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Spoutil F, Dlugosova S, Varga I, Aranaz-Novaliches G, Novosadova V, Prochazkova M, Sedlacek R, Prochazka J. Semi-Automated MicroCT Analysis of Bone Anatomy and Mineralization in Mouse Models. Curr Protoc 2024; 4:e980. [PMID: 38385868 DOI: 10.1002/cpz1.980] [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] [Indexed: 02/23/2024]
Abstract
The skeletal system mirrors several processes in the vertebrate body that impact developmental malfunctions, hormonal disbalance, malfunction of calcium metabolism and turn over, and inflammation processes such as arthrosis. X-ray micro computed tomography is a useful tool for 3D in situ evaluation of the skeletal system in a time-related manner, but results depend highly on resolution. Here, we provide the methodological background for a graduated evaluation from whole-body analysis of skeletal morphology and mineralization to high-resolution analysis of femoral and vertebral microstructure. We combine an expert-based evaluation with a machine-learning-based computational approach, including pre-setup analytical task lists. © 2024 Wiley Periodicals LLC. Basic Protocol 1: In vivo microCT scanning and skeletal analysis in mice Basic Protocol 2: Ex vivo high-resolution microCT scanning and microstructural analysis of the femur and L4 vertebra.
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Affiliation(s)
- Frantisek Spoutil
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Sylvie Dlugosova
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Igor Varga
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Cybernetics, Czech Technical University in Prague, Prague, Czech Republic
| | - Goretti Aranaz-Novaliches
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Vendula Novosadova
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michaela Prochazkova
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Prochazka
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
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2
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Benes J, Kroupova K, Kotrc M, Petrak J, Jarolim P, Novosadova V, Kautzner J, Melenovsky V. FGF-23 is a biomarker of RV dysfunction and congestion in patients with HFrEF. Sci Rep 2023; 13:16004. [PMID: 37749114 PMCID: PMC10520041 DOI: 10.1038/s41598-023-42558-4] [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: 04/03/2023] [Accepted: 09/12/2023] [Indexed: 09/27/2023] Open
Abstract
There is no biomarker reflecting right ventricular dysfunction in HFrEF patients used in clinical practice. We have aimed to look for a circulating marker of RV dysfunction employing a quantitative proteomic strategy. The Olink Proteomics Multiplex panels (Cardiovascular Disease II, III, Cardiometabolic, and Inflammation Target Panels) identified FGF-23 to be the most differentially abundant (more than 2.5-fold) in blood plasma of HF patients with severe RV dysfunction (n = 30) compared to those with preserved RV function (n = 31). A subsequent ELISA-based confirmatory analysis of circulating FGF-23 in a large cohort of patients (n = 344, 72.7% NYHA III/IV, LVEF 22.5%, 54.1% with moderate/severe RV dysfunction), followed by multivariable regression analysis, revealed that the plasma FGF-23 level was most significantly associated with RV dysfunction grade (p = 0.0004) and congestion in the systemic circulation (p = 0.03), but not with LV-ejection fraction (p = 0.69) or estimated glomerular filtration rate (eGFR, p = 0.08). FGF-23 was associated with the degree of RV dysfunction in both sub-cohorts (i.e. in patients with and without congestion, p < 0.0001). The association between FGF-23 and RV-dysfunction remained significant after the adjustment for BNP (p = 0.01). In contrast, when adjusted for BNP, FGF-23 was no longer associated with LV dysfunction (p = 0.59). The Cox proportional hazard model revealed that circulating FGF-23 was significantly associated with adverse outcomes even after adjusting for BNP, LVEF, RV dysfunction grade and eGFR. Circulating FGF-23 is thus a biomarker of right ventricular dysfunction in HFrEF patients regardless of congestion status.
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Affiliation(s)
- Jan Benes
- Department of Cardiology, Institute for Clinical and Experimental Medicine-IKEM, Videnska 1958/9, 140 21 Praha 4, Prague, Czech Republic.
| | - Katerina Kroupova
- Department of Cardiology, Institute for Clinical and Experimental Medicine-IKEM, Videnska 1958/9, 140 21 Praha 4, Prague, Czech Republic
- Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Martin Kotrc
- Department of Cardiology, Institute for Clinical and Experimental Medicine-IKEM, Videnska 1958/9, 140 21 Praha 4, Prague, Czech Republic
| | - Jiri Petrak
- BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic
| | - Petr Jarolim
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Vendula Novosadova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Josef Kautzner
- Department of Cardiology, Institute for Clinical and Experimental Medicine-IKEM, Videnska 1958/9, 140 21 Praha 4, Prague, Czech Republic
| | - Vojtech Melenovsky
- Department of Cardiology, Institute for Clinical and Experimental Medicine-IKEM, Videnska 1958/9, 140 21 Praha 4, Prague, Czech Republic
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3
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Syding LA, Kubik-Zahorodna A, Reguera DP, Nickl P, Hruskova B, Kralikova M, Kopkanova J, Novosadova V, Kasparek P, Prochazka J, Rozman J, Turecek R, Sedlacek R. Ablation of Gabra5 Influences Corticosterone Levels and Anxiety-like Behavior in Mice. Genes (Basel) 2023; 14:genes14020285. [PMID: 36833213 PMCID: PMC9956889 DOI: 10.3390/genes14020285] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/07/2023] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
Stress responses are activated by the hypothalamic-pituitary-adrenal axis (HPA axis), culminating in the release of glucocorticoids. During prolonged periods of secretion of glucocorticoids or inappropriate behavioral responses to a stressor, pathologic conditions may occur. Increased glucocorticoid concentration is linked to generalized anxiety, and there are knowledge gaps regarding its regulation. It is known that the HPA axis is under GABAergic control, but the contribution of the individual subunits of the GABA receptor is largely unknown. In this study, we investigated the relationship between the α5 subunit and corticosterone levels in a new mouse model deficient for Gabra5, which is known to be linked to anxiety disorders in humans and phenologs observed in mice. We observed decreased rearing behavior, suggesting lower anxiety in the Gabra5-/- animals; however, such a phenotype was absent in the open field and elevated plus maze tests. In addition to decreased rearing behavior, we also found decreased levels of fecal corticosterone metabolites in Gabra5-/- mice indicating a lowered stress response. Moreover, based on the electrophysiological recordings where we observed a hyperpolarized state of hippocampal neurons, we hypothesize that the constitutive ablation of the Gabra5 gene leads to functional compensation with other channels or GABA receptor subunits in this model.
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Affiliation(s)
- Linn Amanda Syding
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, 25250 Vestec, Czech Republic
| | - Agnieszka Kubik-Zahorodna
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the CAS, 25250 Vestec, Czech Republic
- Correspondence: (A.K.-Z.); (R.S.)
| | - David Pajuelo Reguera
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the CAS, 25250 Vestec, Czech Republic
| | - Petr Nickl
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, 25250 Vestec, Czech Republic
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the CAS, 25250 Vestec, Czech Republic
| | - Bohdana Hruskova
- Department of Auditory Neuroscience, Institute of Experimental Medicine of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Michaela Kralikova
- Department of Auditory Neuroscience, Institute of Experimental Medicine of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Jana Kopkanova
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the CAS, 25250 Vestec, Czech Republic
| | - Vendula Novosadova
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the CAS, 25250 Vestec, Czech Republic
| | - Petr Kasparek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the CAS, 25250 Vestec, Czech Republic
| | - Jan Prochazka
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, 25250 Vestec, Czech Republic
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the CAS, 25250 Vestec, Czech Republic
| | - Jan Rozman
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the CAS, 25250 Vestec, Czech Republic
| | - Rostislav Turecek
- Department of Auditory Neuroscience, Institute of Experimental Medicine of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Radislav Sedlacek
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, 25250 Vestec, Czech Republic
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the CAS, 25250 Vestec, Czech Republic
- Correspondence: (A.K.-Z.); (R.S.)
