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Vetrivel S, Tamburello M, Oßwald A, Zhang R, Khan A, Jung S, Baker JE, Rainey WE, Nowak E, Altieri B, Detomas M, Watts D, Williams TA, Wielockx B, Beuschlein F, Reincke M, Sbiera S, Riester A. PPARG dysregulation as a potential molecular target in adrenal Cushing's syndrome. Front Endocrinol (Lausanne) 2023; 14:1265794. [PMID: 38098864 PMCID: PMC10720662 DOI: 10.3389/fendo.2023.1265794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 11/07/2023] [Indexed: 12/17/2023] Open
Abstract
Background We performed a transcriptomic analysis of adrenal signaling pathways in various forms of endogenous Cushing's syndrome (CS) to define areas of dysregulated and druggable targets. Methodology Next-generation sequencing was performed on adrenal samples of patients with primary bilateral macronodular adrenal hyperplasia (PBMAH, n=10) and control adrenal samples (n=8). The validation groups included cortisol-producing adenoma (CPA, n=9) and samples from patients undergoing bilateral adrenalectomy for Cushing's disease (BADX-CD, n=8). In vivo findings were further characterized using three adrenocortical cell-lines (NCI-H295R, CU-ACC2, MUC1). Results Pathway mapping based on significant expression patterns identified PPARG (peroxisome proliferator-activated receptor gamma) pathway as the top hit. Quantitative PCR (QPCR) confirmed that PPARG (l2fc<-1.5) and related genes - FABP4 (l2fc<-5.5), PLIN1 (l2fc<-4.1) and ADIPOQ (l2fc<-3.3) - were significantly downregulated (p<0.005) in PBMAH. Significant downregulation of PPARG was also found in BADX-CD (l2fc<-1.9, p<0.0001) and CPA (l2fc<-1.4, p<0.0001). In vitro studies demonstrated that the PPARG activator rosiglitazone resulted in decreased cell viability in MUC1 and NCI-H295R (p<0.0001). There was also a significant reduction in the production of aldosterone, cortisol, and cortisone in NCI-H295R and in Dihydrotestosterone (DHT) in MUC1 (p<0.05), respectively. Outcome This therapeutic effect was independent of the actions of ACTH, postulating a promising application of PPARG activation in endogenous hypercortisolism.
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Affiliation(s)
- Sharmilee Vetrivel
- Department of Medicine IV, LMU University Hospital, LMU Munich, Munich, Germany
| | - Mariangela Tamburello
- Division of Endocrinology and Diabetes, Department of Internal Medicine I, University Hospital, University of Würzburg, Würzburg, Germany
- Section of Pharmacology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Andrea Oßwald
- Department of Medicine IV, LMU University Hospital, LMU Munich, Munich, Germany
| | - Ru Zhang
- Department of Medicine IV, LMU University Hospital, LMU Munich, Munich, Germany
| | - Ali Khan
- Division of Endocrinology and Diabetes, Department of Internal Medicine I, University Hospital, University of Würzburg, Würzburg, Germany
| | - Sara Jung
- Department of Medicine IV, LMU University Hospital, LMU Munich, Munich, Germany
| | - Jessica E. Baker
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - William E. Rainey
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Elisabeth Nowak
- Department of Medicine IV, LMU University Hospital, LMU Munich, Munich, Germany
| | - Barbara Altieri
- Division of Endocrinology and Diabetes, Department of Internal Medicine I, University Hospital, University of Würzburg, Würzburg, Germany
| | - Mario Detomas
- Division of Endocrinology and Diabetes, Department of Internal Medicine I, University Hospital, University of Würzburg, Würzburg, Germany
| | - Deepika Watts
- Institute of Clinical Chemistry and Laboratory Medicine, Technische Universität Dresden (TUD)/Universitätsklinikum Carl Gustav Carus Dresden (UKD), Dresden, Germany
| | - Tracy Ann Williams
- Department of Medicine IV, LMU University Hospital, LMU Munich, Munich, Germany
| | - Ben Wielockx
- Institute of Clinical Chemistry and Laboratory Medicine, Technische Universität Dresden (TUD)/Universitätsklinikum Carl Gustav Carus Dresden (UKD), Dresden, Germany
| | - Felix Beuschlein
- Department of Medicine IV, LMU University Hospital, LMU Munich, Munich, Germany
- Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH), Zurich, Switzerland
| | - Martin Reincke
- Department of Medicine IV, LMU University Hospital, LMU Munich, Munich, Germany
| | - Silviu Sbiera
- Division of Endocrinology and Diabetes, Department of Internal Medicine I, University Hospital, University of Würzburg, Würzburg, Germany
