, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - T M van Gulik
- Department of Experimental Surgery, University of Amsterdam, Amsterdam, The Netherlands
| | - M Heger
- Department of Experimental Surgery, University of Amsterdam, Amsterdam, The Netherlands
| | - R F van Golen
- Department of Experimental Surgery, University of Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
23
|
van Wenum M, Adam AAA, van der Mark VA, Chang JC, Wildenberg ME, Hendriks EJ, Jongejan A, Moerland PD, van Gulik TM, Oude Elferink RP, Chamuleau RAFM, Hoekstra R. Oxygen drives hepatocyte differentiation and phenotype stability in liver cell lines. J Cell Commun Signal 2018; 12:575-588. [PMID: 29399736 PMCID: PMC6039343 DOI: 10.1007/s12079-018-0456-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/25/2018] [Indexed: 02/07/2023] Open
Abstract
The in vitro generation of terminally differentiated hepatocytes is an unmet need. We investigated the contribution of oxygen concentration to differentiation in human liver cell lines HepaRG and C3A. HepaRG cells were cultured under hypoxia (5%O2), normoxia (21%O2) or hyperoxia (40%O2). Cultures were analysed for hepatic functions, gene transcript levels, and protein expression of albumin, hepatic transcription factor CEBPα, hepatic progenitor marker SOX9, and hypoxia inducible factor (HIF)1α. C3A cells were analysed after exposure to normoxia or hyperoxia. In hyperoxic HepaRG cultures, urea cycle activity, bile acid synthesis, CytochromeP450 3A4 (CYP3A4) activity and ammonia elimination were 165-266% increased. These effects were reproduced in C3A cells. Whole transcriptome analysis of HepaRG cells revealed that 240 (of 23.223) probes were differentially expressed under hyperoxia, with an overrepresentation of genes involved in hepatic differentiation, metabolism and extracellular signalling. Under hypoxia, CYP3A4 activity and ammonia elimination were inhibited almost completely and 5/5 tested hepatic genes and 2/3 tested hepatic transcription factor genes were downregulated. Protein expression of SOX9 and HIF1α was strongly positive in hypoxic cultures, variable in normoxic cultures and predominantly negative in hyperoxic cultures. Conversely, albumin and CEBPα expression were highest in hyperoxic cultures. HepaRG cells that were serially passaged under hypoxia maintained their capacity to differentiate under normoxia, in contrast to cells passaged under normoxia. Hyperoxia increases hepatocyte differentiation in HepaRG and C3A cells. In contrast, hypoxia maintains stem cell characteristics and inhibits hepatic differentiation of HepaRG cells, possibly through the activity of HIF1α.
Collapse
Affiliation(s)
- Martien van Wenum
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center (AMC), Meibergdreef 69-71, 1105BK, Amsterdam, The Netherlands
- Surgical Laboratory, Department of Surgery, Academic Medical Center, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - Aziza A A Adam
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center (AMC), Meibergdreef 69-71, 1105BK, Amsterdam, The Netherlands
| | - Vincent A van der Mark
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center (AMC), Meibergdreef 69-71, 1105BK, Amsterdam, The Netherlands
- Surgical Laboratory, Department of Surgery, Academic Medical Center, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - Jung-Chin Chang
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center (AMC), Meibergdreef 69-71, 1105BK, Amsterdam, The Netherlands
| | - Manon E Wildenberg
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center (AMC), Meibergdreef 69-71, 1105BK, Amsterdam, The Netherlands
| | - Erik J Hendriks
- Surgical Laboratory, Department of Surgery, Academic Medical Center, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - Aldo Jongejan
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - Perry D Moerland
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - Thomas M van Gulik
- Surgical Laboratory, Department of Surgery, Academic Medical Center, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - Ronald P Oude Elferink
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center (AMC), Meibergdreef 69-71, 1105BK, Amsterdam, The Netherlands
| | - Robert A F M Chamuleau
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center (AMC), Meibergdreef 69-71, 1105BK, Amsterdam, The Netherlands
| | - Ruurdtje Hoekstra
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center (AMC), Meibergdreef 69-71, 1105BK, Amsterdam, The Netherlands.
- Surgical Laboratory, Department of Surgery, Academic Medical Center, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.
| |
Collapse
|
24
|
van Wenum M, Treskes P, Adam AAA, van der Mark VA, Jongejan A, Moerland PD, van Gulik TM, Oude Elferink RPJ, Chamuleau RAFM, Hoekstra R. HepaRG-Progenitor Cell Derived Hepatocytes Cultured in Bioartificial Livers Are Protected from Healthy- and Acute Liver Failure-Plasma Induced Toxicity. Cell Physiol Biochem 2018; 48:2189-2204. [PMID: 30110678 DOI: 10.1159/000492560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 07/31/2018] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIMS For applicability of cell-based therapies aimed at the treatment of liver failure, such as bioartificial livers (BALs) and hepatocyte transplantation, it is essential that the applied hepatocytes tolerate exposure to the patient plasma. However, plasma from both healthy donors and acute liver failure (ALF) patients is detrimental to hepatocytes and hepatic cell lines, such as HepaRG. We aimed to elucidate the underlying mechanisms of plasma-induced toxicity against HepaRG cells in order to ultimately develop methods to reduce this toxicity and render HepaRG-BAL treatment more effective. METHODS Differentiated HepaRG cells cultured in monolayers and laboratory-scale BALs were exposed to culture medium, healthy human plasma, healthy porcine plasma and ALF porcine plasma. Healthy human plasma was fractionated based on size- and polarity, albumin depleted and heat treated to characterize the toxic fraction. The cells were assessed for viability by total protein content and trypan blue staining. Their hepatic differentiation was assessed on transcript level through qRT-PCR and microarray analysis, and on functional level for Cytochrome P450 3A4 activity and ammonia elimination. Mitochondrial damage was assessed by JC-1 staining and mitochondrial gene transcription. RESULTS Sixteen hours of healthy human plasma exposure did not affect viability, however, hepatic gene-transcript levels decreased dramatically and dose-dependently within four hours of exposure. These changes were associated with early NF-kB signaling and a shift from mitochondrial energy metabolism towards glycolysis. Healthy human plasma-toxicity was associated with the dose-dependent presence of heat-resistant, albumin-bound and (partly) hydrophobic toxic compound(s). HepaRG cells cultured in BALs were partially protected from plasma-toxicity, which was mainly attributable to medium perfusion and/or 3D configuration applied during BAL culturing. The detrimental human plasma effects were reversible in BAL-cultured cells. Porcine ALF-plasma elicited mitotoxicity additional to the basal detrimental effect of porcine healthy plasma, which were only partially reversible. CONCLUSION A specific fraction of human plasma reduces hepatic differentiation of HepaRG cultures, in association with early NF-κB activation. In addition, ALF-plasma elicits mitotoxic effects. These findings allow for a targeted approach in preventing plasma-induced cell damage.
Collapse
Affiliation(s)
- Martien van Wenum
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center (AMC), Amsterdam, the Netherlands.,Surgical Laboratory, Department of Surgery, Academic Medical Center, Amsterdam, the Netherlands
| | - Philipp Treskes
- Hepatology Laboratory, University of Edinburgh, Chancellor's Building, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Aziza A A Adam
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center (AMC), Amsterdam, the Netherlands
| | - Vincent A van der Mark
- Surgical Laboratory, Department of Surgery, Academic Medical Center, Amsterdam, the Netherlands
| | - Aldo Jongejan
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health research institute, Academic Medical Center, Amsterdam, the Netherlands
| | - Perry D Moerland
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health research institute, Academic Medical Center, Amsterdam, the Netherlands
| | - Thomas M van Gulik
- Surgical Laboratory, Department of Surgery, Academic Medical Center, Amsterdam, the Netherlands
| | - Ronald P J Oude Elferink
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center (AMC), Amsterdam, the Netherlands
| | - Robert A F M Chamuleau
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center (AMC), Amsterdam, the Netherlands
| | - Ruurdtje Hoekstra
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center (AMC), Amsterdam, the Netherlands.,Surgical Laboratory, Department of Surgery, Academic Medical Center, Amsterdam, the Netherlands
| |
Collapse
|
25
|
Bennis A, Jacobs JG, Catsburg LAE, Ten Brink JB, Koster C, Schlingemann RO, van Meurs J, Gorgels TGMF, Moerland PD, Heine VM, Bergen AA. Stem Cell Derived Retinal Pigment Epithelium: The Role of Pigmentation as Maturation Marker and Gene Expression Profile Comparison with Human Endogenous Retinal Pigment Epithelium. Stem Cell Rev Rep 2018; 13:659-669. [PMID: 28730556 PMCID: PMC5602068 DOI: 10.1007/s12015-017-9754-0] [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] [Indexed: 11/03/2022]
Abstract
In age-related macular degeneration (AMD) the retinal pigment epithelium (RPE) deteriorates, leading to photoreceptor decay and severe vision loss. New therapeutic strategies aim at RPE replacement by transplantation of pluripotent stem cell (PSC)-derived RPE. Several protocols to generate RPE have been developed where appearance of pigmentation is commonly used as indicator of RPE differentiation and maturation. It is, however, unclear how different pigmentation stages reflect developmental stages and functionality of PSC-derived RPE cells. We generated human embryonic stem cell-derived RPE (hESC-RPE) cells and investigated their gene expression profiles at early pigmentation (EP) and late pigmentation (LP) stages. In addition, we compared the hESC-RPE samples with human endogenous RPE. We used a common reference design microarray (44 K). Our analysis showed that maturing hESC-RPE, upon acquiring pigmentation, expresses markers specific for human RPE. Interestingly, our analysis revealed that EP and LP hESC-RPE do not differ much in gene expression. Our data further showed that pigmented hESC-RPE has a significant lower expression than human endogenous RPE in the visual cycle and oxidative stress pathways. In contrast, we observed a significantly higher expression of pathways related to the process adhesion-to-polarity model that is typical of developing epithelial cells. We conclude that, in vitro, the first appearance of pigmentation hallmarks differentiated RPE. However, further increase in pigmentation does not result in much significant gene expression changes and does not add important RPE functionalities. Consequently, our results suggest that the time span for obtaining differentiated hESC-RPE cells, that are suitable for transplantation, may be greatly reduced.