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4
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Sojka L, Opattova A, Bartu L, Horak J, Korenkova V, Novosadova V, Krizkova V, Bruha J, Liska V, Schneiderova M, Kubecek O, Vodickova L, Urbanova M, Simsa J, Vodicka P, Vymetalkova V. MUC13-miRNA-4647 axis in colorectal cancer: Prospects to identifications of risk factors and clinical outcomes. Oncol Lett 2022; 25:72. [PMID: 36688110 PMCID: PMC9843305 DOI: 10.3892/ol.2022.13658] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 12/09/2022] [Indexed: 01/01/2023] Open
Abstract
MUC13, a transmembrane mucin glycoprotein, is overexpressed in colorectal cancer (CRC), however, its regulation and functions are not fully understood. It has been shown that MUC13 protects colonic epithelial cells from apoptosis. Therefore, studying MUC13 and MUC13-regulated pathways may reveal promising therapeutic approaches for CRC treatment. Growing evidence suggests that microRNAs (miRs) are involved in the development and progression of CRC. In the present study, the MUC13-miR-4647 axis was addressed in association with survival of patients. miR-4647 is predicted in silico to bind to the MUC13 gene and was analyzed by RT-qPCR in 187 tumors and their adjacent non-malignant mucosa of patients with CRC. The impact of previously mentioned genes on survival and migration abilities of cancer cells was validated in vitro. Significantly upregulated MUC13 (P=0.02) in was observed tumor tissues compared with non-malignant adjacent mucosa, while miR-4647 (P=0.05) showed an opposite trend. Higher expression levels of MUC13 (log-rank P=0.05) were associated with worse patient's survival. The ectopic overexpression of studied miR resulted in decreased migratory abilities and worse survival of cells. Attenuated MUC13 expression levels confirmed the suppression of colony forming of CRC cells. In summary, the present data suggested the essential role of MUC13-miR-4647 in patients' survival, and this axis may serve as a novel therapeutic target. It is anticipated MUC13 may hold significant potential in the screening, diagnosis and treatment of CRC.
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Affiliation(s)
- Ladislav Sojka
- Department of Surgery, Thomayer Hospital, 14200 Prague, Czech Republic,Institute of Experimental Medicine, 1st Medical Faculty, Charles University, 12108 Prague, Czech Republic
| | - Alena Opattova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of The Czech Academy of Sciences, 14200 Prague, Czech Republic,Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, 12108 Prague, Czech Republic,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic
| | - Linda Bartu
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of The Czech Academy of Sciences, 14200 Prague, Czech Republic
| | - Josef Horak
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of The Czech Academy of Sciences, 14200 Prague, Czech Republic,Department of Medical Genetics, 3rd Medical Faculty, Charles University, 10000 Prague, Czech Republic
| | - Vlasta Korenkova
- Institute of Immunology and Microbiology, 1st Faculty of Medicine, Charles University, 12108 Prague, Czech Republic
| | - Vendula Novosadova
- Centre for Phenogenomics, Institute of Molecular Genetics, BIOCEV, 25250 Vestec, Czech Republic
| | - Vera Krizkova
- Department of Histology and Embryology, Faculty of Medicine in Pilsen, Charles University, 30166 Pilsen, Czech Republic
| | - Jan Bruha
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of The Czech Academy of Sciences, 14200 Prague, Czech Republic,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic,Department of Surgery, University Hospital and Faculty of Medicine in Pilsen, Charles University, 30166 Pilsen, Czech Republic
| | - Vaclav Liska
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of The Czech Academy of Sciences, 14200 Prague, Czech Republic,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic,Department of Surgery, University Hospital and Faculty of Medicine in Pilsen, Charles University, 30166 Pilsen, Czech Republic
| | - Michaela Schneiderova
- Department of Surgery, University Hospital Kralovske Vinohrady and Third Faculty of Medicine, Charles University, 10034 Prague, Czech Republic
| | - Ondrej Kubecek
- Department of Oncology and Radiotherapy, University Hospital and Faculty of Medicine in Hradec Kralove, Charles University, 50005 Hradec Kralove, Czech Republic
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of The Czech Academy of Sciences, 14200 Prague, Czech Republic,Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, 12108 Prague, Czech Republic,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic
| | - Marketa Urbanova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of The Czech Academy of Sciences, 14200 Prague, Czech Republic
| | - Jaromir Simsa
- Department of Surgery, Thomayer Hospital, 14200 Prague, Czech Republic
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of The Czech Academy of Sciences, 14200 Prague, Czech Republic,Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, 12108 Prague, Czech Republic,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of The Czech Academy of Sciences, 14200 Prague, Czech Republic,Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, 12108 Prague, Czech Republic,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic,Correspondence to: Dr Veronika Vymetalkova, Department of Molecular Biology of Cancer, Institute of Experimental Medicine of The Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic, E-mail:
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5
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Malinka F, Zareie A, Prochazka J, Sedlacek R, Novosadova V. Batch alignment via retention orders for preprocessing large-scale multi-batch LC-MS experiments. Bioinformatics 2022; 38:3759-3767. [PMID: 35748696 DOI: 10.1093/bioinformatics/btac407] [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] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 05/20/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Meticulous selection of chromatographic peak detection parameters and algorithms is a crucial step in preprocessing LC-MS data. However, as mass-to-charge ratio (m/z) and retention time shifts are larger between batches than within batches, finding apt parameters for all samples of a large-scale multi-batch experiment with the aim of minimizing information loss becomes a challenging task. Preprocessing independent batches individually can curtail said problems but requires a method for aligning and combining them for further downstream analysis. RESULTS We present two methods for aligning and combining individually preprocessed batches in multi-batch LC-MS experiments. Our developed methods were tested on six sets of simulated and six sets of real datasets. Furthermore, by estimating the probabilities of peak insertion, deletion, and swap between batches in authentic datasets we demonstrate that retention order swaps are not rare in untargeted LC-MS data. AVAILABILITY kmersAlignment and rtcorrectedAlignment algorithms are made available as an R package with raw data at https://metabocombiner.img.cas.cz. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- František Malinka
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Průmyslova 595, 252 50, Vestec, Czech Republic
| | - Ashkan Zareie
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Průmyslova 595, 252 50, Vestec, Czech Republic
| | - Jan Prochazka
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Průmyslova 595, 252 50, Vestec, Czech Republic
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Průmyslova 595, 252 50, Vestec, Czech Republic
| | - Vendula Novosadova
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Průmyslova 595, 252 50, Vestec, Czech Republic
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6
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Iatsiuk V, Malinka F, Pickova M, Tureckova J, Klema J, Spoutil F, Novosadova V, Prochazka J, Sedlacek R. Semantic clustering analysis of E3-ubiquitin ligases in gastrointestinal tract defines genes ontology clusters with tissue expression patterns. BMC Gastroenterol 2022; 22:186. [PMID: 35413796 PMCID: PMC9006408 DOI: 10.1186/s12876-022-02265-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 04/01/2022] [Indexed: 11/20/2022] Open
Abstract
Background Ubiquitin ligases (Ub-ligases) are essential intracellular enzymes responsible for the regulation of proteome homeostasis, signaling pathway crosstalk, cell differentiation and stress responses. Individual Ub-ligases exhibit their unique functions based on the nature of their substrates. They create a complex regulatory network with alternative and feedback pathways to maintain cell homeostasis, being thus important players in many physiological and pathological conditions. However, the functional classification of Ub-ligases needs to be revised and extended. Methods In the current study, we used a novel semantic biclustering technique for expression profiling of Ub-ligases and ubiquitination-related genes in the murine gastrointestinal tract (GIT). We accommodated a general framework of the algorithm for finding tissue-specific gene expression clusters in GIT. In order to test identified clusters in a biological system, we used a model of epithelial regeneration. For this purpose, a dextran sulfate sodium (DSS) mouse model, following with in situ hybridization, was used to expose genes with possible compensatory features. To determine cell-type specific distribution of Ub-ligases and ubiquitination-related genes, principal component analysis (PCA) and Uniform Manifold Approximation and Projection technique (UMAP) were used to analyze the Tabula Muris scRNA-seq data of murine colon followed by comparison with our clustering results. Results Our established clustering protocol, that incorporates the semantic biclustering algorithm, demonstrated the potential to reveal interesting expression patterns. In this manner, we statistically defined gene clusters consisting of the same genes involved in distinct regulatory pathways vs distinct genes playing roles in functionally similar signaling pathways. This allowed us to uncover the potentially redundant features of GIT-specific Ub-ligases and ubiquitination-related genes. Testing the statistically obtained results on the mouse model showed that genes clustered to the same ontology group simultaneously alter their expression pattern after induced epithelial damage, illustrating their complementary role during tissue regeneration. Conclusions An optimized semantic clustering protocol demonstrates the potential to reveal a readable and unique pattern in the expression profiling of GIT-specific Ub-ligases, exposing ontologically relevant gene clusters with potentially redundant features. This extends our knowledge of ontological relationships among Ub-ligases and ubiquitination-related genes, providing an alternative and more functional gene classification. In a similar way, semantic cluster analysis could be used for studding of other enzyme families, tissues and systems. Supplementary Information The online version contains supplementary material available at 10.1186/s12876-022-02265-2.