| | - Anna Riester
- Department of Medicine IV, LMU University Hospital, LMU Munich, Munich, Germany
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Maassen S, Coenen B, Dulk S, van der Werff M, Warner H, Spada F, Frischmuth T, Incarnato D, van den Bogaart G. 5-Ethynyluridine: A Bio-orthogonal Uridine Variant for mRNA-Based Therapies and Vaccines. Chembiochem 2023; 24:e202200658. [PMID: 36594506 DOI: 10.1002/cbic.202200658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/17/2022] [Accepted: 01/02/2023] [Indexed: 01/04/2023]
Abstract
The identification of pseudo- and N1 -methylpseudo-uridine (Ψ and mΨ, respectively) as immunosilent uridine analogues has propelled the development of mRNA-based vaccines and therapeutics. Here, we have characterised another uridine analogue, 5-ethynyluridine (EU), which has an ethynyl moiety. We show that this uridine analogue does not cause immune activation in human macrophages, as it does not induce interleukin-6 secretion or expression of the inflammatory and antiviral genes MX1, PKR, and TAP2. Moreover, EU allows for prolonged expression, as shown with mRNA coding for yellow fluorescent protein (YFP). Side-by-side comparisons of EU with unmodified, Ψ, and mΨ revealed that EU-modified mRNA is expressed at lower levels, but confers similar stability and low immunogenicity to the other uridine analogues. Furthermore, structure analysis of modified mRNAs suggests that the observed phenotype is largely independent of RNA folding. Thus, EU is a potential candidate for RNA-based vaccines and therapeutics.
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Affiliation(s)
- Sjors Maassen
- Department of Molecular Immunology, GBB, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Britt Coenen
- Department of Molecular Immunology, GBB, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Sara Dulk
- Department of Molecular Genetics, GBB, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Martijn van der Werff
- Department of Molecular Immunology, GBB, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Harry Warner
- Department of Molecular Immunology, GBB, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Fabio Spada
- Baseclick GmbH, Floriansbogen 2, 82061, Neuried, Germany
| | | | - Danny Incarnato
- Department of Molecular Genetics, GBB, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Geert van den Bogaart
- Department of Molecular Immunology, GBB, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.,Department of Medical Biology and Pathology, UMCG, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
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Isolating mineralized bone and bone marrow mRNA from transiliac bone biopsies stored in a stabilizing solution: A comparative study. Bone Rep 2022; 17:101624. [PMID: 36238088 PMCID: PMC9551114 DOI: 10.1016/j.bonr.2022.101624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/24/2022] Open
Abstract
The molecular mechanisms underlying metabolic bone diseases, including renal osteodystrophy, are poorly understood. Transcriptomics are increasingly used to characterize biological molecular networks and prove promising in identifying therapeutic targets and biomarkers. A reliable method for obtaining sufficient amounts of high quality RNA from human bone biopsies is a prerequisite for the implementation of molecular diagnostics in clinical research and practice. The present study aimed to develop a simple and adequate method for isolating bone and bone marrow mRNA from transiliac bone biopsies. Several storage, separation, and extraction procedures were compared. The procedure was optimized in pig samples and subsequently validated in human samples. Appropriate amounts of mineralized bone and bone marrow mRNA of moderate to high quality were obtained from transiliac bone biopsies that were immersed in the stabilizing solution Allprotect Tissue Reagent at room temperature for up to 3 days prior to freezing. After thawing, bone marrow and mineralized bone were separated by a multistep centrifugation procedure and subsequently disrupted and homogenized by a bead crusher. Appropriate separation of mineralized bone and bone marrow was confirmed by discriminatory gene expression profiles. Molecular diagnostics increasingly gain interest in clinical practice. A bone biopsy immersed in a stabilization reagent yields moderate mRNA quality. Use of a stabilization reagent allows for easy separation of bone and bone marrow.