Collapse
Affiliation(s)
- A Bennis
- Department of Clinical Genetics, AMC, Amsterdam, The Netherlands.,The Netherlands Institute for Neuroscience (NIN-KNAW), Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - J G Jacobs
- Department of Pediatrics/Child Neurology, VU University Medical Center, Amsterdam, The Netherlands
| | - L A E Catsburg
- Department of Clinical Genetics, AMC, Amsterdam, The Netherlands
| | - J B Ten Brink
- Department of Clinical Genetics, AMC, Amsterdam, The Netherlands.,The Netherlands Institute for Neuroscience (NIN-KNAW), Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - C Koster
- Department of Clinical Genetics, AMC, Amsterdam, The Netherlands
| | - R O Schlingemann
- Ocular Angiogenesis Group, AMC, Amsterdam, The Netherlands.,Department of Ophthalmology, AMC, Amsterdam, The Netherlands.,Department of Cell Biology and Histology, AMC, Amsterdam, The Netherlands
| | - J van Meurs
- Rotterdam Eye Hospital, Amsterdam, The Netherlands
| | - T G M F Gorgels
- The Netherlands Institute for Neuroscience (NIN-KNAW), Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands.,University Eye Clinic Maastricht, MUMC+, Amsterdam, The Netherlands
| | - P D Moerland
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, AMC, Amsterdam, The Netherlands
| | - V M Heine
- Department of Pediatrics/Child Neurology, VU University Medical Center, Amsterdam, The Netherlands. .,Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, Amsterdam, The Netherlands.
| | - A A Bergen
- Department of Clinical Genetics, AMC, Amsterdam, The Netherlands. .,The Netherlands Institute for Neuroscience (NIN-KNAW), Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands. .,Department of Ophthalmology, AMC, Amsterdam, The Netherlands.
| |
Collapse
|
26
|
de Ronde MWJ, Ruijter JM, Moerland PD, Creemers EE, Pinto-Sietsma SJ. Study Design and qPCR Data Analysis Guidelines for Reliable Circulating miRNA Biomarker Experiments: A Review. Clin Chem 2018; 64:1308-1318. [PMID: 29903876 DOI: 10.1373/clinchem.2017.285288] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 05/08/2018] [Indexed: 01/07/2023]
Abstract
BACKGROUND In the past decade, the search for circulating microRNA (miRNA) biomarkers has yielded numerous associations between miRNAs and different types of disease. However, many of these relations could not be replicated in subsequent studies under similar experimental conditions. Although this lack of replicability may be explained by the variation in experimental design and analysis methods, guidelines on the most appropriate design and analysis methods to study circulating miRNAs are scarce. CONTENT miRNA biomarker experiments generally consist of a discovery phase and a validation phase. In the discovery phase, typically hundreds of miRNAs are measured in parallel to identify candidate biomarkers. Because of the costs of such high-throughput experiments, the number of individuals included in those studies is often too small, which can easily lead to false positives and false negatives. In the validation phase, a small number of identified biomarker candidates are measured in a large cohort of cases and controls, generally by quantitative PCR (qPCR). Although qPCR is a sensitive method to measure miRNAs in the circulation, experimental design and qPCR data analysis remain challenging. Omitting some crucial steps in the design and analysis of the qPCR experiment or performing them incorrectly can cause serious biases, ultimately leading to false conclusions. SUMMARY In this review, we aim to expose and discuss the most common sources of interstudy variation in miRNA research from a methodological point of view and to provide guidelines on how to perform these steps correctly to increase replicability of studies on circulating miRNAs.
Collapse
Affiliation(s)
- Maurice W J de Ronde
- Departments of Vascular Medicine.,Clinical Epidemiology, Biostatistics and Bioinformatics
| | | | | | - Esther E Creemers
- Experimental Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | | |
Collapse
|
27
|
Oja AE, Piet B, Helbig C, Stark R, van der Zwan D, Blaauwgeers H, Remmerswaal EBM, Amsen D, Jonkers RE, Moerland PD, Nolte MA, van Lier RAW, Hombrink P. Trigger-happy resident memory CD4 + T cells inhabit the human lungs. Mucosal Immunol 2018; 11:654-667. [PMID: 29139478 DOI: 10.1038/mi.2017.94] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/18/2017] [Indexed: 02/04/2023]
Abstract
Resident memory T cells (TRM) reside in the lung epithelium and mediate protective immunity against respiratory pathogens. Although lung CD8+ TRM have been extensively characterized, the properties of CD4+ TRM remain unclear. Here we determined the transcriptional signature of CD4+ TRM, identified by the expression of CD103, retrieved from human lung resection material. Various tissue homing molecules were specifically upregulated on CD4+ TRM, whereas expression of tissue egress and lymph node homing molecules were low. CD103+ TRM expressed low levels of T-bet, only a small portion expressed Eomesodermin (Eomes), and although the mRNA levels for Hobit were increased, protein expression was absent. On the other hand, the CD103+ TRM showed a Notch signature. CD4+CD103+ TRM constitutively expressed high transcript levels of numerous cytotoxic mediators that was functionally reflected by a fast recall response, magnitude of cytokine production, and a high degree of polyfunctionality. Interestingly, the superior cytokine production appears to be because of an accessible interferon-γ (IFNγ) locus and was partially because of rapid translation of preformed mRNA. Our studies provide a molecular understanding of the maintenance and potential function of CD4+ TRM in the human lung. Understanding the specific properties of CD4+ TRM is required to rationally improve vaccine design.
Collapse
Affiliation(s)
- A E Oja
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam, The Netherlands
| | - B Piet
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam, The Netherlands.,Department of Respiratory Medicine, OLVG, Amsterdam, The Netherlands
| | - C Helbig
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam, The Netherlands
| | - R Stark
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam, The Netherlands
| | - D van der Zwan
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam, The Netherlands
| | - H Blaauwgeers
- Department of Pathology, OLVG, Amsterdam, The Netherlands
| | - E B M Remmerswaal
- Department of Experimental Immunology, Academic Medical Center, Amsterdam, The Netherlands.,Renal Transplant Unit, Division of Internal Medicine, Academic Medical Center, Amsterdam The Netherlands
| | - D Amsen
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam, The Netherlands
| | - R E Jonkers
- Department of Respiratory Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - P D Moerland
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics and Department of Immunology, Academic Medical Center, Amsterdam, The Netherlands
| | - M A Nolte
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam, The Netherlands
| | - R A W van Lier
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam, The Netherlands
| | - P Hombrink
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam, The Netherlands
| |
Collapse
|
28
|
Kok MGM, de Ronde MWJ, Moerland PD, Ruijter JM, Creemers EE, Pinto-Sietsma SJ. Small sample sizes in high-throughput miRNA screens: A common pitfall for the identification of miRNA biomarkers. Biomol Detect Quantif 2017; 15:1-5. [PMID: 29276692 PMCID: PMC5737945 DOI: 10.1016/j.bdq.2017.11.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/02/2017] [Accepted: 11/27/2017] [Indexed: 02/08/2023]
Abstract
Since the discovery of microRNAs (miRNAs), circulating miRNAs have been proposed as biomarkers for disease. Consequently, many groups have tried to identify circulating miRNA biomarkers for various types of diseases including cardiovascular disease and cancer. However, the replicability of these experiments has been disappointingly low. In order to identify circulating miRNA candidate biomarkers, in general, first an unbiased high-throughput screen is performed in which a large number of miRNAs is detected and quantified in the circulation. Because these are costly experiments, many of such studies have been performed using a low number of study subjects (small sample size). Due to lack of power in small sample size experiments, true effects are often missed and many of the detected effects are wrong. Therefore, it is important to have a good estimate of the appropriate sample size for a miRNA high-throughput screen. In this review, we discuss the effects of small sample sizes in high-throughput screens for circulating miRNAs. Using data from a miRNA high-throughput experiment on isolated monocytes, we illustrate that the implementation of power calculations in a high-throughput miRNA discovery experiment will avoid unnecessarily large and expensive experiments, while still having enough power to be able to detect clinically important differences.
