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Rade M, Kreuz M, Borkowetz A, Sommer U, Blumert C, Füssel S, Bertram C, Löffler D, Otto DJ, Wöller LA, Schimmelpfennig C, Köhl U, Gottschling AC, Hönscheid P, Baretton GB, Wirth M, Thomas C, Horn F, Reiche K. A reliable transcriptomic risk-score applicable to formalin-fixed paraffin-embedded biopsies improves outcome prediction in localized prostate cancer. Mol Med 2024; 30:19. [PMID: 38302875 PMCID: PMC10835874 DOI: 10.1186/s10020-024-00789-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 01/22/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Clinical manifestation of prostate cancer (PCa) is highly variable. Aggressive tumors require radical treatment while clinically non-significant ones may be suitable for active surveillance. We previously developed the prognostic ProstaTrend RNA signature based on transcriptome-wide microarray and RNA-sequencing (RNA-Seq) analyses, primarily of prostatectomy specimens. An RNA-Seq study of formalin-fixed paraffin-embedded (FFPE) tumor biopsies has now allowed us to use this test as a basis for the development of a novel test that is applicable to FFPE biopsies as a tool for early routine PCa diagnostics. METHODS All patients of the FFPE biopsy cohort were treated by radical prostatectomy and median follow-up for biochemical recurrence (BCR) was 9 years. Based on the transcriptome data of 176 FFPE biopsies, we filtered ProstaTrend for genes susceptible to FFPE-associated degradation via regression analysis. ProstaTrend was additionally restricted to genes with concordant prognostic effects in the RNA-Seq TCGA prostate adenocarcinoma (PRAD) cohort to ensure robust and broad applicability. The prognostic relevance of the refined Transcriptomic Risk Score (TRS) was analyzed by Kaplan-Meier curves and Cox-regression models in our FFPE-biopsy cohort and 9 other public datasets from PCa patients with BCR as primary endpoint. In addition, we developed a prostate single-cell atlas of 41 PCa patients from 5 publicly available studies to analyze gene expression of ProstaTrend genes in different cell compartments. RESULTS Validation of the TRS using the original ProstaTrend signature in the cohort of FFPE biopsies revealed a relevant impact of FFPE-associated degradation on gene expression and consequently no significant association with prognosis (Cox-regression, p-value > 0.05) in FFPE tissue. However, the TRS based on the new version of the ProstaTrend-ffpe signature, which included 204 genes (of originally 1396 genes), was significantly associated with BCR in the FFPE biopsy cohort (Cox-regression p-value < 0.001) and retained prognostic relevance when adjusted for Gleason Grade Groups. We confirmed a significant association with BCR in 9 independent cohorts including 1109 patients. Comparison of the prognostic performance of the TRS with 17 other prognostically relevant PCa panels revealed that ProstaTrend-ffpe was among the best-ranked panels. We generated a PCa cell atlas to associate ProstaTrend genes with cell lineages or cell types. Tumor-specific luminal cells have a significantly higher TRS than normal luminal cells in all analyzed datasets. In addition, TRS of epithelial and luminal cells was correlated with increased Gleason score in 3 studies. CONCLUSIONS We developed a prognostic gene-expression signature for PCa that can be applied to FFPE biopsies and may be suitable to support clinical decision-making.
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Affiliation(s)
- Michael Rade
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Markus Kreuz
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Angelika Borkowetz
- Department of Urology, Faculty of Medicine, University Hospital, Technische Universität Dresden, Dresden, Germany
| | - Ulrich Sommer
- Institute of Pathology, Faculty of Medicine, University Hospital, Technische Universität Dresden, Dresden, Germany
| | - Conny Blumert
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Susanne Füssel
- Department of Urology, Faculty of Medicine, University Hospital, Technische Universität Dresden, Dresden, Germany
| | - Catharina Bertram
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Dennis Löffler
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Dominik J Otto
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
- Basic Science Division, Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Livia A Wöller
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Carolin Schimmelpfennig
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Ulrike Köhl
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
- Institute of Clinical Immunology, University of Leipzig, Leipzig, Germany
| | - Ann-Cathrin Gottschling
- Department of Urology, Faculty of Medicine, University Hospital, Technische Universität Dresden, Dresden, Germany
| | - Pia Hönscheid
- Institute of Pathology, Faculty of Medicine, University Hospital, Technische Universität Dresden, Dresden, Germany
| | - Gustavo B Baretton
- Institute of Pathology, Faculty of Medicine, University Hospital, Technische Universität Dresden, Dresden, Germany
| | - Manfred Wirth
- Department of Urology, Faculty of Medicine, University Hospital, Technische Universität Dresden, Dresden, Germany
| | - Christian Thomas
- Department of Urology, Faculty of Medicine, University Hospital, Technische Universität Dresden, Dresden, Germany
| | - Friedemann Horn
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Kristin Reiche
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany.