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Cerón-Pisa N, Shafiek H, Martín-Medina A, Verdú J, Jordana-Lluch E, Escobar-Salom M, Barceló IM, López-Causapé C, Oliver A, Juan C, Iglesias A, Cosío BG. Effects of Inhaled Corticosteroids on the Innate Immunological Response to Pseudomonas aeruginosa Infection in Patients with COPD. Int J Mol Sci 2022; 23:ijms23158127. [PMID: 35897707 PMCID: PMC9332726 DOI: 10.3390/ijms23158127] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 11/16/2022] Open
Abstract
Inhaled corticosteroids (ICS) use is associated with an increased risk of Pseudomonas aeruginosa (PA) infection in patients with COPD. We aimed to evaluate the effects of ICS on alveolar macrophages in response to PA in COPD patients with and without baseline ICS treatment (COPD and COPD + ICS, respectively) as well as smoker and nonsmoker controls. To do so, cells were infected with PA and cotreated with budesonide (BUD) or fluticasone propionate (FLU). The analysis of NF-κB and c-jun activity revealed a significant increase in both factors in response to PA cotreated with BUD/FLU in smokers but not in COPD or COPD + ICS patients when compared with PA infection alone. The expression of Toll-like receptor 2 (TLR2) and the transcription factor c-jun were induced upon PA infection in nonsmokers only. Moreover, in the smoker and COPD groups, there was a significant increase in TLR2 and a decrease in c-jun expression when treated with BUD/FLU after PA infection, which were not observed in COPD + ICS patients. Therefore, the chronic use of ICS seemingly makes the macrophages tolerant to BUD/FLU stimulation compared with those from patients not treated with ICS, promoting an impaired recognition of PA and activity of alveolar macrophages in terms of altered expression of TLR2 and cytokine production, which could explain the increased risk of PA infection in COPD patients under ICS treatment.
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Affiliation(s)
- Noemi Cerón-Pisa
- Instituto de Investigación Sanitaria de Les Illes Balears (IdISBa), Hospital Universitario Son Espases, 07120 Palma de Mallorca, Spain; (N.C.-P.); (A.M.-M.); (J.V.); (E.J.-L.); (M.E.-S.); (I.M.B.); (C.L.-C.); (A.O.); (C.J.)
| | - Hanaa Shafiek
- Chest Diseases Department, Faculty of Medicine, Alexandria University, Alexandria 21526, Egypt;
| | - Aina Martín-Medina
- Instituto de Investigación Sanitaria de Les Illes Balears (IdISBa), Hospital Universitario Son Espases, 07120 Palma de Mallorca, Spain; (N.C.-P.); (A.M.-M.); (J.V.); (E.J.-L.); (M.E.-S.); (I.M.B.); (C.L.-C.); (A.O.); (C.J.)
| | - Javier Verdú
- Instituto de Investigación Sanitaria de Les Illes Balears (IdISBa), Hospital Universitario Son Espases, 07120 Palma de Mallorca, Spain; (N.C.-P.); (A.M.-M.); (J.V.); (E.J.-L.); (M.E.-S.); (I.M.B.); (C.L.-C.); (A.O.); (C.J.)
- Department of Respiratory Medicine, Hospital Universitario Son Espases, 07120 Palma de Mallorca, Spain
| | - Elena Jordana-Lluch
- Instituto de Investigación Sanitaria de Les Illes Balears (IdISBa), Hospital Universitario Son Espases, 07120 Palma de Mallorca, Spain; (N.C.-P.); (A.M.-M.); (J.V.); (E.J.-L.); (M.E.-S.); (I.M.B.); (C.L.-C.); (A.O.); (C.J.)