Collapse
Affiliation(s)
- M G M Kok
- Departments of Vascular Medicine, University of Amsterdam, Amsterdam, The Netherlands
| | - M W J de Ronde
- Departments of Vascular Medicine, University of Amsterdam, Amsterdam, The Netherlands.,Departments of Clinical Epidemiology, Biostatistics and Bioinformatics, University of Amsterdam, Amsterdam, The Netherlands
| | - P D Moerland
- Departments of Clinical Epidemiology, Biostatistics and Bioinformatics, University of Amsterdam, Amsterdam, The Netherlands
| | - J M Ruijter
- Departments of Anatomy, Embryology and Physiology, University of Amsterdam, Amsterdam, The Netherlands
| | - E E Creemers
- Departments of Experimental Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - S J Pinto-Sietsma
- Departments of Vascular Medicine, University of Amsterdam, Amsterdam, The Netherlands.,Departments of Clinical Epidemiology, Biostatistics and Bioinformatics, University of Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
29
|
Duijvis NW, Moerland PD, Kunne C, Slaman MMW, van Dooren FH, Vogels EW, de Jonge WJ, Meijer SL, Fluiter K, te Velde AA. Inhibition of miR-142-5P ameliorates disease in mouse models of experimental colitis. PLoS One 2017; 12:e0185097. [PMID: 29059189 PMCID: PMC5653202 DOI: 10.1371/journal.pone.0185097] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 09/06/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are epigenetically involved in regulating gene expression. They may be of importance in the pathogenesis of inflammatory bowel disease (IBD). The aim of this study was to determine the role of miRNAs by their specific blocking in the CD4+CB45RBhi T-cell transfer model of chronic experimental colitis. METHODS Colitis caused by transfer of WT CD4+CD45RBhi T cells in severe combined immunodeficiency (SCID) mice shares many features with human IBD. Colonic miRNA expression levels were measured at three time points in colitic mice, where a time-dependent upregulation of multiple miRNAs was seen. To inhibit these miRNAs, specific locked-nucleic-acid-modified (LNA) oligonucleotides were administered in further experiments at the moment the mice demonstrated the first signs of colitis. As controls, PBS and a scrambled sequence of anti-miRNA were used. Genome-wide expression analyses were also performed in order to detect candidate target genes of miR-142-5p, of which inhibition resulted in most effective amelioration of colitis. RESULTS Anti-miR-142-5p reduced colitis and related wasting disease when administered in the T-cell transfer model, reflected in reduced weight loss and a lower disease activity index (DAI). In further validation experiments we also observed a higher survival rate and less colonic histological inflammation in the antagomir-treated mice. Moreover, by genome-wide expression analyses, we found downstream activation of the anti-inflammatory IL10RA pathway, including three genes also found in the top-20 candidate target genes of miR-142-5p. CONCLUSION In conclusion, CD4+CD45RBhi-transfer colitis induces miR-142-5p. Blocking miR-142-5p reduced colitis and prevented wasting disease, possibly by activation of the IL10RA pathway.
Collapse
Affiliation(s)
- Nicolette W. Duijvis
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center (AMC), Amsterdam, the Netherlands
- * E-mail: (NWD); (AAV)
| | - Perry D. Moerland
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, Amsterdam, the Netherlands
| | - Cindy Kunne
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center (AMC), Amsterdam, the Netherlands
| | - Monique M. W. Slaman
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center (AMC), Amsterdam, the Netherlands
| | - Faas H. van Dooren
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center (AMC), Amsterdam, the Netherlands
| | - Esther W. Vogels
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center (AMC), Amsterdam, the Netherlands
| | - Wouter J. de Jonge
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center (AMC), Amsterdam, the Netherlands
| | - Sybren L. Meijer
- Department of Pathology, Academic Medical Center (AMC), Amsterdam, the Netherlands
| | - Kees Fluiter
- Department of Clinical Genetics, Academic Medical Center (AMC), Amsterdam, the Netherlands
| | - Anje A. te Velde
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center (AMC), Amsterdam, the Netherlands
- * E-mail: (NWD); (AAV)
| |
Collapse
|
30
|
Adam AAA, van Wenum M, van der Mark VA, Jongejan A, Moerland PD, Houtkooper RH, Wanders RJA, Oude Elferink RP, Chamuleau RAFM, Hoekstra R. AMC-Bio-Artificial Liver culturing enhances mitochondrial biogenesis in human liver cell lines: The role of oxygen, medium perfusion and 3D configuration. Mitochondrion 2017; 39:30-42. [PMID: 28844938 DOI: 10.1016/j.mito.2017.08.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/15/2017] [Accepted: 08/23/2017] [Indexed: 12/18/2022]
Abstract
BACKGROUND Human liver cell lines, like HepaRG and C3A, acquire higher functionality when cultured in the AMC-Bio-Artificial Liver (AMC-BAL). The three main differences between BAL and monolayer culture are the oxygenation (40% vs 20%O2), dynamic vs absent medium perfusion and 3D vs 2D configuration. Here, we investigated the background of the differences between BAL-cultures and monolayers. METHODS We performed whole-genome microarray analysis on HepaRG monolayer and BAL-cultures. Next, mitochondrial biogenesis was studied in monolayer and BAL-cultures of HepaRG and C3A. The driving forces for mitochondrial biogenesis by BAL-culturing were investigated in representative culture models differing in oxygenation level, medium flow or 2D vs 3D configuration. RESULTS Gene-sets related to mitochondrial energy metabolism were most prominently up-regulated in HepaRG-BAL vs monolayer cultures. This was confirmed by a 2.4-fold higher mitochondrial abundance with increased expression of mitochondrial OxPhos complexes. Moreover, the transcript levels of mitochondria-encoded genes were up to 3.6-fold induced and mitochondrial membrane potential activity was 8.3-fold increased in BAL vs monolayers. Culturing with 40% O2, dynamic medium flow and/or in 3D increased the mitochondrial abundance and expression of mitochondrial complexes vs standard monolayer culturing. The stimulatory effect of the BAL culture on mitochondrial biogenesis was confirmed in C3A cells in which mitochondrial abundance increased 2.2-fold with induction of mitochondria-encoded genes. CONCLUSIONS AND GENERAL SIGNIFICANCE The increased functionality of liver cell lines upon AMC-BAL culturing is associated with increased mitochondrial biogenesis. High oxygenation, medium perfusion and 3D configuration contribute to the up-regulation of the mitochondrial biogenesis.
Collapse
Affiliation(s)
- Aziza A A Adam
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center (AMC), University of Amsterdam, Postbus 22660, 1100 DD Amsterdam, The Netherlands
| | - Martien van Wenum
- Surgical Laboratory, Academic Medical Center (AMC), University of Amsterdam, Postbus 22660, 1100 DD Amsterdam, The Netherlands
| | - Vincent A van der Mark
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center (AMC), University of Amsterdam, Postbus 22660, 1100 DD Amsterdam, The Netherlands; Surgical Laboratory, Academic Medical Center (AMC), University of Amsterdam, Postbus 22660, 1100 DD Amsterdam, The Netherlands
| | - Aldo Jongejan
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health Research Institute, Academic Medical Center (AMC), University of Amsterdam, Postbus 22660, 1100 DD Amsterdam, The Netherlands
| | - Perry D Moerland
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health Research Institute, Academic Medical Center (AMC), University of Amsterdam, Postbus 22660, 1100 DD Amsterdam, The Netherlands
| | - Riekelt H Houtkooper
- Laboratory Genetic and Metabolic Diseases, Academic Medical Center (AMC), University of Amsterdam, Postbus 22660, 1100 DD Amsterdam, The Netherlands
| | - Ronald J A Wanders
- Laboratory Genetic and Metabolic Diseases, Academic Medical Center (AMC), University of Amsterdam, Postbus 22660, 1100 DD Amsterdam, The Netherlands
| | - Ronald P Oude Elferink
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center (AMC), University of Amsterdam, Postbus 22660, 1100 DD Amsterdam, The Netherlands
| | - Robert A F M Chamuleau
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center (AMC), University of Amsterdam, Postbus 22660, 1100 DD Amsterdam, The Netherlands
| | - Ruurdtje Hoekstra
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center (AMC), University of Amsterdam, Postbus 22660, 1100 DD Amsterdam, The Netherlands; Surgical Laboratory, Academic Medical Center (AMC), University of Amsterdam, Postbus 22660, 1100 DD Amsterdam, The Netherlands.
| |
Collapse
|
31
|
Bennis A, ten Brink JB, Moerland PD, Heine VM, Bergen AA. Comparative gene expression study and pathway analysis of the human iris- and the retinal pigment epithelium. PLoS One 2017; 12:e0182983. [PMID: 28827822 PMCID: PMC5565104 DOI: 10.1371/journal.pone.0182983] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 07/27/2017] [Indexed: 11/25/2022] Open
Abstract
Background The retinal pigment epithelium (RPE) is a neural monolayer lining the back of the eye. Degeneration of the RPE leads to severe vision loss in, so far incurable, diseases such as age-related macular degeneration and some forms of retinitis pigmentosa. A promising future replacement therapy may be autologous iris epithelial cell transdifferentiation into RPE in vitro and, subsequently, transplantation. In this study we compared the gene expression profiles of the iris epithelium (IE) and the RPE. Methods We collected both primary RPE- and IE cells from 5 freshly frozen human donor eyes, using respectively laser dissection microscopy and excision. We performed whole-genome expression profiling using 44k Agilent human microarrays. We investigated the gene expression profiles on both gene and functional network level, using R and the knowledge database Ingenuity. Results The major molecular pathways related to the RPE and IE were quite similar and yielded basic neuro-epithelial cell functions. Nonetheless, we also found major specific differences: For example, genes and molecular pathways, related to the visual cycle and retinol biosynthesis are significantly higher expressed in the RPE than in the IE. Interestingly, Wnt and aryl hydrocarbon receptor (AhR-) signaling pathways are much higher expressed in the IE than in the RPE, suggesting, respectively, a possible pluripotent and high detoxification state of the IE. Conclusions This study provides a valuation of the similarities and differences between the expression profiles of the RPE and IE. Our data combined with that of the literature, represent a most comprehensive perspective on transcriptional variation, which may support future research in the development of therapeutic transplantation of IE.