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Affiliation(s)
- Veronika Iatsiuk
- Laboratory of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Frantisek Malinka
- Laboratory of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.,Department of Computer Science, Czech Technical University in Prague, Prague, Czech Republic
| | - Marketa Pickova
- Laboratory of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jolana Tureckova
- Laboratory of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jiri Klema
- Department of Computer Science, Czech Technical University in Prague, Prague, Czech Republic
| | - Frantisek Spoutil
- Laboratory of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Vendula Novosadova
- Laboratory of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Prochazka
- Laboratory of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Radislav Sedlacek
- Laboratory of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.
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7
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Kovacech B, Fialova L, Filipcik P, Skrabana R, Zilkova M, Paulenka-Ivanovova N, Kovac A, Palova D, Rolkova GP, Tomkova K, Csokova NT, Markova K, Skrabanova M, Sinska K, Basheer N, Majerova P, Hanes J, Parrak V, Prcina M, Cehlar O, Cente M, Piestansky J, Fresser M, Novak M, Slavikova M, Borsova K, Cabanova V, Brejova B, Vinař T, Nosek J, Klempa B, Eyer L, Hönig V, Palus M, Ruzek D, Vyhlidalova T, Strakova P, Mrazkova B, Zudova D, Koubkova G, Novosadova V, Prochazka J, Sedlacek R, Zilka N, Kontsekova E. Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. EBioMedicine 2022; 76:103818. [PMID: 35078012 PMCID: PMC8782626 DOI: 10.1016/j.ebiom.2022.103818] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/05/2022] [Accepted: 01/05/2022] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The emergence of new SARS-CoV-2 variants of concern B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma) and B.1.617.2 (Delta) that harbor mutations in the viral S protein raised concern about activity of current vaccines and therapeutic antibodies. Independent studies have shown that mutant variants are partially or completely resistant against some of the therapeutic antibodies authorized for emergency use. METHODS We employed hybridoma technology, ELISA-based and cell-based S-ACE2 interaction assays combined with authentic virus neutralization assays to develop second-generation antibodies, which were specifically selected for their ability to neutralize the new variants of SARS-CoV-2. FINDINGS AX290 and AX677, two monoclonal antibodies with non-overlapping epitopes, exhibit subnanomolar or nanomolar affinities to the receptor binding domain of the viral Spike protein carrying amino acid substitutions N501Y, N439K, E484K, K417N, and a combination N501Y/E484K/K417N found in the circulating virus variants. The antibodies showed excellent neutralization of an authentic SARS-CoV-2 virus representing strains circulating in Europe in spring 2020 and also the variants of concern B.1.1.7 (Alpha), B.1.351 (Beta) and B.1.617.2 (Delta). In addition, AX677 is able to bind Omicron Spike protein just like the wild type Spike. The combination of the two antibodies prevented the appearance of escape mutations of the authentic SARS-CoV-2 virus. Prophylactic administration of AX290 and AX677, either individually or in combination, effectively reduced viral burden and inflammation in the lungs, and prevented disease in a mouse model of SARS-CoV-2 infection. INTERPRETATION The virus-neutralizing properties were fully reproduced in chimeric mouse-human versions of the antibodies, which may represent a promising tool for COVID-19 therapy. FUNDING The study was funded by AXON Neuroscience SE and AXON COVIDAX a.s.
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Affiliation(s)
- Branislav Kovacech
- AXON COVIDAX a. s.; Bratislava, 811 02, Slovakia; AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia.
| | - Lubica Fialova
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | - Peter Filipcik
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia; Institute of Neuroimmunology, Slovak Academy of Sciences; Bratislava, 845 10, Slovakia
| | | | - Monika Zilkova
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | | | - Andrej Kovac
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | - Denisa Palova
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | | | | | - Natalia Turic Csokova
- Institute of Neuroimmunology, Slovak Academy of Sciences; Bratislava, 845 10, Slovakia
| | - Karina Markova
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | - Michaela Skrabanova
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia; Institute of Neuroimmunology, Slovak Academy of Sciences; Bratislava, 845 10, Slovakia
| | - Kristina Sinska
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | - Neha Basheer
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | - Petra Majerova
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | - Jozef Hanes
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia; Institute of Neuroimmunology, Slovak Academy of Sciences; Bratislava, 845 10, Slovakia
| | - Vojtech Parrak
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | - Michal Prcina
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | - Ondrej Cehlar
- Institute of Neuroimmunology, Slovak Academy of Sciences; Bratislava, 845 10, Slovakia
| | - Martin Cente
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia; Institute of Neuroimmunology, Slovak Academy of Sciences; Bratislava, 845 10, Slovakia
| | | | - Michal Fresser
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | | | - Monika Slavikova
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences; Bratislava, 845 05, Slovakia
| | - Kristina Borsova
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences; Bratislava, 845 05, Slovakia; Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava; Bratislava, 842 15, Slovakia
| | - Viktoria Cabanova
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences; Bratislava, 845 05, Slovakia
| | - Bronislava Brejova
- Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava; Bratislava, 842 48, Slovakia
| | - Tomas Vinař
- Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava; Bratislava, 842 48, Slovakia
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava; Bratislava, 842 15, Slovakia
| | - Boris Klempa
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences; Bratislava, 845 05, Slovakia
| | - Ludek Eyer
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, CZ-37005 Ceske Budejovice, Czech Republic; Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic
| | - Vaclav Hönig
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, CZ-37005 Ceske Budejovice, Czech Republic; Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic
| | - Martin Palus
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, CZ-37005 Ceske Budejovice, Czech Republic; Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic
| | - Daniel Ruzek
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, CZ-37005 Ceske Budejovice, Czech Republic; Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
| | - Tereza Vyhlidalova
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, CZ-37005 Ceske Budejovice, Czech Republic
| | - Petra Strakova
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, CZ-37005 Ceske Budejovice, Czech Republic; Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic
| | - Blanka Mrazkova
- Czech Centre of Phenogenomics, Institute of Molecular Genetics, ASCR v.v.i, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Dagmar Zudova
- Czech Centre of Phenogenomics, Institute of Molecular Genetics, ASCR v.v.i, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Gizela Koubkova
- Czech Centre of Phenogenomics, Institute of Molecular Genetics, ASCR v.v.i, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Vendula Novosadova
- Czech Centre of Phenogenomics, Institute of Molecular Genetics, ASCR v.v.i, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Jan Prochazka
- Czech Centre of Phenogenomics, Institute of Molecular Genetics, ASCR v.v.i, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Radislav Sedlacek
- Czech Centre of Phenogenomics, Institute of Molecular Genetics, ASCR v.v.i, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Norbert Zilka
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia; Institute of Neuroimmunology, Slovak Academy of Sciences; Bratislava, 845 10, Slovakia.
| | - Eva Kontsekova
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia; Institute of Neuroimmunology, Slovak Academy of Sciences; Bratislava, 845 10, Slovakia
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8
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Gazdarica M, Noda J, Durydivka O, Novosadova V, Mackie K, Pin JP, Prezeau L, Blahos J. SGIP1 modulates kinetics and interactions of the cannabinoid receptor 1 and G protein-coupled receptor kinase 3 signalosome. J Neurochem 2021; 160:625-642. [PMID: 34970999 PMCID: PMC9306533 DOI: 10.1111/jnc.15569] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 12/23/2021] [Accepted: 12/23/2021] [Indexed: 12/05/2022]
Abstract
Cannabinoid receptor 1 (CB1R), a G protein‐coupled receptor, plays a fundamental role in synaptic plasticity. Abnormal activity and deregulation of CB1R signaling result in a broad spectrum of pathological conditions. CB1R signaling is regulated by receptor desensitization including phosphorylation of residues within the intracellular C terminus by G protein‐coupled receptor kinases (GRKs) that may lead to endocytosis. Furthermore, CB1R signaling is regulated by the protein Src homology 3‐domain growth factor receptor‐bound 2‐like (SGIP1) that hinders receptor internalization, while enhancing CB1R association with β‐arrestin. It has been postulated that phosphorylation of two clusters of serine/threonine residues, 425SMGDS429 and 460TMSVSTDTS468, within the CB1R C‐tail controls dynamics of the association between receptor and its interaction partners involved in desensitization. Several molecular determinants of these events are still not well understood. We hypothesized that the dynamics of these interactions are modulated by SGIP1. Using a panel of CB1Rs mutated in the aforementioned serine and threonine residues, together with an array of Bioluminescence energy transfer‐based (BRET) sensors, we discovered that GRK3 forms complexes with Gβγ subunits of G proteins that largely independent of GRK3’s interaction with CB1R. Furthermore, CB1R interacts only with activated GRK3. Interestingly, phosphorylation of two specific residues on CB1R triggers GRK3 dissociation from the desensitized receptor. SGIP1 increases the association of GRK3 with Gβγ subunits of G proteins, and with CB1R. Altogether, our data suggest that the CB1R signalosome complex is dynamically controlled by sequential phosphorylation of the receptor C‐tail and is also modified by SGIP1.