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III (CIBERINFEC), 28029 Madrid, Spain
- Department of Microbiology, Hospital Universitario Son Espases, 07120 Palma de Mallorca, Spain
| | - Maria Escobar-Salom
- Instituto de Investigación Sanitaria de Les Illes Balears (IdISBa), Hospital Universitario Son Espases, 07120 Palma de Mallorca, Spain; (N.C.-P.); (A.M.-M.); (J.V.); (E.J.-L.); (M.E.-S.); (I.M.B.); (C.L.-C.); (A.O.); (C.J.)
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III (CIBERINFEC), 28029 Madrid, Spain
- Department of Microbiology, Hospital Universitario Son Espases, 07120 Palma de Mallorca, Spain
| | - Isabel M. Barceló
- Instituto de Investigación Sanitaria de Les Illes Balears (IdISBa), Hospital Universitario Son Espases, 07120 Palma de Mallorca, Spain; (N.C.-P.); (A.M.-M.); (J.V.); (E.J.-L.); (M.E.-S.); (I.M.B.); (C.L.-C.); (A.O.); (C.J.)
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III (CIBERINFEC), 28029 Madrid, Spain
- Department of Microbiology, Hospital Universitario Son Espases, 07120 Palma de Mallorca, Spain
| | - Carla López-Causapé
- Instituto de Investigación Sanitaria de Les Illes Balears (IdISBa), Hospital Universitario Son Espases, 07120 Palma de Mallorca, Spain; (N.C.-P.); (A.M.-M.); (J.V.); (E.J.-L.); (M.E.-S.); (I.M.B.); (C.L.-C.); (A.O.); (C.J.)
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III (CIBERINFEC), 28029 Madrid, Spain
- Department of Microbiology, Hospital Universitario Son Espases, 07120 Palma de Mallorca, Spain
| | - Antonio Oliver
- Instituto de Investigación Sanitaria de Les Illes Balears (IdISBa), Hospital Universitario Son Espases, 07120 Palma de Mallorca, Spain; (N.C.-P.); (A.M.-M.); (J.V.); (E.J.-L.); (M.E.-S.); (I.M.B.); (C.L.-C.); (A.O.); (C.J.)
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III (CIBERINFEC), 28029 Madrid, Spain
- Department of Microbiology, Hospital Universitario Son Espases, 07120 Palma de Mallorca, Spain
| | - Carlos Juan
- Instituto de Investigación Sanitaria de Les Illes Balears (IdISBa), Hospital Universitario Son Espases, 07120 Palma de Mallorca, Spain; (N.C.-P.); (A.M.-M.); (J.V.); (E.J.-L.); (M.E.-S.); (I.M.B.); (C.L.-C.); (A.O.); (C.J.)
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III (CIBERINFEC), 28029 Madrid, Spain
- Department of Microbiology, Hospital Universitario Son Espases, 07120 Palma de Mallorca, Spain
| | - Amanda Iglesias
- Instituto de Investigación Sanitaria de Les Illes Balears (IdISBa), Hospital Universitario Son Espases, 07120 Palma de Mallorca, Spain; (N.C.-P.); (A.M.-M.); (J.V.); (E.J.-L.); (M.E.-S.); (I.M.B.); (C.L.-C.); (A.O.); (C.J.)
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III (CIBERES), 28029 Madrid, Spain
- Correspondence: (A.I.); (B.G.C.); Tel.: +34-871-205-050 (ext. 64521) (A.I. & B.G.C.)
| | - Borja G. Cosío
- Instituto de Investigación Sanitaria de Les Illes Balears (IdISBa), Hospital Universitario Son Espases, 07120 Palma de Mallorca, Spain; (N.C.-P.); (A.M.-M.); (J.V.); (E.J.-L.); (M.E.-S.); (I.M.B.); (C.L.-C.); (A.O.); (C.J.)
- Department of Respiratory Medicine, Hospital Universitario Son Espases, 07120 Palma de Mallorca, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III (CIBERES), 28029 Madrid, Spain
- Correspondence: (A.I.); (B.G.C.); Tel.: +34-871-205-050 (ext. 64521) (A.I. & B.G.C.)