Collapse
Affiliation(s)
- Anna Bennis
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
- The Netherlands Institute for Neuroscience (NIN-KNAW), Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - Jacoline B. ten Brink
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
| | - Perry D. Moerland
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, Amsterdam, The Netherlands
| | - Vivi M. Heine
- Department of Pediatrics / Child Neurology, Neuroscience Campus Amsterdam, VU University Medical Centre, Amsterdam, The Netherlands
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, Vrije Universiteit, Amsterdam, The Netherlands
| | - Arthur A. Bergen
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
- The Netherlands Institute for Neuroscience (NIN-KNAW), Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
- Department of Ophthalmology, Academic Medical Centre, Amsterdam, The Netherlands
- * E-mail:
| |
Collapse
|
32
|
van Hagen M, Piebes DGE, de Leeuw WC, Vuist IM, van Roon-Mom WMC, Moerland PD, Verschure PJ. The dynamics of early-state transcriptional changes and aggregate formation in a Huntington's disease cell model. BMC Genomics 2017; 18:373. [PMID: 28499347 PMCID: PMC5429582 DOI: 10.1186/s12864-017-3745-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [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: 07/15/2016] [Accepted: 05/01/2017] [Indexed: 11/17/2022] Open
Abstract
Background Huntington’s disease (HD) is a fatal neurodegenerative disorder caused by a CAG expansion in the Huntingtin (HTT) gene. Proteolytic cleavage of mutant huntingtin (Htt) protein with an expanded polyglutamine (polyQ) stretch results in production of Htt fragments that aggregate and induce impaired ubiquitin proteasome, mitochondrial functioning and transcriptional dysregulation. To understand the time-resolved relationship between aggregate formation and transcriptional changes at early disease stages, we performed temporal transcriptome profiling and quantification of aggregate formation in living cells in an inducible HD cell model. Results Rat pheochromocytoma (PC12) cells containing a stably integrated, doxycycline-inducible, eGFP-tagged N-terminal human Htt fragment with an expanded polyQ domain were used to analyse gene expression changes at different stages of mutant Htt aggregation. At earliest time points after doxycycline induction no detectable aggregates and few changes in gene expression were observed. Aggregates started to appear at intermediate time points. Aggregate formation and subsequent enlargement of aggregates coincided with a rapid increase in the number of differentially expressed (DE) genes. The increase in number of large aggregates coincided with a decrease in the number of smaller aggregates whereas the transcription profile reverted towards the profile observed before mutant Htt induction. Cluster-based analysis of the 2,176 differentially expressed genes revealed fourteen distinct clusters responding differently over time. Functional enrichment analysis of the two major gene clusters revealed that genes in the up-regulated cluster were mainly involved in metabolic (antioxidant activity and cellular ketone metabolic processes) and genes in the down-regulated cluster in developmental processes, respectively. Promoter-based analysis of the identified gene clusters resulted in identification of a transcription factor network of which several previously have been linked to HD. Conclusions We demonstrate a time-resolved relationship between Htt aggregation and changes in the transcriptional profile. We identified two major gene clusters showing involvement of (i) mitochondrial dysfunction and (ii) developmental processes implying cellular homeostasis defects. We identified novel and known HD-linked transcription factors and show their interaction with known and predicted regulatory proteins. Our data provide a novel resource for hypothesis building on the role of transcriptional key regulators in early stages of HD and possibly other polyQ-dependent diseases. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3745-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Martijn van Hagen
- Synthetic, Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.,Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Diewertje G E Piebes
- Synthetic, Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Wim C de Leeuw
- MicroArray Department, University of Amsterdam, Amsterdam, The Netherlands
| | - Ilona M Vuist
- Synthetic, Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Perry D Moerland
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Pernette J Verschure
- Synthetic, Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
33
|
Hakimzadeh N, Elias J, Wijntjens GWM, Theunissen R, van Weert A, Smulders MW, van den Akker N, Moerland PD, Verberne HJ, Hoebers LP, Henriques JPS, van der Laan AM, Ilhan M, Post M, Bekkers SCAM, Piek JJ. Monocytic microRNA profile associated with coronary collateral artery function in chronic total occlusion patients. Sci Rep 2017; 7:1532. [PMID: 28484274 PMCID: PMC5431477 DOI: 10.1038/s41598-017-01695-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 12/12/2016] [Accepted: 03/31/2017] [Indexed: 11/09/2022] Open
Abstract
An expansive collateral artery network is correlated with improved survival in case of adverse cardiac episodes. We aimed to identify cellular microRNAs (miRNA; miR) important for collateral artery growth. Chronic total occlusion (CTO) patients (n = 26) were dichotomized using pressure-derived collateral flow index (CFIp) measurements; high collateral capacity (CFIp > 0.39; n = 14) and low collateral (CFIp < 0.39; n = 12) capacity. MiRNA profiling via next generation sequencing from various monocyte phenotypes (freshly isolated monocytes, monocytes cultured without stimulant, or stimulation with lipopolysaccharide, interleukin 4, transforming growth factor beta-1, or interferon gamma) revealed significantly different miRNA expression patterns between high versus low collateral capacity patients. Validation by real-time polymerase chain reaction demonstrated significantly decreased expression of miR339-5p in all stimulated monocyte phenotypes of low collateral capacity patients. MiR339-5p showed significant correlation with CFIp values in stimulated monocytes. Ingenuity pathway analysis of predicted gene targets of miR339-5p and differential gene expression data from high versus low CFIp patients (n = 20), revealed significant association with STAT3 pathway, and also suggested a possible regulatory role for this signaling pathway. These results identify a novel association between miR339-5p and coronary collateral function. Future work examining modulation of miR339-5p and downstream effects on the STAT3 pathway and subsequent collateral vessel growth are warranted.
Collapse
Affiliation(s)
- Nazanin Hakimzadeh
- Department of Biomedical Engineering & Physics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Department of Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Joëlle Elias
- Department of Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Gilbert W M Wijntjens
- Department of Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Ruud Theunissen
- Department of Physiology, Maastricht University Medical Center, University of Maastricht, Maastricht, The Netherlands.,Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - Angela van Weert
- Department of Biomedical Engineering & Physics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Martijn W Smulders
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands.,Department of Cardiology, Maastricht University Medical Center, University of Maastricht, Maastricht, The Netherlands
| | - Nynke van den Akker
- Department of Physiology, Maastricht University Medical Center, University of Maastricht, Maastricht, The Netherlands.,Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - Perry D Moerland
- Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Hein J Verberne
- Department of Nuclear Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Loes P Hoebers
- Department of Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Jose P S Henriques
- Department of Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Anja M van der Laan
- Department of Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Mustafa Ilhan
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - Mark Post
- Department of Physiology, Maastricht University Medical Center, University of Maastricht, Maastricht, The Netherlands.,Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - Sebastiaan C A M Bekkers
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands.,Department of Cardiology, Maastricht University Medical Center, University of Maastricht, Maastricht, The Netherlands
| | - Jan J Piek
- Department of Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
34
|
van Attekum MHA, Terpstra S, Slinger E, von Lindern M, Moerland PD, Jongejan A, Kater AP, Eldering E. Macrophages confer survival signals via CCR1-dependent translational MCL-1 induction in chronic lymphocytic leukemia. Oncogene 2017; 36:3651-3660. [PMID: 28192408 PMCID: PMC5584520 DOI: 10.1038/onc.2016.515] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [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: 10/19/2015] [Revised: 12/05/2016] [Accepted: 12/12/2016] [Indexed: 12/22/2022]
Abstract
Protective interactions with bystander cells in micro-environmental niches, such as lymph nodes (LNs), contribute to survival and therapy resistance of chronic lymphocytic leukemia (CLL) cells. This is caused by a shift in expression of B-cell lymphoma 2 (BCL-2) family members. Pro-survival proteins B-cell lymphoma-extra large (BCL-XL), BCL-2-related protein A1 (BFL-1) and myeloid leukemia cell differentiation protein 1 (MCL-1) are upregulated by LN-residing T cells through CD40L interaction, presumably via nuclear factor (NF)-κB signaling. Macrophages (Mφs) also reside in the LN, and are assumed to provide important supportive functions for CLL cells. However, if and how Mφs are able to induce survival is incompletely known. We first established that Mφs induced survival because of an exclusive upregulation of MCL-1. Next, we investigated the mechanism underlying MCL-1 induction by Mφs in comparison with CD40L. Genome-wide expression profiling of in vitro Mφ- and CD40L-stimulated CLL cells indicated activation of the phosphoinositide 3-kinase (PI3K)-V-Akt murine thymoma viral oncogene homolog (AKT)-mammalian target of rapamycin (mTOR) pathway, which was confirmed in ex vivo CLL LN material. Inhibition of PI3K-AKT-mTOR signaling abrogated MCL-1 upregulation and survival by Mφs, as well as CD40 stimulation. MCL-1 can be regulated at multiple levels, and we established that AKT leads to increased MCL-1 translation, but does not affect MCL-1 transcription or protein stabilization. Furthermore, among Mφ-secreted factors that could activate AKT, we found that induction of MCL-1 and survival critically depended on C-C motif chemokine receptor-1 (CCR1). In conclusion, this study indicates that two distinct micro-environmental factors, CD40L and Mφs, signal via CCR1 to induce AKT activation resulting in translational stabilization of MCL-1, and hence can contribute to CLL cell survival.