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Affiliation(s)
- Matej Gazdarica
- Institute of Molecular Genetics, Czech Academy of Science, Videnska 1083, 14220, Prague 4, Czech Republic.,Institut de Génomique Fonctionnelle, Université Montpellier 1 and 2, Montpellier, France
| | - Judith Noda
- Institute of Molecular Genetics, Czech Academy of Science, Videnska 1083, 14220, Prague 4, Czech Republic
| | - Oleh Durydivka
- Institute of Molecular Genetics, Czech Academy of Science, Videnska 1083, 14220, Prague 4, Czech Republic
| | - Vendula Novosadova
- The Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Ken Mackie
- Department of Psychological and Brain Sciences, Gill Center for Molecular Bioscience, Indiana University, 1101 E. 10th St, Bloomington, IN, USA, 47405
| | - Jean-Philippe Pin
- Institut de Génomique Fonctionnelle, Université Montpellier 1 and 2, Montpellier, France
| | - Laurent Prezeau
- Institut de Génomique Fonctionnelle, Université Montpellier 1 and 2, Montpellier, France
| | - Jaroslav Blahos
- Institute of Molecular Genetics, Czech Academy of Science, Videnska 1083, 14220, Prague 4, Czech Republic
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9
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Cervena K, Novosadova V, Pardini B, Naccarati A, Opattova A, Horak J, Vodenkova S, Buchler T, Skrobanek P, Levy M, Vodicka P, Vymetalkova V. Analysis of MicroRNA Expression Changes During the Course of Therapy In Rectal Cancer Patients. Front Oncol 2021; 11:702258. [PMID: 34540669 PMCID: PMC8444897 DOI: 10.3389/fonc.2021.702258] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/16/2021] [Indexed: 12/28/2022] Open
Abstract
MicroRNAs (miRNAs) regulate gene expression in a tissue-specific manner. However, little is known about the miRNA expression changes induced by the therapy in rectal cancer (RC) patients. We evaluated miRNA expression levels before and after therapy and identified specific miRNA signatures reflecting disease course and treatment responses of RC patients. First, miRNA expression levels were assessed by next-generation sequencing in two plasma samplings (at the time of diagnosis and a year after) from 20 RC patients. MiR-122-5p and miR-142-5p were classified for subsequent validation in plasma and plasma extracellular vesicles (EVs) on an independent group of RC patients (n=107). Due to the intrinsic high differences in miRNA expression levels between samplings, cancer-free individuals (n=51) were included in the validation phase to determine the baseline expression levels of the selected miRNAs. Expression levels of these miRNAs were significantly different between RC patients and controls (for all p <0.001). A year after diagnosis, miRNA expression profiles were significantly modified in patients responding to treatment and were no longer different from those measured in cancer-free individuals. On the other hand, patients not responding to therapy maintained low expression levels in their second sampling (miR-122-5p: plasma: p=0.05, EVs: p=0.007; miR-142-5p: plasma: p=0.008). Besides, overexpression of miR-122-5p and miR-142-5p in RC cell lines inhibited cell growth and survival. This study provides novel evidence that circulating miR-122-5p and miR-142-5p have a high potential for RC screening and early detection as well as for the assessment of patients' outcomes and the effectiveness of treatment schedule.
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Affiliation(s)
- Klara Cervena
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia.,Institute of Biology and Medical Genetics, 1stMedical Faculty, Charles University, Prague, Czechia
| | - Vendula Novosadova
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Prague, Czechia
| | - Barbara Pardini
- Molecular Genetics Epidemiology Unit, Italian Institute for Genomic Medicine, c/o IRCCS Candiolo,, Turin, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Alessio Naccarati
- Molecular Genetics Epidemiology Unit, Italian Institute for Genomic Medicine, c/o IRCCS Candiolo,, Turin, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Alena Opattova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia.,Institute of Biology and Medical Genetics, 1stMedical Faculty, Charles University, Prague, Czechia.,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
| | - Josef Horak
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia.,Third Faculty of Medicine, Charles University, Prague, Czechia
| | - Sona Vodenkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia.,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
| | - Tomas Buchler
- Department of Oncology, First Faculty of Medicine, Charles University and Thomayer Hospital, Prague, Czechia
| | - Pavel Skrobanek
- Department of Oncology, First Faculty of Medicine, Charles University and Thomayer Hospital, Prague, Czechia
| | - Miroslav Levy
- Department of Surgery, First Faculty of Medicine, Charles University and Thomayer Hospital, Prague, Czechia
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia.,Institute of Biology and Medical Genetics, 1stMedical Faculty, Charles University, Prague, Czechia.,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia.,Institute of Biology and Medical Genetics, 1stMedical Faculty, Charles University, Prague, Czechia.,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
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10
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Gresakova V, Novosadova V, Prochazkova M, Bhargava S, Jenickova I, Prochazka J, Sedlacek R. Retraction notice to "Fam208a orchestrates interaction protein network essential for early embryonic development and cell division" [Exp. Cell Res. 382 (1) (2019) 111437]. Exp Cell Res 2021; 405:112718. [PMID: 34272044 DOI: 10.1016/j.yexcr.2021.112718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Veronika Gresakova
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the ASCR, v.v.i, Průmyslova 595, 252 50, Vestec, Czech Republic; Palacky University in Olomouc, Faculty of Medicine and Dentistry, Hněvotínská, 3775 15, Olomouc, Czech Republic
| | - Vendula Novosadova
- Czech Centre of Phenogenomics, Institute of Molecular Genetics, ASCR v.v.i, Průmyslova 595, 252 50, Vestec, Czech Republic
| | - Michaela Prochazkova
- Czech Centre of Phenogenomics, Institute of Molecular Genetics, ASCR v.v.i, Průmyslova 595, 252 50, Vestec, Czech Republic
| | - Shohag Bhargava
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the ASCR, v.v.i, Průmyslova 595, 252 50, Vestec, Czech Republic
| | - Irena Jenickova
- Czech Centre of Phenogenomics, Institute of Molecular Genetics, ASCR v.v.i, Průmyslova 595, 252 50, Vestec, Czech Republic
| | - Jan Prochazka
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the ASCR, v.v.i, Průmyslova 595, 252 50, Vestec, Czech Republic; Czech Centre of Phenogenomics, Institute of Molecular Genetics, ASCR v.v.i, Průmyslova 595, 252 50, Vestec, Czech Republic.
| | - Radislav Sedlacek
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the ASCR, v.v.i, Průmyslova 595, 252 50, Vestec, Czech Republic; Czech Centre of Phenogenomics, Institute of Molecular Genetics, ASCR v.v.i, Průmyslova 595, 252 50, Vestec, Czech Republic.
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11
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Gresakova V, Novosadova V, Prochazkova M, Prochazka J, Sedlacek R. Dual role of Fam208a during zygotic cleavage and early embryonic development. Exp Cell Res 2021; 406:112723. [PMID: 34216590 DOI: 10.1016/j.yexcr.2021.112723] [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: 06/11/2021] [Accepted: 06/27/2021] [Indexed: 11/15/2022]
Abstract
Maintenance of genome stability is essential for every living cell as genetic information is repeatedly challenged during DNA replication in each cell division event. Errors, defects, delays, and mistakes that arise during mitosis or meiosis lead to an activation of DNA repair processes and in case of their failure, programmed cell death, i.e. apoptosis, could be initiated. Fam208a is a protein whose importance in heterochromatin maintenance has been described recently. In this work, we describe the crucial role of Fam208a in sustaining genome stability during cellular division. The targeted depletion of Fam208a in mice using CRISPR/Cas9 led to embryonic lethality before E12.5. We also used the siRNA approach to downregulate Fam208a in zygotes to avoid the influence of maternal RNA in the early stages of development. This early downregulation increased arresting of the embryonal development at the two-cell stage and the occurrence of multipolar spindles formation. To investigate this further, we used the yeast two-hybrid (Y2H) system and identified new putative interaction partners Gpsm2, Svil, and Itgb3bp. Their co-expression with Fam208a was assessed by RT-qPCR profiling and in situ hybridization [1] in multiple murine tissues. Based on these results we proposed that Fam208a functions within the HUSH complex by interaction with Mphosph8 as these proteins are not only able to physically interact but also co-localise. We are bringing new evidence that Fam208a is a multi-interacting protein affecting genome stability on the cell division level at the earliest stages of development and by interaction with methylation complex in adult tissues. In addition to its epigenetic functions, Fam208a appears to have an important role in the zygotic division, possibly via interaction with newly identified putative partners Gpsm2, Svil, and Itgb3bp.