- Institute of Clinical Immunology, University of Leipzig, Leipzig, Germany.
- Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), University of Leipzig, 04105, Leipzig, Germany.
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Rade M, Böhlen S, Neuhaus V, Löffler D, Blumert C, Merz M, Köhl U, Dehmel S, Sewald K, Reiche K. A time-resolved meta-analysis of consensus gene expression profiles during human T-cell activation. Genome Biol 2023; 24:287. [PMID: 38098113 PMCID: PMC10722659 DOI: 10.1186/s13059-023-03120-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 11/22/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND The coordinated transcriptional regulation of activated T-cells is based on a complex dynamic behavior of signaling networks. Given an external stimulus, T-cell gene expression is characterized by impulse and sustained patterns over the course. Here, we analyze the temporal pattern of activation across different T-cell populations to develop consensus gene signatures for T-cell activation. RESULTS Here, we identify and verify general biomarker signatures robustly evaluating T-cell activation in a time-resolved manner. We identify time-resolved gene expression profiles comprising 521 genes of up to 10 disjunct time points during activation and different polarization conditions. The gene signatures include central transcriptional regulators of T-cell activation, representing successive waves as well as sustained patterns of induction. They cover sustained repressed, intermediate, and late response expression rates across multiple T-cell populations, thus defining consensus biomarker signatures for T-cell activation. In addition, intermediate and late response activation signatures in CAR T-cell infusion products are correlated to immune effector cell-associated neurotoxicity syndrome. CONCLUSION This study is the first to describe temporally resolved gene expression patterns across T-cell populations. These biomarker signatures are a valuable source, e.g., monitoring transcriptional changes during T-cell activation with a reasonable number of genes, annotating T-cell states in single-cell transcriptome studies, or assessing dysregulated functions of human T-cell immunity.
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Affiliation(s)
- Michael Rade
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103, Leipzig, Germany.
| | - Sebastian Böhlen
- Department of Preclinical Pharmacology and In-Vitro Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, ITEM, Nikolai-Fuchs-Strasse 1, 30625, Hannover, Germany
| | - Vanessa Neuhaus
- Department of Preclinical Pharmacology and In-Vitro Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, ITEM, Nikolai-Fuchs-Strasse 1, 30625, Hannover, Germany
| | - Dennis Löffler
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103, Leipzig, Germany
| | - Conny Blumert
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103, Leipzig, Germany
| | - Maximilian Merz
- Department of Hematology, Cellular Therapy, Hemostaseology and Infectiology, University Hospital of Leipzig, Leipzig, Germany
| | - Ulrike Köhl
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103, Leipzig, Germany
- Institute for Clinical Immunology, Leipzig University, Johannisallee 30, 04103, Leipzig, Germany
| | - Susann Dehmel
- Department of Preclinical Pharmacology and In-Vitro Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, ITEM, Nikolai-Fuchs-Strasse 1, 30625, Hannover, Germany
| | - Katherina Sewald
- Department of Preclinical Pharmacology and In-Vitro Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, ITEM, Nikolai-Fuchs-Strasse 1, 30625, Hannover, Germany
| | - Kristin Reiche
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103, Leipzig, Germany
- Institute for Clinical Immunology, Leipzig University, Johannisallee 30, 04103, Leipzig, Germany
- Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), Dresden, Leipzig, Germany
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Schimmelpfennig C, Rade M, Füssel S, Löffler D, Blumert C, Bertram C, Borkowetz A, Otto DJ, Puppel SH, Hönscheid P, Sommer U, Baretton GB, Köhl U, Wirth M, Thomas C, Horn F, Kreuz M, Reiche K. Characterization and evaluation of gene fusions as a measure of genetic instability and disease prognosis in prostate cancer. BMC Cancer 2023; 23:575. [PMID: 37349736 DOI: 10.1186/s12885-023-11019-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/27/2023] [Indexed: 06/24/2023] Open