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Vetrivel S, Zhang R, Engel M, Oßwald A, Watts D, Chen A, Wielockx B, Sbiera S, Reincke M, Riester A. Characterization of Adrenal miRNA-Based Dysregulations in Cushing's Syndrome. Int J Mol Sci 2022; 23:ijms23147676. [PMID: 35887024 PMCID: PMC9320303 DOI: 10.3390/ijms23147676] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/04/2022] [Accepted: 07/10/2022] [Indexed: 02/05/2023] Open
Abstract
MiRNAs are important epigenetic players with tissue- and disease-specific effects. In this study, our aim was to investigate the putative differential expression of miRNAs in adrenal tissues from different forms of Cushing’s syndrome (CS). For this, miRNA-based next-generation sequencing was performed in adrenal tissues taken from patients with ACTH-independent cortisol-producing adrenocortical adenomas (CPA), from patients with ACTH-dependent pituitary Cushing’s disease (CD) after bilateral adrenalectomy, and from control subjects. A confirmatory QPCR was also performed in adrenals from patients with other CS subtypes, such as primary bilateral macronodular hyperplasia and ectopic CS. Sequencing revealed significant differences in the miRNA profiles of CD and CPA. QPCR revealed the upregulated expression of miR-1247-5p in CPA and PBMAH (log2 fold change > 2.5, p < 0.05). MiR-379-5p was found to be upregulated in PBMAH and CD (log2 fold change > 1.8, p < 0.05). Analyses of miR-1247-5p and miR-379-5p expression in the adrenals of mice which had been exposed to short-term ACTH stimulation showed no influence on the adrenal miRNA expression profiles. For miRNA-specific target prediction, RNA-seq data from the adrenals of CPA, PBMAH, and control samples were analyzed with different bioinformatic platforms. The analyses revealed that both miR-1247-5p and miR-379-5p target specific genes in the WNT signaling pathway. In conclusion, this study identified distinct adrenal miRNAs as being associated with CS subtypes.
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Affiliation(s)
- Sharmilee Vetrivel
- Medizinische Klinik und Poliklinik IV, LMU Klinikum, Ludwig-Maximilians-University, 80336 Munich, Germany; (S.V.); (R.Z.); (A.O.); (M.R.)
| | - Ru Zhang
- Medizinische Klinik und Poliklinik IV, LMU Klinikum, Ludwig-Maximilians-University, 80336 Munich, Germany; (S.V.); (R.Z.); (A.O.); (M.R.)
| | - Mareen Engel
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, 80804 Munich, Germany; (M.E.); (A.C.)
| | - Andrea Oßwald
- Medizinische Klinik und Poliklinik IV, LMU Klinikum, Ludwig-Maximilians-University, 80336 Munich, Germany; (S.V.); (R.Z.); (A.O.); (M.R.)
| | - Deepika Watts
- Institute of Clinical Chemistry and Laboratory Medicine, Technische Universität Dresden, 01307 Dresden, Germany; (D.W.); (B.W.)
| | - Alon Chen
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, 80804 Munich, Germany; (M.E.); (A.C.)
- Department of Neurobiology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ben Wielockx
- Institute of Clinical Chemistry and Laboratory Medicine, Technische Universität Dresden, 01307 Dresden, Germany; (D.W.); (B.W.)
| | - Silviu Sbiera
- Department of Internal Medicine I, Division of Endocrinology and Diabetes, University Hospital, University of Würzburg, 97080 Würzburg, Germany;
| | - Martin Reincke
- Medizinische Klinik und Poliklinik IV, LMU Klinikum, Ludwig-Maximilians-University, 80336 Munich, Germany; (S.V.); (R.Z.); (A.O.); (M.R.)
| | - Anna Riester
- Medizinische Klinik und Poliklinik IV, LMU Klinikum, Ludwig-Maximilians-University, 80336 Munich, Germany; (S.V.); (R.Z.); (A.O.); (M.R.)