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Affiliation(s)
- Veronika Gresakova
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, Prumyslova 595, 252 50, Vestec, Czech Republic; Palacky University in Olomouc, Faculty of Medicine and Dentistry, Hněvotínská 3, 775 15, Olomouc, Czech Republic.
| | - Vendula Novosadova
- Czech Centre of Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prumyslova 595, 252 50, Vestec, Czech Republic.
| | - Michaela Prochazkova
- Czech Centre of Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prumyslova 595, 252 50, Vestec, Czech Republic.
| | - Jan Prochazka
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, Prumyslova 595, 252 50, Vestec, Czech Republic; Czech Centre of Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prumyslova 595, 252 50, Vestec, Czech Republic.
| | - Radislav Sedlacek
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, Prumyslova 595, 252 50, Vestec, Czech Republic; Czech Centre of Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prumyslova 595, 252 50, Vestec, Czech Republic.
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12
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Cacheiro P, Muñoz-Fuentes V, Murray SA, Dickinson ME, Bucan M, Nutter LMJ, Peterson KA, Haselimashhadi H, Flenniken AM, Morgan H, Westerberg H, Konopka T, Hsu CW, Christiansen A, Lanza DG, Beaudet AL, Heaney JD, Fuchs H, Gailus-Durner V, Sorg T, Prochazka J, Novosadova V, Lelliott CJ, Wardle-Jones H, Wells S, Teboul L, Cater H, Stewart M, Hough T, Wurst W, Sedlacek R, Adams DJ, Seavitt JR, Tocchini-Valentini G, Mammano F, Braun RE, McKerlie C, Herault Y, de Angelis MH, Mallon AM, Lloyd KCK, Brown SDM, Parkinson H, Meehan TF, Smedley D. Human and mouse essentiality screens as a resource for disease gene discovery. Nat Commun 2020; 11:655. [PMID: 32005800 PMCID: PMC6994715 DOI: 10.1038/s41467-020-14284-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [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: 05/23/2019] [Accepted: 12/12/2019] [Indexed: 12/31/2022] Open
Abstract
The identification of causal variants in sequencing studies remains a considerable challenge that can be partially addressed by new gene-specific knowledge. Here, we integrate measures of how essential a gene is to supporting life, as inferred from viability and phenotyping screens performed on knockout mice by the International Mouse Phenotyping Consortium and essentiality screens carried out on human cell lines. We propose a cross-species gene classification across the Full Spectrum of Intolerance to Loss-of-function (FUSIL) and demonstrate that genes in five mutually exclusive FUSIL categories have differing biological properties. Most notably, Mendelian disease genes, particularly those associated with developmental disorders, are highly overrepresented among genes non-essential for cell survival but required for organism development. After screening developmental disorder cases from three independent disease sequencing consortia, we identify potentially pathogenic variants in genes not previously associated with rare diseases. We therefore propose FUSIL as an efficient approach for disease gene discovery.
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Grants
- UM1 HG008900 NHGRI NIH HHS
- UM1 HG006504 NHGRI NIH HHS
- MC_UP_1502/1 Medical Research Council
- UM1 HG006542 NHGRI NIH HHS
- UM1 OD023221 NIH HHS
- MC_U142684171 Medical Research Council
- MR/S006753/1 Medical Research Council
- UM1 HG006370 NHGRI NIH HHS
- UM1 HG006493 NHGRI NIH HHS
- U54 HG006370 NHGRI NIH HHS
- U54 HG006364 NHGRI NIH HHS
- MC_U142684172 Medical Research Council
- UM1 HG006348 NHGRI NIH HHS
- U42 OD011174 NIH HHS
- U42 OD011175 NIH HHS
- Wellcome Trust
- This work was supported by NIH grant U54 HG006370. IMPC-related mouse production and phenotyping was funded by the Government of Canada through Genome Canada and Ontario Genomics (OGI-051) for NorCOMM2 (C.M.) and the National Institutes of Health and OD, NCRR, NIDDK and NHLBI for KOMP and KOMP2 Projects U42 OD011175 and UM1OD023221 (C.M., K.C.K.L), Infrafrontier grant 01KX1012, EU Horizon2020: IPAD-MD funding 653961 (M.H.d.A); EUCOMM: LSHM-CT-2005-018931, EUCOMMTOOLS: FP7-HEALTH-F4-2010-261492 (W.G.W). UM1 HG006348; U42 OD011174; U54 HG005348 (A.L.B), NIH U54706HG006364 (A.L.B). Wellcome Trust grants WT098051 and WT206194 (D.A). The French National Centre for Scientific Research (CNRS), the French National Institute of Health and Medical Research (INSERM), the University of Strasbourg and the “Centre Europeen de Recherche en Biomedecine”, and the French state funds through the “Agence Nationale de la Recherche” under the frame programme Investissements d’Avenir labelled (ANR-10-IDEX-0002-02, ANR-10-LABX-0030-INRT, ANR-10-INBS-07 PHENOMIN (J.H.). This research was made possible through access to the data and findings generated by the 100,000 Genomes Project. The 100,000 Genomes Project is managed by Genomics England Limited (a wholly owned company of the Department of Health). The 100,000 Genomes Project is funded by the National Institute for Health Research and NHS England. The Wellcome Trust, Cancer Research UK and the Medical Research Council have also funded research infrastructure. The 100,000 Genomes Project uses data provided by patients and collected by the National Health Service as part of their care and support. We are also grateful for the data access provided by the DDD and CMG projects. The DDD study presents independent research commissioned by the Health Innovation Challenge Fund [grant number HICF-1009-003], a parallel funding partnership between Wellcome and the Department of Health, and the Wellcome Sanger Institute [grant number WT098051]. The views expressed in this publication are those of the author(s) and not necessarily those of Wellcome or the Department of Health. The study has UK Research Ethics Committee approval (10/H0305/83, granted by the Cambridge South REC, and GEN/284/12 granted by the Republic of Ireland REC). The research team acknowledges the support of the National Institute for Health Research, through the Comprehensive Clinical Research Network. The Centers for Mendelian Genomics are funded by the National Human Genome Research Institute, the National Heart, Lung, and Blood Institute, and the National Eye Institute. Broad Institute (UM1 HG008900), Johns Hopkins University School of Medicine/Baylor College of Medicine (UM1 HG006542), University of Washington (UM1 HG006493), Yale University (UM1 HG006504).
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Affiliation(s)
- Pilar Cacheiro
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Violeta Muñoz-Fuentes
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | - Mary E Dickinson
- Departments of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Maja Bucan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, The Hospital for Sick Children, Toronto, ON, M5T 3H7, Canada
| | | | - Hamed Haselimashhadi
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Ann M Flenniken
- The Centre for Phenogenomics, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5T 3H7, Canada
| | - Hugh Morgan
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Henrik Westerberg
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Tomasz Konopka
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Chih-Wei Hsu
- Departments of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Audrey Christiansen
- Departments of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Denise G Lanza
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Arthur L Beaudet
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jason D Heaney
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Tania Sorg
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404, Illkirch, France
| | - Jan Prochazka
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, 252 50, Prague, Czech Republic
| | - Vendula Novosadova
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, 252 50, Prague, Czech Republic
| | | | | | - Sara Wells
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Lydia Teboul
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Heather Cater
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Michelle Stewart
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Tertius Hough
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764, Neuherberg, Germany
- Department of Developmental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85764, Neuherberg, Germany
- Deutsches Institut für Neurodegenerative Erkrankungen (DZNE) Site Munich, Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, 80336, Munich, Germany
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, 252 50, Prague, Czech Republic
| | - David J Adams
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - John R Seavitt
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Glauco Tocchini-Valentini
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, 00015, Monterotondo Scalo, Italy
| | - Fabio Mammano
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, 00015, Monterotondo Scalo, Italy
| | | | - Colin McKerlie
- The Centre for Phenogenomics, The Hospital for Sick Children, Toronto, ON, M5T 3H7, Canada
- Translational Medicine, The Hospital for Sick Children, Toronto, ON, M5T 3H7, Canada
| | - Yann Herault
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique, Biologie Moléculaire et Cellulaire, Institut Clinique de la Souris, IGBMC, PHENOMIN-ICS, 67404, Illkirch, France
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
- Department of Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354, Freising-Weihenstephan, Germany
- German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany
| | - Ann-Marie Mallon
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - K C Kent Lloyd
- Mouse Biology Program, University of California, Davis, CA, 95618, USA
| | - Steve D M Brown
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Terrence F Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Damian Smedley
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK.