Collapse
Affiliation(s)
- M H A van Attekum
- Department of Hematology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Department of Experimental Immunology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - S Terpstra
- Department of Hematology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Department of Experimental Immunology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - E Slinger
- Department of Hematology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Department of Experimental Immunology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - M von Lindern
- Department of Hematopoiesis, Sanquin Research, Amsterdam, The Netherlands
| | - P D Moerland
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - A Jongejan
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - A P Kater
- Department of Hematology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, The Netherlands
| | - E Eldering
- Department of Experimental Immunology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, The Netherlands
| |
Collapse
|
35
|
van Oorschot B, Uitterhoeve L, Oomen I, Ten Cate R, Medema JP, Vrieling H, Stalpers LJA, Moerland PD, Franken NAP. Prostate Cancer Patients with Late Radiation Toxicity Exhibit Reduced Expression of Genes Involved in DNA Double-Strand Break Repair and Homologous Recombination. Cancer Res 2017; 77:1485-1491. [PMID: 28108515 DOI: 10.1158/0008-5472.can-16-1966] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 11/17/2016] [Accepted: 11/18/2016] [Indexed: 11/16/2022]
Abstract
Severe late damage to normal tissue is a major limitation of cancer radiotherapy in prostate cancer patients. In a recent retrospective study, late radiation toxicity was found to relate to a decreased decay of γ-H2AX foci and reduced induction of DNA double-strand break repair genes. Here, we report evidence of prognostic utility in prostate cancer for γ-H2AX foci decay ratios and gene expression profiles derived from ex vivo-irradiated patient lymphocytes. Patients were followed ≥2 years after radiotherapy. Clinical characteristics were assembled, and toxicity was recorded using the Common Terminology Criteria (CTCAE) v4.0. No clinical factor was correlated with late radiation toxicity. The γ-H2AX foci decay ratio correlated negatively with toxicity grade, with a significant difference between grade ≥3 and grade 0 patients (P = 0.02). A threshold foci decay ratio, determined in our retrospective study, correctly classified 23 of 28 patients with grade ≥3 toxicity (sensitivity 82%) and 9 of 14 patients with grade 0 toxicity (specificity 64%). Induction of homologous recombination (HR) repair genes was reduced with increasing toxicity grade. The difference in fold induction of the HR gene set was most pronounced between grade 0 and grade ≥3 toxicity (P = 0.008). Notably, reduced responsiveness of HR repair genes to irradiation and inefficient double-strand break repair correlated with severe late radiation toxicity. Using a decay ratio classifier, we correctly classified 82% of patients with grade ≥3 toxicity, suggesting a prognostic biomarker for cancer patients with a genetically enhanced risk for late radiation toxicity to normal tissues after radiotherapy. Cancer Res; 77(6); 1485-91. ©2017 AACR.
Collapse
Affiliation(s)
- Bregje van Oorschot
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Molecular Medicine (CEMM), Department of Radiation Oncology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
| | - Lon Uitterhoeve
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Molecular Medicine (CEMM), Department of Radiation Oncology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Ilja Oomen
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Molecular Medicine (CEMM), Department of Radiation Oncology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Rosemarie Ten Cate
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Molecular Medicine (CEMM), Department of Radiation Oncology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Jan Paul Medema
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Molecular Medicine (CEMM), Department of Radiation Oncology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Harry Vrieling
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Lukas J A Stalpers
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Molecular Medicine (CEMM), Department of Radiation Oncology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Perry D Moerland
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Nicolaas A P Franken
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Molecular Medicine (CEMM), Department of Radiation Oncology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| |
Collapse
|
36
|
Hombrink P, Helbig C, Backer RA, Piet B, Oja AE, Stark R, Brasser G, Jongejan A, Jonkers RE, Nota B, Basak O, Clevers HC, Moerland PD, Amsen D, van Lier RAW. Programs for the persistence, vigilance and control of human CD8+ lung-resident memory T cells. Nat Immunol 2016; 17:1467-1478. [DOI: 10.1038/ni.3589] [Citation(s) in RCA: 287] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 09/21/2016] [Indexed: 12/13/2022]
|
37
|
Sontrop HMJ, Reinders MJT, Moerland PD. Erratum to: Breast cancer subtype predictors revisited: from consensus to concordance? BMC Med Genomics 2016; 9:39. [PMID: 27417682 PMCID: PMC4944428 DOI: 10.1186/s12920-016-0209-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 07/05/2016] [Indexed: 12/02/2022] Open
Affiliation(s)
- Herman M J Sontrop
- Molecular Diagnostics Department, Philips Research, High Tech Campus 11, Eindhoven, 5656 AE, The Netherlands.,Friss Fraud and Risk Solutions, Orteliuslaan 15, Utrecht, 3528 BA, The Netherlands
| | - Marcel J T Reinders
- Delft Bioinformatics Lab, Delft University of Technology, Mekelweg 4, Delft, 2628 CD, The Netherlands
| | - Perry D Moerland
- Bioinformatics Laboratory, Academic Medical Center, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands.
| |
Collapse
|
38
|
Nandal UK, van Kampen AHC, Moerland PD. compendiumdb: an R package for retrieval and storage of functional genomics data. Bioinformatics 2016; 32:2856-7. [DOI: 10.1093/bioinformatics/btw335] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 05/23/2016] [Indexed: 01/28/2023] Open
|
39
|
Sontrop HMJ, Reinders MJT, Moerland PD. Breast cancer subtype predictors revisited: from consensus to concordance? BMC Med Genomics 2016; 9:26. [PMID: 27259591 PMCID: PMC4893290 DOI: 10.1186/s12920-016-0185-6] [Citation(s) in RCA: 6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 05/09/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND At the molecular level breast cancer comprises a heterogeneous set of subtypes associated with clear differences in gene expression and clinical outcomes. Single sample predictors (SSPs) are built via a two-stage approach consisting of clustering and subtype predictor construction based on the cluster labels of individual cases. SSPs have been criticized because their subtype assignments for the same samples were only moderately concordant (Cohen's κ<0.6). METHODS We propose a semi-supervised approach where for five datasets, consensus sets were constructed consisting of those samples that were concordantly subtyped by a number of different predictors. Next, nine subtype predictors - three SSPs, three subtype classification models (SCMs) and three novel rule-based predictors based on the St. Gallen surrogate intrinsic subtype definitions (STGs) - were constructed on the five consensus sets and their associated consensus subtype labels. The predictors were validated on a compendium of over 4,000 uniformly preprocessed Affymetrix microarrays. Concordance between subtype predictors was assessed using Cohen's kappa statistic. RESULTS In this standardized setup, subtype predictors of the same type (either SCM, SSP, or STG) but with a different gene list and/or consensus training set were associated with almost perfect levels of agreement (median κ>0.8). Interestingly, for a given predictor type a change in consensus set led to higher concordance than a change to another gene list. The more challenging scenario where the predictor type, gene list and training set were all different resulted in predictors with only substantial levels of concordance (median κ=0.74) on independent validation data. CONCLUSIONS Our results demonstrate that for a given subtype predictor type stringent standardization of the preprocessing stage, combined with carefully devised consensus training sets, leads to predictors that show almost perfect levels of concordance. However, predictors of a different type are only substantially concordant, despite reaching almost perfect levels of concordance on training data.
Collapse
Affiliation(s)
- Herman M J Sontrop
- Molecular Diagnostics Department, Philips Research, High Tech Campus 11, Eindhoven, 5656 AE, The Netherlands.,Friss Fraud and Risk Solutions, Orteliuslaan 15, Utrecht, 3528 BA, The Netherlands
| | - Marcel J T Reinders
- Delft Bioinformatics Lab, Delft University of Technology, Mekelweg 4, Delft, 2628 CD, The Netherlands
| | - Perry D Moerland
- Bioinformatics Laboratory, Academic Medical Center, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands.
| |
Collapse
|
40
|
Hamers AAJ, Argmann C, Moerland PD, Koenis DS, Marinković G, Sokolović M, de Vos AF, de Vries CJM, van Tiel CM. Nur77-deficiency in bone marrow-derived macrophages modulates inflammatory responses, extracellular matrix homeostasis, phagocytosis and tolerance. BMC Genomics 2016; 17:162. [PMID: 26932821 PMCID: PMC4774191 DOI: 10.1186/s12864-016-2469-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [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: 04/24/2015] [Accepted: 02/12/2016] [Indexed: 02/08/2023] Open
Abstract
Background The nuclear orphan receptor Nur77 (NR4A1, TR3, or NGFI-B) has been shown to modulate the inflammatory response of macrophages. To further elucidate the role of Nur77 in macrophage physiology, we compared the transcriptome of bone marrow-derived macrophages (BMM) from wild-type (WT) and Nur77-knockout (KO) mice. Results In line with previous observations, SDF-1α (CXCL12) was among the most upregulated genes in Nur77-deficient BMM and we demonstrated that Nur77 binds directly to the SDF-1α promoter, resulting in inhibition of SDF-1α expression. The cytokine receptor CX3CR1 was strongly downregulated in Nur77-KO BMM, implying involvement of Nur77 in macrophage tolerance. Ingenuity pathway analyses (IPA) to identify canonical pathways regulation and gene set enrichment analyses (GSEA) revealed a potential role for Nur77 in extracellular matrix homeostasis. Nur77-deficiency increased the collagen content of macrophage extracellular matrix through enhanced expression of several collagen subtypes and diminished matrix metalloproteinase (MMP)-9 activity. IPA upstream regulator analyses discerned the small GTPase Rac1 as a novel regulator of Nur77-mediated gene expression. We identified an inhibitory feedback loop with increased Rac1 activity in Nur77-KO BMM, which may explain the augmented phagocytic activity of these cells. Finally, we predict multiple chronic inflammatory diseases to be influenced by macrophage Nur77 expression. GSEA and IPA associated Nur77 to osteoarthritis, chronic obstructive pulmonary disease, rheumatoid arthritis, psoriasis, and allergic airway inflammatory diseases. Conclusions Altogether these data identify Nur77 as a modulator of macrophage function and an interesting target to treat chronic inflammatory disease. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2469-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Anouk A J Hamers
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands. .,Present address: Department of Inflammation Biology, La Jolla Institute for Allergy and Immunology, San Diego, USA.
| | - Carmen Argmann
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands. .,Present address: Institute for Genomics and Multiscale Biology Mount Sinai Hospital, New York, USA.
| | - Perry D Moerland
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
| | - Duco S Koenis
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
| | - Goran Marinković
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
| | - Milka Sokolović
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands. .,Present address: European Food Information Council, Brussels, Belgium.