- Correspondence: ; Tel.: +49-89-440052111
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Sorber L, Van Dorst B, Bellon E, Zwaenepoel K, Lambin S, De Winne K, Lardon F, Pauwels P, Siozopoulou V. NTRK Gene Fusion Detection in a Pan-Cancer Setting Using the Idylla GeneFusion Assay. J Mol Diagn 2022; 24:750-759. [PMID: 35550184 DOI: 10.1016/j.jmoldx.2022.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/14/2022] [Accepted: 03/23/2022] [Indexed: 10/18/2022] Open
Abstract
Recently, approval of tyrosine receptor kinase (TRK) inhibitors by Food and Drug Administration and European Medicines Agency in NTRK fusion-positive cancer types has led to a variety of proposed testing algorithms. In this study, performance of the fully automated Idylla GeneFusion Assay was assessed in a set of clinically relevant cancer types, including glioblastoma, non-small-cell lung cancer, microsatellite instability-positive colorectal cancer, and thyroid carcinoma. Analysis with the Idylla GeneFusion Assay revealed significant differences in baseline RNA expression profile between the different cancer types, which corresponded to both literature and pan-TRK immunohistochemistry staining. Compared with the RNA-based Oncomine Focus Assay, the Idylla GeneFusion Assay demonstrated an overall percentage agreement, positive percentage agreement, and negative percentage agreement of 92.7%, 81.8%, and 93.8%, respectively; and the pan-TRK immunohistochemistry demonstrated an overall percentage agreement, positive percentage agreement, and negative percentage agreement of 82.1%, 45.5%, and 85.7%, respectively. These findings highlighted the importance of tailoring NTRK testing algorithms per cancer type. In a small subset, data from the RNA-based Archer FusionPlex Assay were also available. NTRK fusion detection efficiency was compared between the four NTRK testing modalities, with a high concordance between the PCR-based methods. Last, RNA degradation was observed when using the Idylla GeneFusion Assay on snap frozen tissue samples as these are nonfixated. This might be countered by increasing the amount of sample input. To conclude, the Idylla GeneFusion Assay has shown a clear potential in identifying NTRK fusions.
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Affiliation(s)
- Laure Sorber
- Center for Oncological Research, Integrated Personalized and Precision Oncology Network, University of Antwerp, Wilrijk, Belgium.
| | | | | | - Karen Zwaenepoel
- Center for Oncological Research, Integrated Personalized and Precision Oncology Network, University of Antwerp, Wilrijk, Belgium; Department of Pathology, University Hospital Antwerp, Edegem, Belgium
| | - Suzan Lambin
- Department of Pathology, University Hospital Antwerp, Edegem, Belgium
| | - Koen De Winne
- Department of Pathology, University Hospital Antwerp, Edegem, Belgium
| | - Filip Lardon
- Center for Oncological Research, Integrated Personalized and Precision Oncology Network, University of Antwerp, Wilrijk, Belgium
| | - Patrick Pauwels
- Department of Pathology, University Hospital Antwerp, Edegem, Belgium
| | - Vasiliki Siozopoulou
- Center for Oncological Research, Integrated Personalized and Precision Oncology Network, University of Antwerp, Wilrijk, Belgium; Department of Pathology, University Hospital Antwerp, Edegem, Belgium
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Somiari SB, Shuss S, Liu J, Mamula K, O’Donnell A, Deyarmin B, Kane J, Greenawalt A, Larson C, Rigby S, Hu H, Shriver CD. Assessing the quality of RNA isolated from human breast tissue after ambient room temperature exposure. PLoS One 2022; 17:e0262654. [PMID: 35041696 PMCID: PMC8765617 DOI: 10.1371/journal.pone.0262654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 01/03/2022] [Indexed: 11/19/2022] Open
Abstract