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13
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Szczerkowska KI, Petrezselyova S, Lindovsky J, Palkova M, Dvorak J, Makovicky P, Fang M, Jiang C, Chen L, Shi M, Liu X, Zhang J, Kubik-Zahorodna A, Schuster B, Beck IM, Novosadova V, Prochazka J, Sedlacek R. Myopia disease mouse models: a missense point mutation (S673G) and a protein-truncating mutation of the Zfp644 mimic human disease phenotype. Cell Biosci 2019; 9:21. [PMID: 30834109 PMCID: PMC6385473 DOI: 10.1186/s13578-019-0280-4] [Citation(s) in RCA: 4] [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: 01/18/2019] [Accepted: 02/01/2019] [Indexed: 12/24/2022] Open
Abstract
Zinc finger 644 (Zfp644 in mouse, ZNF644 in human) gene is a transcription factor whose mutation S672G is considered a potential genetic factor of inherited high myopia. ZNF644 interacts with G9a/GLP complex, which functions as a H3K9 methyltransferase to silence transcription. In this study, we generated mouse models to unravel the mechanisms leading to symptoms associated with high myopia. Employing TALEN technology, two mice mutants were generated, either with the disease-carrying mutation (Zfp644S673G) or with a truncated form of Zfp644 (Zfp644Δ8). Eye morphology and visual functions were analysed in both mutants, revealing a significant difference in a vitreous chamber depth and lens diameter, however the physiological function of retina was preserved as found under the high-myopia conditions. Our findings prove that ZNF644/Zfp644 is involved in the development of high-myopia, indicating that mutations such as, Zfp644S673G and Zfp644Δ8 are causative for changes connected with the disease. The developed models represent a valuable tool to investigate the molecular basis of myopia pathogenesis and its potential treatment.
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Affiliation(s)
- Katarzyna I Szczerkowska
- 1Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics CAS, Prumyslova 595, Vestec, 252 50 Prague, Czech Republic
| | - Silvia Petrezselyova
- 1Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics CAS, Prumyslova 595, Vestec, 252 50 Prague, Czech Republic.,2Czech Centre for Phenogenomics, Institute of Molecular Genetics CAS, Prague, Czech Republic
| | - Jiri Lindovsky
- 2Czech Centre for Phenogenomics, Institute of Molecular Genetics CAS, Prague, Czech Republic
| | - Marcela Palkova
- 2Czech Centre for Phenogenomics, Institute of Molecular Genetics CAS, Prague, Czech Republic
| | - Jan Dvorak
- 1Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics CAS, Prumyslova 595, Vestec, 252 50 Prague, Czech Republic
| | - Peter Makovicky
- 2Czech Centre for Phenogenomics, Institute of Molecular Genetics CAS, Prague, Czech Republic
| | - Mingyan Fang
- 3Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden.,4BGI-Shenzhen, Shenzhen, 518083 China.,5China National GeneBank, BGI-Shenzhen, Shenzhen, 518120 China
| | - Chongyi Jiang
- 4BGI-Shenzhen, Shenzhen, 518083 China.,5China National GeneBank, BGI-Shenzhen, Shenzhen, 518120 China
| | - Lingyan Chen
- 4BGI-Shenzhen, Shenzhen, 518083 China.,5China National GeneBank, BGI-Shenzhen, Shenzhen, 518120 China
| | - Mingming Shi
- 4BGI-Shenzhen, Shenzhen, 518083 China.,5China National GeneBank, BGI-Shenzhen, Shenzhen, 518120 China
| | - Xiao Liu
- 4BGI-Shenzhen, Shenzhen, 518083 China.,5China National GeneBank, BGI-Shenzhen, Shenzhen, 518120 China
| | - Jianguo Zhang
- 4BGI-Shenzhen, Shenzhen, 518083 China.,5China National GeneBank, BGI-Shenzhen, Shenzhen, 518120 China
| | | | - Bjoern Schuster
- 2Czech Centre for Phenogenomics, Institute of Molecular Genetics CAS, Prague, Czech Republic
| | - Inken M Beck
- 2Czech Centre for Phenogenomics, Institute of Molecular Genetics CAS, Prague, Czech Republic.,6Animal Research Center, Ulm University, Ulm, Germany
| | - Vendula Novosadova
- 2Czech Centre for Phenogenomics, Institute of Molecular Genetics CAS, Prague, Czech Republic
| | - Jan Prochazka
- 1Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics CAS, Prumyslova 595, Vestec, 252 50 Prague, Czech Republic.,2Czech Centre for Phenogenomics, Institute of Molecular Genetics CAS, Prague, Czech Republic
| | - Radislav Sedlacek
- 1Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics CAS, Prumyslova 595, Vestec, 252 50 Prague, Czech Republic.,2Czech Centre for Phenogenomics, Institute of Molecular Genetics CAS, Prague, Czech Republic
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14
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Kral J, Korenkova V, Novosadova V, Langerova L, Schneiderova M, Liska V, Levy M, Veskrnova V, Spicak J, Opattova A, Jiraskova K, Vymetalkova V, Vodicka P, Slyskova J. Expression profile of miR-17/92 cluster is predictive of treatment response in rectal cancer. Carcinogenesis 2018; 39:1359-1367. [DOI: 10.1093/carcin/bgy100] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/05/2018] [Indexed: 12/11/2022] Open
Affiliation(s)
- Jan Kral
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Gastroenterology and Hepatology, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Vlasta Korenkova
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Vendula Novosadova
- Laboratory of Transgenic Models of Diseases, Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Division BIOCEV, Vestec, Czech Republic
| | - Lucie Langerova
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czech Republic
| | | | - Vaclav Liska
- Department of Surgery, Teaching Hospital and Medical School of Charles University, Pilsen, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University in Prague, Pilsen, Czech Republic
| | - Miroslav Levy
- Department of Surgery, First Faculty of Medicine, Charles University and Thomayer Hospital, Prague, Czech Republic
| | - Veronika Veskrnova
- Department of Oncology, First Faculty of Medicine, Charles University and Thomayer Hospital, Prague, Czech Republic
| | - Julius Spicak
- Department of Gastroenterology and Hepatology, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Alena Opattova
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Czech Republic
| | - Katerina Jiraskova
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Czech Republic
| | - Veronika Vymetalkova
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Czech Republic
| | - Pavel Vodicka
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University in Prague, Pilsen, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Czech Republic
| | - Jana Slyskova
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
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15
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Gorges TM, Kuske A, Röck K, Mauermann O, Müller V, Peine S, Verpoort K, Novosadova V, Kubista M, Riethdorf S, Pantel K. Accession of Tumor Heterogeneity by Multiplex Transcriptome Profiling of Single Circulating Tumor Cells. Clin Chem 2016; 62:1504-1515. [DOI: 10.1373/clinchem.2016.260299] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 08/15/2016] [Indexed: 01/06/2023]
Abstract
Abstract
BACKGROUND
Transcriptome analysis of circulating tumor cells (CTCs) holds great promise to unravel the biology of cancer cell dissemination and identify expressed genes and signaling pathways relevant to therapeutic interventions.
METHODS
CTCs were enriched based on their EpCAM expression (CellSearch®) or by size and deformability (ParsortixTM), identified by EpCAM and/or pan-keratin–specific antibodies, and isolated for single cell multiplex RNA profiling.
RESULTS
Distinct breast and prostate CTC expression signatures could be discriminated from RNA profiles of leukocytes. Some CTCs positive for epithelial transcripts (EpCAM and KRT19) also coexpressed leukocyte/mesenchymal associated markers (PTPRC and VIM). Additional subsets of CTCs within individual patients were characterized by divergent expression of genes involved in epithelial–mesenchymal transition (e.g., CDH2, MMPs, VIM, or ZEB1 and 2), DNA repair (RAD51), resistance to cancer therapy (e.g., AR, AR-V7, ERBB2, EGFR), cancer stemness (e.g., CD24 and CD44), activated signaling pathways involved in tumor progression (e.g., PIK3CA and MTOR) or cross talks between tumors and immune cells (e.g., CCL4, CXCL2, CXCL9, IL15, IL1B, or IL8).
CONCLUSIONS
Multimarker RNA profiling of single CTCs reveals distinct CTC subsets and provides important insights into gene regulatory networks relevant for cancer progression and therapy.