Abstract
BACKGROUND Prostate cancer (PCa) is one of the most prevalent cancers worldwide. The clinical manifestations and molecular characteristics of PCa are highly variable. Aggressive types require radical treatment, whereas indolent ones may be suitable for active surveillance or organ-preserving focal therapies. Patient stratification by clinical or pathological risk categories still lacks sufficient precision. Incorporating molecular biomarkers, such as transcriptome-wide expression signatures, improves patient stratification but so far excludes chromosomal rearrangements. In this study, we investigated gene fusions in PCa, characterized potential novel candidates, and explored their role as prognostic markers for PCa progression. METHODS We analyzed 630 patients in four cohorts with varying traits regarding sequencing protocols, sample conservation, and PCa risk group. The datasets included transcriptome-wide expression and matched clinical follow-up data to detect and characterize gene fusions in PCa. With the fusion calling software Arriba, we computationally predicted gene fusions. Following detection, we annotated the gene fusions using published databases for gene fusions in cancer. To relate the occurrence of gene fusions to Gleason Grading Groups and disease prognosis, we performed survival analyses using the Kaplan-Meier estimator, log-rank test, and Cox regression. RESULTS Our analyses identified two potential novel gene fusions, MBTTPS2,L0XNC01::SMS and AMACR::AMACR. These fusions were detected in all four studied cohorts, providing compelling evidence for the validity of these fusions and their relevance in PCa. We also found that the number of gene fusions detected in a patient sample was significantly associated with the time to biochemical recurrence in two of the four cohorts (log-rank test, p-value < 0.05 for both cohorts). This was also confirmed after adjusting the prognostic model for Gleason Grading Groups (Cox regression, p-values < 0.05). CONCLUSIONS Our gene fusion characterization workflow revealed two potential novel fusions specific for PCa. We found evidence that the number of gene fusions was associated with the prognosis of PCa. However, as the quantitative correlations were only moderately strong, further validation and assessment of clinical value is required before potential application.
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Affiliation(s)
- Carolin Schimmelpfennig
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Michael Rade
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Susanne Füssel
- Department of Urology, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Dennis Löffler
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Conny Blumert
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Catharina Bertram
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Angelika Borkowetz
- Department of Urology, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Dominik J Otto
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Sven-Holger Puppel
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Pia Hönscheid
- Institute of Pathology, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Ulrich Sommer
- Institute of Pathology, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Gustavo B Baretton
- Institute of Pathology, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Ulrike Köhl
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
- Institute of Clinical Immunology, Medical Faculty, University Hospital, University of Leipzig, Leipzig, Germany
| | - Manfred Wirth
- Department of Urology, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Christian Thomas
- Department of Urology, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Friedemann Horn
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Markus Kreuz
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Kristin Reiche
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany.
- Institute of Clinical Immunology, Medical Faculty, University Hospital, University of Leipzig, Leipzig, Germany.