High quality human tissue is essential for molecular research, but pre-analytical conditions encountered during tissue collection could degrade tissue RNA. We evaluated how prolonged exposure of non-diseased breast tissue to ambient room temperature (22±1°C) impacted RNA quality. Breast tissue received between 70 to 190 minutes after excision was immediately flash frozen (FF) or embedded in Optimal Cutting Temperature (OCT) compound upon receipt (T0). Additional breast tissue pieces were further exposed to increments of 60 (T1 = T0+60 mins), 120 (T2 = T0+120 mins) and 180 (T3 = T0+180 mins) minutes of ambient room temperature before processing into FF and OCT. Total exposure, T3 (T0+180 mins) ranged from 250 minutes to 370 minutes. All samples (FF and OCT) were stored at -80°C before RNA isolation. The RNA quality assessment based on RNA Integrity Number (RIN) showed RINs for both FF and OCT samples were within the generally acceptable range (mean 7.88±0.90 to 8.52±0.66). No significant difference was observed when RIN at T0 was compared to RIN at T1, T2 and T3 (FF samples, p = 0.43, 0.56, 0.44; OCT samples, p = 0.25, 0.82, 1.0), or when RIN was compared between T1, T2 and T3. RNA quality assessed by quantitative real-time PCR (qRT-PCR) analysis of beta-actin (ACTB), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), cyclophilin A (CYPA), and porphobilinogen deaminase (PBGD) transcripts showed threshold values (Ct) that indicate abundant and intact target nucleic acid in all samples (mean ranging from 14.1 to 25.3). The study shows that higher RIN values were obtained for non-diseased breast tissue up to 190 minutes after resection and prior to stabilization. Further experimental exposure up to 180 minutes had no significant effect on RIN values. This study strengthens the rationale for assessing RIN and specific gene transcript levels as an objective method for determining how suitable RNA will be for a specific research purpose (“fit-for purpose”).
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Affiliation(s)
- Stella B. Somiari
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, Pennsylvania, United States of America
- * E-mail:
| | - Susan Shuss
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, Pennsylvania, United States of America
| | - Jianfang Liu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, Pennsylvania, United States of America
| | - Kimberly Mamula
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, Pennsylvania, United States of America
| | - Amy O’Donnell
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, Pennsylvania, United States of America
| | - Brenda Deyarmin
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, Pennsylvania, United States of America
| | - Jennifer Kane
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, Pennsylvania, United States of America
| | - Amber Greenawalt
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, Pennsylvania, United States of America
| | - Caroline Larson
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, Pennsylvania, United States of America
| | - Sean Rigby
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, Pennsylvania, United States of America
| | - Hai Hu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, Pennsylvania, United States of America
- Murtha Cancer Center Research Program, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Craig D. Shriver
- Murtha Cancer Center Research Program, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
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8
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Veryaskina YA, Titov SE, Zhimulev IF. Reference Genes for qPCR-Based miRNA Expression Profiling in 14 Human Tissues. Med Princ Pract 2022; 31:322-332. [PMID: 35354155 PMCID: PMC9485981 DOI: 10.1159/000524283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/22/2022] [Indexed: 11/19/2022] Open
Abstract
MicroRNAs (miRNAs) are promising biomarkers for the diagnosis and prognosis of various diseases. Quantitative PCR is the most frequently used method of measuring expression levels of miRNA. However, the lack of validated reference genes represents the main source of potential bias in results. It is normal practice to use small nuclear RNAs as reference genes; however, they often have variable expression. Researchers tend to prefer the most stable reference genes in each experiment. The review includes reference genes for the following tissue types: gliomas, lung cancer, melanoma, gastric cancer, liver cancer, prostate cancer, breast cancer, thyroid cancer, ovarian cancer, cervical cancer, endometrial cancer, rectal cancer, blood tumors, and placental tissues.