| | - Alex F de Vos
- Center for Experimental and Molecular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
| | - Carlie J M de Vries
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
| | - Claudia M van Tiel
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
41
|
Weijer R, Broekgaarden M, van Golen RF, Bulle E, Nieuwenhuis E, Jongejan A, Moerland PD, van Kampen AHC, van Gulik TM, Heger M. Low-power photodynamic therapy induces survival signaling in perihilar cholangiocarcinoma cells. BMC Cancer 2015; 15:1014. [PMID: 26705830 PMCID: PMC4691291 DOI: 10.1186/s12885-015-1994-2] [Citation(s) in RCA: 24] [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: 07/28/2015] [Accepted: 12/11/2015] [Indexed: 12/21/2022] Open
Abstract
Background Photodynamic therapy (PDT) of solid cancers comprises the administration of a photosensitizer followed by illumination of the photosensitizer-replete tumor with laser light. This induces a state of local oxidative stress, culminating in the destruction of tumor tissue and microvasculature and induction of an anti-tumor immune response. However, some tumor types, including perihilar cholangiocarcinoma, are relatively refractory to PDT, which may be attributable to the activation of survival pathways in tumor cells following PDT (i.e., activator protein 1 (AP-1)-, nuclear factor of kappa light polypeptide gene enhancer in B-cells (NF-κB)-, hypoxia-inducible factor 1-alpha (HIF-1α)-, nuclear factor (erythroid-derived 2)-like 2 (NFE2L2)-, and unfolded protein response-mediated pathways). Methods To assess the activation of survival pathways after PDT, human perihilar cholangiocarcinoma (SK-ChA-1) cells were subjected to PDT with zinc phthalocyanine (ZnPC)-encapsulating liposomes. Following 30-minute incubation with liposomes, the cells were either left untreated or treated at low (50 mW) or high (500 mW) laser power (cumulative light dose of 15 J/cm2). Cells were harvested 90 min post-PDT and whole genome expression analysis was performed using Illumina HumanHT-12 v4 expression beadchips. The data were interpreted in the context of the survival pathways. In addition, the safety of ZnPC-encapsulating liposomes was tested both in vitro and in vivo. Results PDT-treated SK-ChA-1 cells exhibited activation of the hypoxia-induced stress response via HIF-1α and initiation of the pro-inflammatory response via NF-кB. PDT at low laser power in particular caused extensive survival signaling, as evidenced by the significant upregulation of HIF-1- (P < 0.001) and NF-кB-related (P < 0.001) genes. Low-power PDT was less lethal to SK-ChA-1 cells 90 min post-PDT, confirmed by annexin V/propidium iodide staining. In vitro toxicogenomics and toxicological testing in chicken embryos and mice revealed that the ZnPC-encapsulating liposomes are non-toxic. Conclusions PDT-treated perihilar cholangiocarcinoma cells exhibit extensive survival signaling that may translate to a suboptimal therapeutic response and possibly tumor recurrence. These findings encourage the development of photosensitizer delivery systems with co-encapsulated inhibitors of survival pathways. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1994-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ruud Weijer
- Department of Experimental Surgery, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105, AZ, Amsterdam, The Netherlands.
| | - Mans Broekgaarden
- Department of Experimental Surgery, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105, AZ, Amsterdam, The Netherlands.
| | - Rowan F van Golen
- Department of Experimental Surgery, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105, AZ, Amsterdam, The Netherlands.
| | - Esther Bulle
- Department of Experimental Surgery, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105, AZ, Amsterdam, The Netherlands.
| | - Esther Nieuwenhuis
- Department of Experimental Surgery, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105, AZ, Amsterdam, The Netherlands.
| | - Aldo Jongejan
- Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105, AZ, Amsterdam, The Netherlands.
| | - Perry D Moerland
- Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105, AZ, Amsterdam, The Netherlands.
| | - Antoine H C van Kampen
- Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105, AZ, Amsterdam, The Netherlands.
| | - Thomas M van Gulik
- Department of Experimental Surgery, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105, AZ, Amsterdam, The Netherlands.
| | - Michal Heger
- Department of Experimental Surgery, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105, AZ, Amsterdam, The Netherlands.
| |
Collapse
|
42
|
Kok MGM, Mandolini C, Moerland PD, de Ronde MWJ, Sondermeijer BM, Halliani A, Nieuwland R, Cipollone F, Creemers EE, Meijers JCM, Pinto-Sietsma SJ. Low miR-19b-1-5p expression in isolated platelets after aspirin use is related to aspirin insensitivity. Int J Cardiol 2015; 203:262-3. [PMID: 26519680 DOI: 10.1016/j.ijcard.2015.10.098] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 10/13/2015] [Indexed: 12/01/2022]
Affiliation(s)
- M G M Kok
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; Department of Experimental Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - C Mandolini
- Department of Experimental Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; Department of Hypertension and Dyslipidemia, Geriatric Clinic and European Center on Atherosclerosis, G. D'Annunzio University, Chieti, Italy
| | - P D Moerland
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - M W J de Ronde
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; Department of Experimental Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - B M Sondermeijer
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - A Halliani
- Department of Experimental Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - R Nieuwland
- Department of Clinical Chemistry, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - F Cipollone
- Department of Hypertension and Dyslipidemia, Geriatric Clinic and European Center on Atherosclerosis, G. D'Annunzio University, Chieti, Italy
| | - E E Creemers
- Department of Experimental Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - J C M Meijers
- Department of Experimental Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; Department of Plasma Proteins, Sanquin, Amsterdam, The Netherlands
| | - S J Pinto-Sietsma
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; Department of Experimental Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
43
|
Palao T, Swärd K, Jongejan A, Moerland PD, de Vos J, van Weert A, Arribas SM, Groma G, vanBavel E, Bakker ENTP. Gene Expression and MicroRNA Expression Analysis in Small Arteries of Spontaneously Hypertensive Rats. Evidence for ER Stress. PLoS One 2015; 10:e0137027. [PMID: 26356734 PMCID: PMC4565692 DOI: 10.1371/journal.pone.0137027] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 08/11/2015] [Indexed: 01/24/2023] Open
Abstract
Small arteries are known to develop functional and structural alterations in hypertension. However, the mechanisms of this remodeling are not fully understood. We hypothesized that altered gene expression is associated with the development of hypertension in mesenteric arteries of spontaneously hypertensive rats (SHR). Three sublines of SHR and normotensive Wistar Kyoto rats (WKY) were studied at 6 weeks and 5 months of age. MiRNA and mRNA microarray experiments were performed and analyzed with bioinformatical tools, including Ingenuity Pathway Analysis (IPA). Principal component analysis showed a clear separation in both miRNA and mRNA expression levels between both ages studied, demonstrating strong age-related changes in expression. At the miRNA level, IPA identified differences between SHR and WKY related to metabolic diseases, cellular growth, and proliferation. The mRNAs differentially expressed between SHR and WKY were related to metabolism, cellular movement and proliferation. The most strongly upregulated gene (9.2-fold) was thrombospondin 4 (Thbs4), a protein involved in the endoplasmic reticulum (ER) stress response that activates transcription factor 6α (ATF6α). ATF6α downstream targets were also differentially expressed in SHR vs. WKY. Differential expression of THBS4, the cleaved form of ATF6α, and two of its targets were further confirmed at the protein level by western blot. In summary, these data revealed a number of genes (n = 202) and miRNAs (n = 3) in mesenteric arteries of SHR that had not been related to hypertension previously. The most prominent of these, Thbs4, is related to vascular ER stress that is associated with hypertension.