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Schmidt JR, Haupt J, Riemschneider S, Kämpf C, Löffler D, Blumert C, Reiche K, Koehl U, Kalkhof S, Lehmann J. Transcriptomic signatures reveal a shift towards an anti-inflammatory gene expression profile but also the induction of type I and type II interferon signaling networks through aryl hydrocarbon receptor activation in murine macrophages. Front Immunol 2023; 14:1156493. [PMID: 37287978 PMCID: PMC10242070 DOI: 10.3389/fimmu.2023.1156493] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/09/2023] [Indexed: 06/09/2023] Open
Abstract
Introduction The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that regulates a broad range of target genes involved in the xenobiotic response, cell cycle control and circadian rhythm. AhR is constitutively expressed in macrophages (Mϕ), acting as key regulator of cytokine production. While proinflammatory cytokines, i.e., IL-1β, IL-6, IL-12, are suppressed through AhR activation, anti-inflammatory IL-10 is induced. However, the underlying mechanisms of those effects and the importance of the specific ligand structure are not yet completely understood. Methods Therefore, we have compared the global gene expression pattern in activated murine bone marrow-derived macrophages (BMMs) subsequently to exposure with either benzo[a]pyrene (BaP) or indole-3-carbinol (I3C), representing high-affinity vs. low-affinity AhR ligands, respectively, by means of mRNA sequencing. AhR dependency of observed effects was proved using BMMs from AhR-knockout (Ahr-/-) mice. Results and discussion In total, more than 1,000 differentially expressed genes (DEGs) could be mapped, covering a plethora of AhR-modulated effects on basal cellular processes, i.e., transcription and translation, but also immune functions, i.e., antigen presentation, cytokine production, and phagocytosis. Among DEGs were genes that are already known to be regulated by AhR, i.e., Irf1, Ido2, and Cd84. However, we identified DEGs not yet described to be AhR-regulated in Mϕ so far, i.e., Slpi, Il12rb1, and Il21r. All six genes likely contribute to shifting the Mϕ phenotype from proinflammatory to anti-inflammatory. The majority of DEGs induced through BaP were not affected through I3C exposure, probably due to higher AhR affinity of BaP in comparison to I3C. Mapping of known aryl hydrocarbon response element (AHRE) sequence motifs in identified DEGs revealed more than 200 genes not possessing any AHRE, and therefore being not eligible for canonical regulation. Bioinformatic approaches modeled a central role of type I and type II interferons in the regulation of those genes. Additionally, RT-qPCR and ELISA confirmed a AhR-dependent expressional induction and AhR-dependent secretion of IFN-γ in response to BaP exposure, suggesting an auto- or paracrine activation pathway of Mϕ.
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Affiliation(s)
- Johannes R. Schmidt
- Department of Preclinical Development and Validation, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
- Fraunhofer Cluster of Excellence Immune-Mediated Diseases (CIMD), Leipzig, Germany
| | - Janine Haupt
- Department of Preclinical Development and Validation, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
- Fraunhofer Cluster of Excellence Immune-Mediated Diseases (CIMD), Leipzig, Germany
| | - Sina Riemschneider
- Department of Preclinical Development and Validation, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Christoph Kämpf
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Dennis Löffler
- Fraunhofer Cluster of Excellence Immune-Mediated Diseases (CIMD), Leipzig, Germany
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Conny Blumert
- Fraunhofer Cluster of Excellence Immune-Mediated Diseases (CIMD), Leipzig, Germany
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Kristin Reiche
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
- Institute for Clinical Immunology, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Ulrike Koehl
- Fraunhofer Cluster of Excellence Immune-Mediated Diseases (CIMD), Leipzig, Germany
- Institute for Clinical Immunology, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Stefan Kalkhof