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Affiliation(s)
- Yulia Andreevna Veryaskina
- Laboratory of Gene Engineering, Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russian Federation
- Department of the Structure and Function of Chromosomes, Laboratory of Molecular Genetics Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russian Federation
- *Yulia Andreevna Veryaskina,
| | - Sergei Evgenievich Titov
- Department of the Structure and Function of Chromosomes, Laboratory of Molecular Genetics Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russian Federation
- AO Vector-Best, Novosibirsk, Russian Federation
| | - Igor Fyodorovich Zhimulev
- Department of the Structure and Function of Chromosomes, Laboratory of Molecular Genetics Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russian Federation
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9
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Vetrivel S, Zhang R, Engel M, Altieri B, Braun L, Osswald A, Bidlingmaier M, Fassnacht M, Beuschlein F, Reincke M, Chen A, Sbiera S, Riester A. Circulating microRNA Expression in Cushing's Syndrome. Front Endocrinol (Lausanne) 2021; 12:620012. [PMID: 33692756 PMCID: PMC7937959 DOI: 10.3389/fendo.2021.620012] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/04/2021] [Indexed: 12/15/2022] Open
Abstract
Context Cushing's syndrome (CS) is a rare disease of endogenous hypercortisolism associated with high morbidity and mortality. Diagnosis and classification of CS is still challenging. Objective Circulating microRNAs (miRNAs) are minimally invasive diagnostic markers. Our aim was to characterize the circulating miRNA profiles of CS patients and to identify distinct profiles between the two major CS subtypes. Methods We included three groups of patients from the German Cushing's registry: ACTH-independent CS (Cortisol-Producing-Adenoma; CPA), ACTH-dependent pituitary CS (Cushing's Disease; CD), and patients in whom CS had been ruled out (controls). Profiling of miRNAs was performed by next-generation-sequencing (NGS) in serum samples of 15 CS patients (each before and after curative surgery) and 10 controls. Significant miRNAs were first validated by qPCR in the discovery cohort and then in an independent validation cohort of 20 CS patients and 11 controls. Results NGS identified 411 circulating miRNAs. Differential expression of 14 miRNAs were found in the pre- and postoperative groups. qPCR in the discovery cohort validated 5 of the significant miRNAs from the preoperative group analyses. Only, miR-182-5p was found to be significantly upregulated in the CD group of the validation cohort. Comparing all CS samples as a group with the controls did not reveal any significant differences in expression. Outcome In conclusion, our study identified miR-182-5p as a possible biomarker for CD, which has to be validated in a prospective cohort. Furthermore, our results suggest that presence or absence of ACTH might be at least as relevant for miRNA expression as hypercortisolism itself.
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Affiliation(s)
- Sharmilee Vetrivel
- Department of Endocrinology, Medizinische Klinik und Poliklinik IV, Ludwig-Maximilians-University, Munich, Germany
| | - Ru Zhang
- Department of Endocrinology, Medizinische Klinik und Poliklinik IV, Ludwig-Maximilians-University, Munich, Germany
| | - Mareen Engel
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
| | - Barbara Altieri
- Division of Endocrinology and Diabetes, Department of Internal Medicine I, University Hospital, University of Würzburg, Würzburg, Germany
| | - Leah Braun
- Department of Endocrinology, Medizinische Klinik und Poliklinik IV, Ludwig-Maximilians-University, Munich, Germany
| | - Andrea Osswald
- Department of Endocrinology, Medizinische Klinik und Poliklinik IV, Ludwig-Maximilians-University, Munich, Germany
| | - Martin Bidlingmaier
- Department of Endocrinology, Medizinische Klinik und Poliklinik IV, Ludwig-Maximilians-University, Munich, Germany
| | - Martin Fassnacht
- Division of Endocrinology and Diabetes, Department of Internal Medicine I, University Hospital, University of Würzburg, Würzburg, Germany
| | - Felix Beuschlein
- Department of Endocrinology, Medizinische Klinik und Poliklinik IV, Ludwig-Maximilians-University, Munich, Germany
- Klinik für Endokrinologie, Diabetologie und Klinische Ernährung, Universitätsspital Zürich, Zürich, Switzerland
| | - Martin Reincke
- Department of Endocrinology, Medizinische Klinik und Poliklinik IV, Ludwig-Maximilians-University, Munich, Germany
| | - Alon Chen
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Silviu Sbiera
- Division of Endocrinology and Diabetes, Department of Internal Medicine I, University Hospital, University of Würzburg, Würzburg, Germany
| | - Anna Riester
- Department of Endocrinology, Medizinische Klinik und Poliklinik IV, Ludwig-Maximilians-University, Munich, Germany
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