Collapse
Affiliation(s)
- Teresa Palao
- Department of Biomedical Engineering and Physics, Academic Medical Center, Amsterdam, The Netherlands
| | - Karl Swärd
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Aldo Jongejan
- Bioinformatics Laboratory, Academic Medical Center, Amsterdam, The Netherlands
| | - Perry D. Moerland
- Bioinformatics Laboratory, Academic Medical Center, Amsterdam, The Netherlands
| | - Judith de Vos
- Department of Biomedical Engineering and Physics, Academic Medical Center, Amsterdam, The Netherlands
| | - Angela van Weert
- Department of Biomedical Engineering and Physics, Academic Medical Center, Amsterdam, The Netherlands
| | - Silvia M. Arribas
- Departamento de Fisiología, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| | - Gergely Groma
- Department of Biomedical Engineering and Physics, Academic Medical Center, Amsterdam, The Netherlands
| | - Ed vanBavel
- Department of Biomedical Engineering and Physics, Academic Medical Center, Amsterdam, The Netherlands
| | - Erik N. T. P. Bakker
- Department of Biomedical Engineering and Physics, Academic Medical Center, Amsterdam, The Netherlands
- * E-mail:
| |
Collapse
|
44
|
Vieira Braga FA, Hertoghs KML, Kragten NAM, Doody GM, Barnes NA, Remmerswaal EBM, Hsiao CC, Moerland PD, Wouters D, Derks IAM, van Stijn A, Demkes M, Hamann J, Eldering E, Nolte MA, Tooze RM, ten Berge IJM, van Gisbergen KPJM, van Lier RAW. Blimp-1 homolog Hobit identifies effector-type lymphocytes in humans. Eur J Immunol 2015; 45:2945-58. [DOI: 10.1002/eji.201545650] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 06/16/2015] [Accepted: 07/13/2015] [Indexed: 01/17/2023]
Affiliation(s)
- Felipe A. Vieira Braga
- Department of Hematopoiesis; Sanquin Research and Landsteiner Laboratory AMC/UvA; Amsterdam The Netherlands
| | | | - Natasja A. M. Kragten
- Department of Hematopoiesis; Sanquin Research and Landsteiner Laboratory AMC/UvA; Amsterdam The Netherlands
- Department of Experimental Immunology; AMC; Amsterdam The Netherlands
| | - Gina M. Doody
- Section of Experimental Haematology; Leeds Institute of Cancer and Pathology; University of Leeds; Leeds UK
| | - Nicholas A. Barnes
- Section of Experimental Haematology; Leeds Institute of Cancer and Pathology; University of Leeds; Leeds UK
| | - Ester B. M. Remmerswaal
- Department of Experimental Immunology; AMC; Amsterdam The Netherlands
- Internal Medicine; Renal Transplant Unit; AMC; Amsterdam The Netherlands
| | - Cheng-Chih Hsiao
- Department of Experimental Immunology; AMC; Amsterdam The Netherlands
| | | | - Diana Wouters
- Department of Hematopoiesis; Sanquin Research and Landsteiner Laboratory AMC/UvA; Amsterdam The Netherlands
| | | | - Amber van Stijn
- Department of Experimental Immunology; AMC; Amsterdam The Netherlands
- Internal Medicine; Renal Transplant Unit; AMC; Amsterdam The Netherlands
| | - Marc Demkes
- Department of Experimental Immunology; AMC; Amsterdam The Netherlands
| | - Jörg Hamann
- Department of Experimental Immunology; AMC; Amsterdam The Netherlands
| | - Eric Eldering
- Department of Experimental Immunology; AMC; Amsterdam The Netherlands
| | - Martijn A. Nolte
- Department of Hematopoiesis; Sanquin Research and Landsteiner Laboratory AMC/UvA; Amsterdam The Netherlands
- Department of Experimental Immunology; AMC; Amsterdam The Netherlands
| | - Reuben M. Tooze
- Section of Experimental Haematology; Leeds Institute of Cancer and Pathology; University of Leeds; Leeds UK
| | | | - Klaas P. J. M. van Gisbergen
- Department of Hematopoiesis; Sanquin Research and Landsteiner Laboratory AMC/UvA; Amsterdam The Netherlands
- Department of Experimental Immunology; AMC; Amsterdam The Netherlands
| | - René A. W. van Lier
- Department of Hematopoiesis; Sanquin Research and Landsteiner Laboratory AMC/UvA; Amsterdam The Netherlands
- Department of Experimental Immunology; AMC; Amsterdam The Netherlands
| |
Collapse
|
45
|
Kok MGM, Halliani A, Moerland PD, Meijers JCM, Creemers EE, Pinto-Sietsma SJ. Normalization panels for the reliable quantification of circulating microRNAs by RT-qPCR. FASEB J 2015; 29:3853-62. [PMID: 26023181 DOI: 10.1096/fj.15-271312] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 05/18/2015] [Indexed: 12/13/2022]
Abstract
Circulating microRNAs (miRNAs) have been reported as biomarkers for disease diagnosis. RT-qPCR is most commonly used to detect miRNAs; however, no consensus on the most appropriate method for data normalization exists. Via a standardized selection method, we aimed to determine separate miRNA normalization panels for RT-qPCR measurements on whole blood, platelets, and serum. Candidate miRNAs were selected from studies describing circulating miRNA microarray data in the Gene Expression Omnibus or ArrayExpress. miRNA expression data of healthy controls were retrieved from each study. For each sample type, we selected those miRNAs that were least variable and sufficiently highly expressed in multiple microarray experiments, performed on at least 2 different platforms. Stability of the candidate miRNAs was assessed using NormFinder and geNorm algorithms in a RT-qPCR cohort of 10 patients with coronary artery disease and 10 healthy controls. We selected miRNA normalization panels for RT-qPCR measurements on whole blood, platelets, and serum. As a validation, we assessed the precision of all 3 panels in 3 independent RT-qPCR cohorts and compared this with normalization for miR-16 or RNU6B. The proposed normalization panels for whole blood, platelets, and serum show better precision than normalization for miR-16 or RNU6B.
Collapse
Affiliation(s)
- Maayke G M Kok
- *Department of Vascular Medicine, Department of Experimental Vascular Medicine, Department of Experimental Cardiology, and Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; and Department of Plasma Proteins, Sanquin, Amsterdam, The Netherlands
| | - Amalia Halliani
- *Department of Vascular Medicine, Department of Experimental Vascular Medicine, Department of Experimental Cardiology, and Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; and Department of Plasma Proteins, Sanquin, Amsterdam, The Netherlands
| | - Perry D Moerland
- *Department of Vascular Medicine, Department of Experimental Vascular Medicine, Department of Experimental Cardiology, and Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; and Department of Plasma Proteins, Sanquin, Amsterdam, The Netherlands
| | - Joost C M Meijers
- *Department of Vascular Medicine, Department of Experimental Vascular Medicine, Department of Experimental Cardiology, and Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; and Department of Plasma Proteins, Sanquin, Amsterdam, The Netherlands
| | - Esther E Creemers
- *Department of Vascular Medicine, Department of Experimental Vascular Medicine, Department of Experimental Cardiology, and Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; and Department of Plasma Proteins, Sanquin, Amsterdam, The Netherlands
| | - Sara-Joan Pinto-Sietsma
- *Department of Vascular Medicine, Department of Experimental Vascular Medicine, Department of Experimental Cardiology, and Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; and Department of Plasma Proteins, Sanquin, Amsterdam, The Netherlands
| |
Collapse
|
46
|
Nandal UK, Vlietstra WJ, Byrman C, Jeeninga RE, Ringrose JH, van Kampen AHC, Speijer D, Moerland PD. Candidate prioritization for low-abundant differentially expressed proteins in 2D-DIGE datasets. BMC Bioinformatics 2015; 16:25. [PMID: 25627479 PMCID: PMC4384356 DOI: 10.1186/s12859-015-0455-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 09/25/2014] [Accepted: 01/09/2015] [Indexed: 01/17/2023] Open
Abstract
Background Two-dimensional differential gel electrophoresis (2D-DIGE) provides a powerful technique to separate proteins on their isoelectric point and apparent molecular mass and quantify changes in protein expression. Abundantly available proteins in spots can be identified using mass spectrometry-based approaches. However, identification is often not possible for low-abundant proteins. Results We present a novel computational approach to prioritize candidate proteins for unidentified spots. Our approach exploits noisy information on the isoelectric point and apparent molecular mass of a protein spot in combination with functional similarities of candidate proteins to already identified proteins to select and rank candidates. We evaluated our method on a 2D-DIGE dataset comparing protein expression in uninfected and HIV-1 infected T-cells. Using leave-one-out cross-validation, we show that the true-positive rate for the top-5 ranked proteins is 43.8%. Conclusions Our approach shows good performance on a 2D-DIGE dataset comparing protein expression in uninfected and HIV-1 infected T-cells. We expect our method to be highly useful in (re-)mining other 2D-DIGE experiments in which especially the low-abundant protein spots remain to be identified. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0455-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Umesh K Nandal
- Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, PO Box 22700, DE Amsterdam, 1100, The Netherlands.
| | - Wytze J Vlietstra
- Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, PO Box 22700, DE Amsterdam, 1100, The Netherlands.
| | - Carsten Byrman
- Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, PO Box 22700, DE Amsterdam, 1100, The Netherlands.
| | - Rienk E Jeeninga
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, PO Box 22700, DE Amsterdam, 1100, The Netherlands.
| | - Jeffrey H Ringrose
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, PO Box 22700, DE Amsterdam, 1100, The Netherlands.
| | - Antoine H C van Kampen
- Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, PO Box 22700, DE Amsterdam, 1100, The Netherlands. .,Biosystems Data Analysis Group, University of Amsterdam, Science Park 9041098, XH Amsterdam, The Netherlands.
| | - Dave Speijer
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, PO Box 22700, DE Amsterdam, 1100, The Netherlands.
| | - Perry D Moerland
- Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, PO Box 22700, DE Amsterdam, 1100, The Netherlands.
| |
Collapse
|
47
|
Kerami Z, Duijvis NW, Vogels EW, van Dooren FH, Moerland PD, Te Velde AA. Effect of interleukin-17 on gene expression profile of fibroblasts from Crohn's disease patients. J Crohns Colitis 2014; 8:1208-16. [PMID: 24637010 DOI: 10.1016/j.crohns.2014.02.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [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: 12/05/2013] [Revised: 02/14/2014] [Accepted: 02/14/2014] [Indexed: 02/08/2023]
Abstract
BACKGROUND AND AIM The expression of interleukin (IL)-17 is upregulated in inflammatory bowel disease (IBD). Since fibroblasts are known to be responsive to IL-17, they may play a role in the modulation of inflammatory responses in IBD. Here, the effects of IL-17 on ileum and colon fibroblasts from Crohn's disease (CD) and ulcerative colitis (UC) patients are investigated, as compared to controls. METHODS Fibroblasts were isolated from surgical specimens taken from the tissue of 21 CD patients, 5 UC patients, and 14 patients undergoing surgery for colorectal carcinoma (control). The fibroblasts were cultured with and without IL-17. We performed mRNA microarray analysis on cultured fibroblasts, isolated from three CD samples and three control samples. Based on these results, the expression of IL-17 induced genes was validated in a larger selection of samples using qRT-PCR and ELISA. RESULTS The mRNA microarray showed that IL-17 induced the expression levels of various genes in fibroblasts of CD patients and controls, among which NFKBIZ, CXCL1, and CXCL6 demonstrated the most prominent response. qRT-PCR validated that IL-17 induced the expression of NFKBIZ significantly (p=0.028) in intestinal fibroblasts of CD patients. By performing an ELISA, we also discovered that, following IL-17 stimulation, CXCL1 levels were significantly increased in fibroblasts from CD patients (p=0.048). IL-17 also stimulated secretion of CXCL6 in fibroblasts from UC patients (p=0.053). CONCLUSION The enhanced expression of IL-17 that is observed in patients with Crohn's disease could act on intestinal fibroblasts to induce expression of transcription factor NFKBIZ and proinflammatory chemokine CXCL1. This can have consequences for fibroblast activity and neutrophil chemotaxis.