- Department of Preclinical Development and Validation, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
- Fraunhofer Cluster of Excellence Immune-Mediated Diseases (CIMD), Leipzig, Germany
- Department of Applied Sciences, Institute for Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Jörg Lehmann
- Department of Preclinical Development and Validation, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
- Fraunhofer Cluster of Excellence Immune-Mediated Diseases (CIMD), Leipzig, Germany
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Anders IM, Schimmelpfennig C, Wiedemann K, Löffler D, Kämpf C, Blumert C, Reiche K, Kunz M, Anderegg U, Simon JC, Ziemer M. Atypisches Fibroxanthom und pleomorphes dermales Sarkom - Genexpressionsanalyse im Vergleich zum entdifferenzierten Plattenepithelkarzinom der Haut. J Dtsch Dermatol Ges 2023; 21:482-492. [PMID: 37183746 DOI: 10.1111/ddg.15006_g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/03/2023] [Indexed: 05/16/2023]
Affiliation(s)
- Iris Marie Anders
- Klinik für Dermatologie, Venerologie und Allergologie, Universitätsklinikum Leipzig
| | | | - Karolin Wiedemann
- Abteilung Diagnostik, Fraunhofer-Institut für Zelltherapie und Immunologie IZI, Leipzig
| | - Dennis Löffler
- Abteilung Diagnostik, Fraunhofer-Institut für Zelltherapie und Immunologie IZI, Leipzig
| | - Christoph Kämpf
- Abteilung Diagnostik, Fraunhofer-Institut für Zelltherapie und Immunologie IZI, Leipzig
| | - Conny Blumert
- Abteilung Diagnostik, Fraunhofer-Institut für Zelltherapie und Immunologie IZI, Leipzig
| | - Kristin Reiche
- Abteilung Diagnostik, Fraunhofer-Institut für Zelltherapie und Immunologie IZI, Leipzig
- Institut für Klinische Immunologie, Universität Leipzig
| | - Manfred Kunz
- Klinik für Dermatologie, Venerologie und Allergologie, Universitätsklinikum Leipzig
| | - Ulf Anderegg
- Klinik für Dermatologie, Venerologie und Allergologie, Universitätsklinikum Leipzig
| | - Jan-Christoph Simon
- Klinik für Dermatologie, Venerologie und Allergologie, Universitätsklinikum Leipzig
| | - Mirjana Ziemer
- Klinik für Dermatologie, Venerologie und Allergologie, Universitätsklinikum Leipzig
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Anders IM, Schimmelpfennig C, Wiedemann K, Löffler D, Kämpf C, Blumert C, Reiche K, Kunz M, Anderegg U, Simon JC, Ziemer M. Atypical fibroxanthoma and pleomorphic dermal sarcoma - gene expression analysis compared with undifferentiated cutaneous squamous cell carcinoma. J Dtsch Dermatol Ges 2023; 21:482-491. [PMID: 37035902 DOI: 10.1111/ddg.15006] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/03/2023] [Indexed: 04/11/2023]
Abstract
BACKGROUND The histogenetic origin of atypical fibroxanthoma (AFX) and pleomorphic dermal sarcoma (PDS) has not been definitively elucidated. In addition to a fibroblastic origin, a keratinocytic differentiation is discussed due to strong clinical, histomorphological and molecular genetic similarities with undifferentiated cutaneous squamous cell carcinoma (cSCC). PATIENTS AND METHODS 56 cases (36 AFXs, 8 PDSs, 12 undifferentiated cSCCs) were evaluated for their clinical, histomorphological, and immunohistochemical characteristics. RNA transcriptome analysis was performed on 18 cases (6 AFXs/PDSs, 6 undifferentiated cSCCs, 6 differentiated cSCCs). RESULTS Clinically, the strong similarities in age, gender and tumor location were confirmed. Without further immunohistochemical staining, histomorphological differentiation between AFX/PDS and undifferentiated cSCC is often impossible. Principal component analysis of the RNA transcriptome analysis showed that AFX/PDS and differentiated cSCC each formed their own cluster, while the undifferentiated cSCCs fall in between these two groups, but without forming a cluster of their own. When examining differentially expressed genes (DEGs), the heat maps showed that there were cases within the undifferentiated cSCC that were more likely to be AFX/PDS than differentiated cSCC based on their expression profile. CONCLUSIONS The results provide evidence of molecular similarities between AFX/PDS and undifferentiated cSCC and suggest a common histogenetic origin.