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Affiliation(s)
- Tobias M Gorges
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andra Kuske
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katharina Röck
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Oliver Mauermann
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Volkmar Müller
- Department of Gynecology, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Sven Peine
- Department of Transfusion Medicine, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Karl Verpoort
- Practice for Haematology and Oncology, Hamburg, Germany
| | - Vendula Novosadova
- Department of Biotechnology, Czech Academy of Sciences, Prague, Czech Republic
| | - Mikael Kubista
- Department of Biotechnology, Czech Academy of Sciences, Prague, Czech Republic
- TATAA Biocenter, Gothenburg, Sweden
| | - Sabine Riethdorf
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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16
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Bredemeier M, Edimiris P, Mach P, Kubista M, Sjoback R, Jindrichova M, Rohlova E, Novosadova V, Kolostova K, Hauch S, Aktas B, Tewes M, Kimmig R, Kasimir-Bauer S. Abstract 502: Gene expression signatures in circulating tumor cells are prognostic for metastatic lesions in breast cancer patients and correlate with response to therapy. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-502] [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] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Circulating tumor cells (CTC) are discussed to be an ideal surrogate marker to monitor disease progression in metastatic breast cancer (MBC). Besides CTC characterization for targeted therapies, it would also be desirable to know where these cells derive from or to which organ site they are going to. Here we investigated whether it is possible to predict the origin of metastatic lesion based on the expression of 46 genes in CTC of MBC patients (pts).
Materials and Methods: 2×5 ml blood of 45 MBC pts and 20 healthy controls was collected at the time of disease progression (T0) and at two consecutive clinical staging (T1 and T2) for the detection of CTC applying immunomagnetic enrichment using the AdnaTest EMT-2/Stem Cell Select (QIAGEN Hannover GmbH, Germany). Pts were grouped a) into overall responders (OR) and overall non-responders (ONR), thus responding or not responding at T1 and T2 and b) according to sites of metastasis. PCR assays, targeting 46 transcripts and reference markers were used for a workflow based on pre-amplification and high throughput profiling (each samples in duplicates) with the full set of markers including also ValidPrime to correct for genomic background and InterPlate Calibrator to even out variations between runs. Data were analyzed using GenEx (MultiD, Sweden) and SAS. qPCR as well as technical reads were normalized using several normalization strategies.
Results: The multidrug resistant protein gene MRP1 was significantly differently expressed if OR and ONR groups were compared. In the following order of significance, VEGFR1, Keratin (KRT) 19, EGFR, MET1, ALDH, progesterone receptor (PR), UPA, Cathepsin D, KIT1 and Ki67 were differentially expressed in CTC of pts who had already developed liver metastasis as compared to pts without liver metastasis. Interestingly, a small group of pts, developing liver metastases in the course of disease, showed the estrogen receptor (ER), PR, HER2, mammaglobin, KRT19 on a significantly lower level as compared to the other pts. Similarly, once CTC were ER and PR positive, the probability of bone metastasis development decreased.
Conclusion: Our preliminary results indicate that the development of metastatic lesions is associated with site-specific CTC. Thus, besides using CTC as a monitoring tool to guide therapy, they might also indicate the site of metastasis which will allow a more precise decision concerning treatment strategy.
Citation Format: Maren Bredemeier, Philippos Edimiris, Pawel Mach, Mikael Kubista, Robert Sjoback, Marie Jindrichova, Eva Rohlova, Vendula Novosadova, Katarina Kolostova, Siegfried Hauch, Bahriye Aktas, Mitra Tewes, Rainer Kimmig, Sabine Kasimir-Bauer. Gene expression signatures in circulating tumor cells are prognostic for metastatic lesions in breast cancer patients and correlate with response to therapy. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 502.
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Affiliation(s)
- Maren Bredemeier
- 1University Hospital Essen, Department of Gynecology and Obstetrics, Essen, Germany
| | - Philippos Edimiris
- 1University Hospital Essen, Department of Gynecology and Obstetrics, Essen, Germany
| | - Pawel Mach
- 1University Hospital Essen, Department of Gynecology and Obstetrics, Essen, Germany
| | | | | | | | | | | | - Katarina Kolostova
- 4University Hospital Kralovske Vinohrady, Department of Laboratory Genetics, Prague, Czech Republic
| | | | - Bahriye Aktas
- 1University Hospital Essen, Department of Gynecology and Obstetrics, Essen, Germany
| | - Mitra Tewes
- 6University Hospital Essen, Department of Medical Oncology, Essen, Germany
| | - Rainer Kimmig
- 1University Hospital Essen, Department of Gynecology and Obstetrics, Essen, Germany
| | - Sabine Kasimir-Bauer
- 1University Hospital Essen, Department of Gynecology and Obstetrics, Essen, Germany
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17
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Korenkova V, Slyskova J, Novosadova V, Pizzamiglio S, Langerova L, Bjorkman J, Vycital O, Liska V, Levy M, Veskrna K, Vodicka P, Vodickova L, Kubista M, Verderio P. The focus on sample quality: Influence of colon tissue collection on reliability of qPCR data. Sci Rep 2016; 6:29023. [PMID: 27383461 PMCID: PMC4935944 DOI: 10.1038/srep29023] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/14/2016] [Indexed: 01/12/2023] Open
Abstract
Successful molecular analyses of human solid tissues require intact biological material with well-preserved nucleic acids, proteins, and other cell structures. Pre-analytical handling, comprising of the collection of material at the operating theatre, is among the first critical steps that influence sample quality. The aim of this study was to compare the experimental outcomes obtained from samples collected and stored by the conventional means of snap freezing and by PAXgene Tissue System (Qiagen). These approaches were evaluated by measuring rRNA and mRNA integrity of the samples (RNA Quality Indicator and Differential Amplification Method) and by gene expression profiling. The collection procedures of the biological material were implemented in two hospitals during colon cancer surgery in order to identify the impact of the collection method on the experimental outcome. Our study shows that the pre-analytical sample handling has a significant effect on the quality of RNA and on the variability of qPCR data. PAXgene collection mode proved to be more easily implemented in the operating room and moreover the quality of RNA obtained from human colon tissues by this method is superior to the one obtained by snap freezing.
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Affiliation(s)
- Vlasta Korenkova
- Institute of Biotechnology, BIOCEV Centre, Czech Academy of Sciences, Průmyslová 595, 252 42, Vestec u Prahy, Czech Republic
| | - Jana Slyskova
- Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czech Republic
| | - Vendula Novosadova
- Institute of Biotechnology, BIOCEV Centre, Czech Academy of Sciences, Průmyslová 595, 252 42, Vestec u Prahy, Czech Republic
| | - Sara Pizzamiglio
- Unit of Medical Statistics, Biometry and Bioinformatics, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Nazionale dei Tumori, Milan, Italy
| | - Lucie Langerova
- Institute of Biotechnology, BIOCEV Centre, Czech Academy of Sciences, Průmyslová 595, 252 42, Vestec u Prahy, Czech Republic
| | | | - Ondrej Vycital
- Deparment of Surgery, Teaching Hospital and Medical School Pilsen, Charles University in Prague, Pilsen, Czech Republic.,Biomedical Centre, Medical School Pilsen, Charles University in Prague, Pilsen, Czech Republic
| | - Vaclav Liska
- Deparment of Surgery, Teaching Hospital and Medical School Pilsen, Charles University in Prague, Pilsen, Czech Republic.,Biomedical Centre, Medical School Pilsen, Charles University in Prague, Pilsen, Czech Republic
| | - Miroslav Levy
- Surgical Department, Thomayer Hospital, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Karel Veskrna
- Surgical Department, Thomayer Hospital, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Pavel Vodicka
- Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czech Republic.,Biomedical Centre, Medical School Pilsen, Charles University in Prague, Pilsen, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Ludmila Vodickova
- Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czech Republic.,Biomedical Centre, Medical School Pilsen, Charles University in Prague, Pilsen, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Mikael Kubista
- Institute of Biotechnology, BIOCEV Centre, Czech Academy of Sciences, Průmyslová 595, 252 42, Vestec u Prahy, Czech Republic.,TATAA Biocenter AB, Göteborg, Sweden
| | - Paolo Verderio
- Unit of Medical Statistics, Biometry and Bioinformatics, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Nazionale dei Tumori, Milan, Italy
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18
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Dzamba D, Honsa P, Valny M, Kriska J, Valihrach L, Novosadova V, Kubista M, Anderova M. Quantitative Analysis of Glutamate Receptors in Glial Cells from the Cortex of GFAP/EGFP Mice Following Ischemic Injury: Focus on NMDA Receptors. Cell Mol Neurobiol 2015; 35:1187-202. [PMID: 25994914 DOI: 10.1007/s10571-015-0212-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [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: 04/21/2015] [Accepted: 05/15/2015] [Indexed: 12/21/2022]
Abstract
Cortical glial cells contain both ionotropic and metabotropic glutamate receptors. Despite several efforts, a comprehensive analysis of the entire family of glutamate receptors and their subunits present in glial cells is still missing. Here, we provide an overall picture of the gene expression of ionotropic (AMPA, kainate, NMDA) and the main metabotropic glutamate receptors in cortical glial cells isolated from GFAP/EGFP mice before and after focal cerebral ischemia. Employing single-cell RT-qPCR, we detected the expression of genes encoding subunits of glutamate receptors in GFAP/EGFP-positive (GFAP/EGFP(+)) glial cells in the cortex of young adult mice. Most of the analyzed cells expressed mRNA for glutamate receptor subunits, the expression of which, in most cases, even increased after ischemic injury. Data analyses disclosed several classes of GFAP/EGFP(+) glial cells with respect to glutamate receptors and revealed in what manner their expression correlates with the expression of glial markers prior to and after ischemia. Furthermore, we also examined the protein expression and functional significance of NMDA receptors in glial cells. Immunohistochemical analyses of all seven NMDA receptor subunits provided direct evidence that the GluN3A subunit is present in GFAP/EGFP(+) glial cells and that its expression is increased after ischemia. In situ and in vitro Ca(2+) imaging revealed that Ca(2+) elevations evoked by the application of NMDA were diminished in GFAP/EGFP(+) glial cells following ischemia. Our results provide a comprehensive description of glutamate receptors in cortical GFAP/EGFP(+) glial cells and may serve as a basis for further research on glial cell physiology and pathophysiology.