Collapse
Affiliation(s)
- Zohra Kerami
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center, Amsterdam, The Netherlands.
| | - Nicolette W Duijvis
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center, Amsterdam, The Netherlands.
| | - Esther W Vogels
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center, Amsterdam, The Netherlands.
| | - Faas H van Dooren
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center, Amsterdam, The Netherlands.
| | - Perry D Moerland
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, Amsterdam, The Netherlands.
| | - Anje A Te Velde
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center, Amsterdam, The Netherlands.
| |
Collapse
|
48
|
Lodder EM, Scicluna BP, Beekman L, Arends D, Moerland PD, Tanck MWT, Adriaens ME, Bezzina CR. Integrative genomic approach identifies multiple genes involved in cardiac collagen deposition. ACTA ACUST UNITED AC 2014; 7:790-8. [PMID: 25217174 DOI: 10.1161/circgenetics.114.000537] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [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: 11/16/2022]
Abstract
BACKGROUND With aging and in cardiac disease, fibrosis caused by collagen deposition is increased, impairing contractility and providing a substrate for arrhythmia. In this study, we set out to identify genetic modifiers of collagen deposition in the heart by exploiting the genetic variability among F2 progeny of 129P2 and FVBN/J mice carrying the Scn5a(tm1Care/+) mutation. METHODS AND RESULTS Relative amounts of collagen were determined in left ventricular myocardium of 65 F2-mice and combined with genome-wide genotypic and cardiac expression data to identify collagen quantitative trait loci (QTLs) and overlapping expression QTLs (eQTLs). A significant collagen QTL was identified on mouse Chr8; an additional collagen QTL was identified on mouse Chr2 after correction for a genetic covariate uncovered on Chr18 using multiple QTL mapping. Of the 24 eQTLs colocalizing with the Chr8-collagen QTL, 6 transcripts were correlated with relative collagen amount. Similarly, of the 7 eQTLs colocalizing with the Chr2-collagen QTL, 1 transcript, Gpr158, correlated with relative collagen. Of the 12 transcripts with an eQTLs in the Chr18-covariate region, only Fgf1 correlated with relative collagen amount. Furthermore, 2 of the transcripts, Pdlim3 (Chr8) and Itga6 (Chr2), with eQTLs overlapping with collagen QTLs, had a genetic covariate on Chr18 that coincided with the Chr18 collagen covariate locus. Application of recombinant human FGF1 to isolated cardiac fibroblasts in culture affected the level of expression of Pdlim3, Itga6, and Gpr158. CONCLUSIONS We here mapped a possible novel genetic network modulating collagen deposition in mouse left ventricular myocardium.
Collapse
Affiliation(s)
- Elisabeth M Lodder
- From the Department of Experimental Cardiology (E.M.L., B.P.S., L.B., M.E.A., C.R.B.), and Department of Clinical Epidemiology, Biostatistics and Bioinformatics (P.D.M., M.W.T.T.), University of Amsterdam, Academic Medical Center, Amsterdam, Netherlands; and Groningen Bioinformatics Centre, University of Groningen, Groningen, Netherlands (D.A.)
| | - Brendon P Scicluna
- From the Department of Experimental Cardiology (E.M.L., B.P.S., L.B., M.E.A., C.R.B.), and Department of Clinical Epidemiology, Biostatistics and Bioinformatics (P.D.M., M.W.T.T.), University of Amsterdam, Academic Medical Center, Amsterdam, Netherlands; and Groningen Bioinformatics Centre, University of Groningen, Groningen, Netherlands (D.A.)
| | - Leander Beekman
- From the Department of Experimental Cardiology (E.M.L., B.P.S., L.B., M.E.A., C.R.B.), and Department of Clinical Epidemiology, Biostatistics and Bioinformatics (P.D.M., M.W.T.T.), University of Amsterdam, Academic Medical Center, Amsterdam, Netherlands; and Groningen Bioinformatics Centre, University of Groningen, Groningen, Netherlands (D.A.)
| | - Danny Arends
- From the Department of Experimental Cardiology (E.M.L., B.P.S., L.B., M.E.A., C.R.B.), and Department of Clinical Epidemiology, Biostatistics and Bioinformatics (P.D.M., M.W.T.T.), University of Amsterdam, Academic Medical Center, Amsterdam, Netherlands; and Groningen Bioinformatics Centre, University of Groningen, Groningen, Netherlands (D.A.)
| | - Perry D Moerland
- From the Department of Experimental Cardiology (E.M.L., B.P.S., L.B., M.E.A., C.R.B.), and Department of Clinical Epidemiology, Biostatistics and Bioinformatics (P.D.M., M.W.T.T.), University of Amsterdam, Academic Medical Center, Amsterdam, Netherlands; and Groningen Bioinformatics Centre, University of Groningen, Groningen, Netherlands (D.A.)
| | - Michael W T Tanck
- From the Department of Experimental Cardiology (E.M.L., B.P.S., L.B., M.E.A., C.R.B.), and Department of Clinical Epidemiology, Biostatistics and Bioinformatics (P.D.M., M.W.T.T.), University of Amsterdam, Academic Medical Center, Amsterdam, Netherlands; and Groningen Bioinformatics Centre, University of Groningen, Groningen, Netherlands (D.A.)
| | - Michiel E Adriaens
- From the Department of Experimental Cardiology (E.M.L., B.P.S., L.B., M.E.A., C.R.B.), and Department of Clinical Epidemiology, Biostatistics and Bioinformatics (P.D.M., M.W.T.T.), University of Amsterdam, Academic Medical Center, Amsterdam, Netherlands; and Groningen Bioinformatics Centre, University of Groningen, Groningen, Netherlands (D.A.)
| | - Connie R Bezzina
- From the Department of Experimental Cardiology (E.M.L., B.P.S., L.B., M.E.A., C.R.B.), and Department of Clinical Epidemiology, Biostatistics and Bioinformatics (P.D.M., M.W.T.T.), University of Amsterdam, Academic Medical Center, Amsterdam, Netherlands; and Groningen Bioinformatics Centre, University of Groningen, Groningen, Netherlands (D.A.).
| |
Collapse
|
49
|
Bakker ENTP, Groma G, Spijkers LJA, Van Veen H, Everts V, Jongejan A, Moerland PD, Arribas SM, Vanbavel E. P454Vascular abnormalities in spontaneously hypertensive rats: a matter of substrains. Cardiovasc Res 2014. [DOI: 10.1093/cvr/cvu091.132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
50
|
Koopmann TT, Adriaens ME, Moerland PD, Marsman RF, Westerveld ML, Lal S, Zhang T, Simmons CQ, Baczko I, dos Remedios C, Bishopric NH, Varro A, George AL, Lodder EM, Bezzina CR. Genome-wide identification of expression quantitative trait loci (eQTLs) in human heart. PLoS One 2014; 9:e97380. [PMID: 24846176 PMCID: PMC4028258 DOI: 10.1371/journal.pone.0097380] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 04/17/2014] [Indexed: 11/23/2022] Open
Abstract
In recent years genome-wide association studies (GWAS) have uncovered numerous chromosomal loci associated with various electrocardiographic traits and cardiac arrhythmia predisposition. A considerable fraction of these loci lie within inter-genic regions. The underlying trait-associated variants likely reside in regulatory regions and exert their effect by modulating gene expression. Hence, the key to unraveling the molecular mechanisms underlying these cardiac traits is to interrogate variants for association with differential transcript abundance by expression quantitative trait locus (eQTL) analysis. In this study we conducted an eQTL analysis of human heart. For a total of 129 left ventricular samples that were collected from non-diseased human donor hearts, genome-wide transcript abundance and genotyping was determined using microarrays. Each of the 18,402 transcripts and 897,683 SNP genotypes that remained after pre-processing and stringent quality control were tested for eQTL effects. We identified 771 eQTLs, regulating 429 unique transcripts. Overlaying these eQTLs with cardiac GWAS loci identified novel candidates for studies aimed at elucidating the functional and transcriptional impact of these loci. Thus, this work provides for the first time a comprehensive eQTL map of human heart: a powerful and unique resource that enables systems genetics approaches for the study of cardiac traits.
Collapse
Affiliation(s)
- Tamara T. Koopmann
- Department of Experimental Cardiology, Heart Failure Research Centre, Academic Medical Center, Amsterdam, The Netherlands
| | - Michiel E. Adriaens
- Department of Experimental Cardiology, Heart Failure Research Centre, Academic Medical Center, Amsterdam, The Netherlands
| | - Perry D. Moerland
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, Amsterdam, The Netherlands
| | - Roos F. Marsman
- Department of Experimental Cardiology, Heart Failure Research Centre, Academic Medical Center, Amsterdam, The Netherlands
| | - Margriet L. Westerveld
- Department of Experimental Cardiology, Heart Failure Research Centre, Academic Medical Center, Amsterdam, The Netherlands
| | - Sean Lal
- Muscle Research Unit, Department of Anatomy, Bosch Institute, The University of Sydney, Sydney, Australia
| | - Taifang Zhang
- Department of Medicine, University of Miami School of Medicine, Miami, Florida, United States of America
| | - Christine Q. Simmons
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Istvan Baczko
- Department of Pharmacology and Pharmacotherapy, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Cristobal dos Remedios
- Muscle Research Unit, Department of Anatomy, Bosch Institute, The University of Sydney, Sydney, Australia
| | - Nanette H. Bishopric
- Department of Medicine, University of Miami School of Medicine, Miami, Florida, United States of America
- Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida, United States of America
| | - Andras Varro
- Department of Pharmacology and Pharmacotherapy, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Alfred L. George
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Elisabeth M. Lodder
- Department of Experimental Cardiology, Heart Failure Research Centre, Academic Medical Center, Amsterdam, The Netherlands
| | - Connie R. Bezzina
- Department of Experimental Cardiology, Heart Failure Research Centre, Academic Medical Center, Amsterdam, The Netherlands
- * E-mail:
| |
Collapse
|