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Affiliation(s)
- Iris Marie Anders
- Department of Dermatology, Venereology and Allergology, University Hospital Leipzig, Leipzig, Germany
| | - Carolin Schimmelpfennig
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Karolin Wiedemann
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Dennis Löffler
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Christoph Kämpf
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Conny Blumert
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Kristin Reiche
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
- Institute of Clinical Immunology, University of Leipzig, Leipzig, Germany
| | - Manfred Kunz
- Department of Dermatology, Venereology and Allergology, University Hospital Leipzig, Leipzig, Germany
| | - Ulf Anderegg
- Department of Dermatology, Venereology and Allergology, University Hospital Leipzig, Leipzig, Germany
| | - Jan-Christoph Simon
- Department of Dermatology, Venereology and Allergology, University Hospital Leipzig, Leipzig, Germany
| | - Mirjana Ziemer
- Department of Dermatology, Venereology and Allergology, University Hospital Leipzig, Leipzig, Germany
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Haehnel S, Rade M, Kaiser N, Reiche K, Horn A, Loeffler D, Blumert C, Rapp F, Horn F, Meixensberger J, Renner C, Mueller W, Gaunitz F, Bechmann I, Winter K. RNA sequencing of glioblastoma tissue slice cultures reveals the effects of treatment at the transcriptional level. FEBS Open Bio 2021; 12:480-493. [PMID: 34923780 PMCID: PMC8804611 DOI: 10.1002/2211-5463.13353] [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: 09/26/2021] [Revised: 11/22/2021] [Accepted: 12/16/2021] [Indexed: 11/30/2022] Open
Abstract
One of the major challenges in cancer research is finding models that closely resemble tumors within patients. Human tissue slice cultures are a promising approach to provide a model of the patient's tumor biology ex vivo. Recently, it was shown that these slices can be successfully analyzed by whole transcriptome sequencing as well as automated histochemistry, increasing their usability as preclinical model. Glioblastoma multiforme (GBM) is a highly malignant brain tumor with poor prognosis and little is known about its genetic background and heterogeneity regarding therapy success. In this study, tissue from the tumors of 25 patients with primary GBM was processed into slice cultures and treated with standard therapy (irradiation and temozolomide). Total RNA sequencing and automated histochemistry were performed to enable analysis of treatment effects at a transcriptional and histological level. Slice cultures from long‐term survivors (overall survival [OS] > 24 months) exhibited more apoptosis than cultures from patients with shorter OS. Proliferation within these slices was slightly increased in contrast to other groups, but not significantly. Among all samples, 58 protein‐coding genes were upregulated and 32 downregulated in treated vs. untreated slice cultures. In general, an upregulation of DNA damage‐related and cell cycle checkpoint genes as well as enrichment of genotoxicity pathways and p53‐dependent signaling was found after treatment. Overall, the current study reproduces knowledge from former studies regarding the feasibility of transcriptomic analyses and automated histology in tissue slice cultures. We further demonstrate that the experimental data merge with the clinical follow‐up of the patients, which improves the applicability of our model system.
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Affiliation(s)
- Susann Haehnel
- Institute of Anatomy, Faculty of Medicine, University of Leipzig, Germany
| | - Michael Rade
- Department of Diagnostics, Fraunhofer Institute of Cell Therapy and Immunology, Leipzig, Germany
| | - Nicole Kaiser
- Institute of Anatomy, Faculty of Medicine, University of Leipzig, Germany
| | - Kristin Reiche
- Department of Diagnostics, Fraunhofer Institute of Cell Therapy and Immunology, Leipzig, Germany
| | - Andreas Horn
- Institute of Anatomy, Faculty of Medicine, University of Leipzig, Germany
| | - Dennis Loeffler
- Department of Diagnostics, Fraunhofer Institute of Cell Therapy and Immunology, Leipzig, Germany
| | - Conny Blumert
- Department of Diagnostics, Fraunhofer Institute of Cell Therapy and Immunology, Leipzig, Germany
| | - Felicitas Rapp
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, Darmstadt, Germany
| | - Friedemann Horn
- Department of Diagnostics, Fraunhofer Institute of Cell Therapy and Immunology, Leipzig, Germany.,Institute of Clinical Immunology, Faculty of Medicine, University of Leipzig, Germany
| | | | | | - Wolf Mueller
- Department of Neuropathology, University Hospital Leipzig, Germany
| | - Frank Gaunitz
- Department of Neurosurgery, University Hospital Leipzig, Germany
| | - Ingo Bechmann