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Affiliation(s)
- David Dzamba
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, Czech Republic.,2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Pavel Honsa
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, Czech Republic
| | - Martin Valny
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, Czech Republic
| | - Jan Kriska
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, Czech Republic.,2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Lukas Valihrach
- Laboratory of Gene Expression, Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Vendula Novosadova
- Laboratory of Gene Expression, Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Mikael Kubista
- Laboratory of Gene Expression, Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Miroslava Anderova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, Czech Republic.
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19
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Svec D, Tichopad A, Novosadova V, Pfaffl MW, Kubista M. How good is a PCR efficiency estimate: Recommendations for precise and robust qPCR efficiency assessments. Biomol Detect Quantif 2015; 3:9-16. [PMID: 27077029 PMCID: PMC4822216 DOI: 10.1016/j.bdq.2015.01.005] [Citation(s) in RCA: 308] [Impact Index Per Article: 34.2] [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: 10/25/2014] [Revised: 01/24/2015] [Accepted: 01/28/2015] [Indexed: 01/22/2023]
Abstract
We have examined the imprecision in the estimation of PCR efficiency by means of standard curves based on strategic experimental design with large number of technical replicates. In particular, how robust this estimation is in terms of a commonly varying factors: the instrument used, the number of technical replicates performed and the effect of the volume transferred throughout the dilution series. We used six different qPCR instruments, we performed 1–16 qPCR replicates per concentration and we tested 2–10 μl volume of analyte transferred, respectively. We find that the estimated PCR efficiency varies significantly across different instruments. Using a Monte Carlo approach, we find the uncertainty in the PCR efficiency estimation may be as large as 42.5% (95% CI) if standard curve with only one qPCR replicate is used in 16 different plates. Based on our investigation we propose recommendations for the precise estimation of PCR efficiency: (1) one robust standard curve with at least 3–4 qPCR replicates at each concentration shall be generated, (2) the efficiency is instrument dependent, but reproducibly stable on one platform, and (3) using a larger volume when constructing serial dilution series reduces sampling error and enables calibration across a wider dynamic range.
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Key Words
- ANCOVA, analysis of covariance
- Amplification efficiency
- CLSI, Clinical and Laboratory Standards Institute
- Cq, cycle of quantification
- Dilution series
- E, PCR efficiency
- EPA, Environmental protection agency
- FDA, food and Drug Administration
- GMO, genetically modified organism
- IEC, International Electrotechnical Commission
- ISO, International Organization for Standardization
- MIQE, minimum information for publication of quantitative real-time PCR experiments
- NTC, no template control
- RIN, RNA Integrity Number
- RT-qPCR, reverse transcription-quantitative polymerase chain reaction
- Real-time quantitative PCR
- Standard curve
- qPCR
- qPCR assay validation
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Affiliation(s)
- David Svec
- Institute of Biotechnology, Academy of Science of the Czech Republic, Prague, Czech Republic; TATAA Biocenter, Gothenburg, Sweden
| | - Ales Tichopad
- Faculty of Medicine Pilsen, Charles University, Pilsen, Czech Republic
| | - Vendula Novosadova
- Institute of Biotechnology, Academy of Science of the Czech Republic, Prague, Czech Republic; TATAA Biocenter, Gothenburg, Sweden
| | - Michael W Pfaffl
- Physiology Weihenstephan, TUM - Technische Universität München, Freising, Germany
| | - Mikael Kubista
- Institute of Biotechnology, Academy of Science of the Czech Republic, Prague, Czech Republic; TATAA Biocenter, Gothenburg, Sweden
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20
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Anderova M, Benesova J, Mikesova M, Dzamba D, Honsa P, Kriska J, Butenko O, Novosadova V, Valihrach L, Kubista M, Dmytrenko L, Cicanic M, Vargova L. Altered astrocytic swelling in the cortex of α-syntrophin-negative GFAP/EGFP mice. PLoS One 2014; 9:e113444. [PMID: 25426721 PMCID: PMC4245134 DOI: 10.1371/journal.pone.0113444] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [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: 07/09/2014] [Accepted: 10/24/2014] [Indexed: 11/30/2022] Open
Abstract
Brain edema accompanying ischemic or traumatic brain injuries, originates from a disruption of ionic/neurotransmitter homeostasis that leads to accumulation of K+ and glutamate in the extracellular space. Their increased uptake, predominantly provided by astrocytes, is associated with water influx via aquaporin-4 (AQP4). As the removal of perivascular AQP4 via the deletion of α-syntrophin was shown to delay edema formation and K+ clearance, we aimed to elucidate the impact of α-syntrophin knockout on volume changes in individual astrocytes in situ evoked by pathological stimuli using three dimensional confocal morphometry and changes in the extracellular space volume fraction (α) in situ and in vivo in the mouse cortex employing the real-time iontophoretic method. RT-qPCR profiling was used to reveal possible differences in the expression of ion channels/transporters that participate in maintaining ionic/neurotransmitter homeostasis. To visualize individual astrocytes in mice lacking α-syntrophin we crossbred GFAP/EGFP mice, in which the astrocytes are labeled by the enhanced green fluorescent protein under the human glial fibrillary acidic protein promoter, with α-syntrophin knockout mice. Three-dimensional confocal morphometry revealed that α-syntrophin deletion results in significantly smaller astrocyte swelling when induced by severe hypoosmotic stress, oxygen glucose deprivation (OGD) or 50 mM K+. As for the mild stimuli, such as mild hypoosmotic or hyperosmotic stress or 10 mM K+, α-syntrophin deletion had no effect on astrocyte swelling. Similarly, evaluation of relative α changes showed a significantly smaller decrease in α-syntrophin knockout mice only during severe pathological conditions, but not during mild stimuli. In summary, the deletion of α-syntrophin markedly alters astrocyte swelling during severe hypoosmotic stress, OGD or high K+.
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Affiliation(s)
- Miroslava Anderova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Department of Neuroscience, Charles University, 2nd Faculty of Medicine, Prague, Czech Republic
- * E-mail:
| | - Jana Benesova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Michaela Mikesova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - David Dzamba
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Pavel Honsa
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jan Kriska
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Olena Butenko
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Vendula Novosadova
- Laboratory of Gene Expression, Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Lukas Valihrach
- Laboratory of Gene Expression, Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Mikael Kubista
- Laboratory of Gene Expression, Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Lesia Dmytrenko
- Department of Neuroscience, Charles University, 2nd Faculty of Medicine, Prague, Czech Republic
| | - Michal Cicanic
- Department of Neuroscience, Charles University, 2nd Faculty of Medicine, Prague, Czech Republic
| | - Lydia Vargova
- Department of Neuroscience, Charles University, 2nd Faculty of Medicine, Prague, Czech Republic
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