- Institute of Anatomy, Faculty of Medicine, University of Leipzig, Germany
| | - Karsten Winter
- Institute of Anatomy, Faculty of Medicine, University of Leipzig, Germany
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8
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Walcher L, Kistenmacher AK, Sommer C, Böhlen S, Ziemann C, Dehmel S, Braun A, Tretbar US, Klöß S, Schambach A, Morgan M, Löffler D, Kämpf C, Blumert C, Reiche K, Beckmann J, König U, Standfest B, Thoma M, Makert GR, Ulbert S, Kossatz-Böhlert U, Köhl U, Dünkel A, Fricke S. Low Energy Electron Irradiation Is a Potent Alternative to Gamma Irradiation for the Inactivation of (CAR-)NK-92 Cells in ATMP Manufacturing. Front Immunol 2021; 12:684052. [PMID: 34149724 PMCID: PMC8212864 DOI: 10.3389/fimmu.2021.684052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/06/2021] [Indexed: 11/18/2022] Open
Abstract
Background With increasing clinical use of NK-92 cells and their CAR-modified derivatives in cancer immunotherapy, there is a growing demand for efficient production processes of these “off-the-shelf” therapeutics. In order to ensure safety and prevent the occurrence of secondary tumors, (CAR-)NK-92 cell proliferation has to be inactivated before transfusion. This is commonly achieved by gamma irradiation. Recently, we showed proof of concept that low energy electron irradiation (LEEI) is a new method for NK-92 inactivation. LEEI has several advantages over gamma irradiation, including a faster reaction time, a more reproducible dose rate and much less requirements on radiation shielding. Here, LEEI was further evaluated as a promising alternative to gamma irradiation yielding cells with highly maintained cytotoxic effector function. Methods Effectiveness and efficiency of LEEI and gamma irradiation were analyzed using NK-92 and CD123-directed CAR-NK-92 cells. LEE-irradiated cells were extensively characterized and compared to gamma-irradiated cells via flow cytometry, cytotoxicity assays, and comet assays, amongst others. Results Our results show that both irradiation methods caused a progressive decrease in cell viability and are, therefore, suitable for inhibition of cell proliferation. Notably, the NK-mediated specific lysis of tumor cells was maintained at stable levels for three days post-irradiation, with a trend towards higher activities after LEEI treatment as compared to gamma irradiation. Both gamma irradiation as well as LEEI led to substantial DNA damage and an accumulation of irradiated cells in the G2/M cell cycle phases. In addition, transcriptomic analysis of irradiated cells revealed approximately 12-fold more differentially expressed genes two hours after gamma irradiation, compared to LEEI. Analysis of surface molecules revealed an irradiation-induced decrease in surface expression of CD56, but no changes in the levels of the activating receptors NKp46, NKG2D, or NKp30. Conclusions The presented data show that LEEI inactivates (CAR-)NK-92 cells as efficiently as gamma irradiation, but with less impact on the overall gene expression. Due to logistic advantages, LEEI might provide a superior alternative for the manufacture of (CAR-)NK-92 cells for clinical application.
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Affiliation(s)
- Lia Walcher
- Department for GMP Process Development/ATMP Design, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
| | - Ann-Kathrin Kistenmacher
- Department for GMP Process Development/ATMP Design, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
| | - Charline Sommer
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Department for Preclinical Pharmacology and Toxicology, Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease (BREATH) research network, Hannover, Germany
| | - Sebastian Böhlen
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Department for Preclinical Pharmacology and Toxicology, Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease (BREATH) research network, Hannover, Germany
| | - Christina Ziemann
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Department for Preclinical Pharmacology and Toxicology, Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease (BREATH) research network, Hannover, Germany
| | - Susann Dehmel
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Department for Preclinical Pharmacology and Toxicology, Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease (BREATH) research network, Hannover, Germany
| | - Armin Braun
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Department for Preclinical Pharmacology and Toxicology, Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease (BREATH) research network, Hannover, Germany
| | - Uta Sandy Tretbar
- Department for GMP Process Development/ATMP Design, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
| | - Stephan Klöß
- Institute of Cellular Therapeutics, Hannover Medical School, Hannover, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Michael Morgan
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Dennis Löffler
- Department for Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
| | - Christoph Kämpf
- Department for Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
| | - Conny Blumert
- Department for Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
| | - Kristin Reiche
- Department for Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany.,Institute for Clinical Immunology, University of Leipzig, Leipzig, Germany
| | - Jana Beckmann
- Division for Medical and Biotechnological Applications, Fraunhofer Institute for Organic Electronics, Electron Beam and Plasma Technology (FEP), Dresden, Germany
| | - Ulla König
- Division for Medical and Biotechnological Applications, Fraunhofer Institute for Organic Electronics, Electron Beam and Plasma Technology (FEP), Dresden, Germany
| | - Bastian Standfest
- Department for Laboratory Automation and Biomanufacturing Engineering, Fraunhofer Institute for Manufacturing Engineering and Automation (IPA), Stuttgart, Germany
| | - Martin Thoma
- Department for Laboratory Automation and Biomanufacturing Engineering, Fraunhofer Institute for Manufacturing Engineering and Automation (IPA), Stuttgart, Germany
| | - Gustavo R Makert
- Department for Vaccines and Infection Models, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
| | - Sebastian Ulbert
- Department for Vaccines and Infection Models, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
| | - Uta Kossatz-Böhlert
- Department for GMP Process Development/ATMP Design, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
| | - Ulrike Köhl
- Institute of Cellular Therapeutics, Hannover Medical School, Hannover, Germany.,Institute for Clinical Immunology, University of Leipzig, Leipzig, Germany.,Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
| | - Anna Dünkel
- Department for GMP Process Development/ATMP Design, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
| | - Stephan Fricke
- Department for GMP Process Development/ATMP Design, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
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9
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Kreuz M, Otto DJ, Fuessel S, Blumert C, Bertram C, Bartsch S, Loeffler D, Puppel SH, Rade M, Buschmann T, Christ S, Erdmann K, Friedrich M, Froehner M, Muders MH, Schreiber S, Specht M, Toma MI, Benigni F, Freschi M, Gandaglia G, Briganti A, Baretton GB, Loeffler M, Hackermüller J, Reiche K, Wirth M, Horn F. ProstaTrend-A Multivariable Prognostic RNA Expression Score for Aggressive Prostate Cancer. Eur Urol 2020; 78:452-459. [PMID: 32631745 DOI: 10.1016/j.eururo.2020.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 06/02/2020] [Indexed: 01/02/2023]
Abstract
BACKGROUND Prostate cancer (PCa) is the most prevalent solid cancer among men in Western Countries. The clinical behavior of localized PCa is highly variable. Some cancers are aggressive leading to death, while others can even be monitored safely. Hence, there is a high clinical need for precise biomarkers for identification of aggressive disease in addition to established clinical parameters. OBJECTIVE To develop an RNA expression-based score for the prediction of PCa prognosis that facilitates clinical decision making. DESIGN, SETTING, AND PARTICIPANTS We assessed 233 tissue specimens of PCa patients with long-term follow-up data from fresh-frozen radical prostatectomies (RPs), from formalin-fixed and paraffin-embedded RP specimens and biopsies by transcriptome-wide next-generation sequencing and customized expression microarrays. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS We applied Cox proportional hazard models to the cohorts from different platforms and specimen types. Evidence from these models was combined by fixed-effect meta-analysis to identify genes predictive of the time to death of disease (DoD). Genes were combined by a weighted median approach into a prognostic score called ProstaTrend and transferred for the prediction of biochemical recurrence (BCR) after RP in an independent cohort of The Cancer Genome Atlas (TCGA). RESULTS AND LIMITATIONS ProstaTrend comprising ∼1400 genes was significantly associated with DoD in the training cohort of PCa patients treated by RP (leave-one-out cross-validation, Cox regression: p=2e-09) and with BCR in the TCGA validation cohort (Cox regression: p=3e-06). The prognostic impact persisted after multivariable Cox regression analysis adjusting for Gleason grading group (GG) ≥3 and resection status (p=0.001; DoD, training cohort) and for GG≥3, pathological stage ≥T3, and resection state (p=0.037; BCR, validation cohort). CONCLUSIONS ProstaTrend is a transcriptome-based score that predicts DoD and BCR in cohorts of PCa patients treated with RP. PATIENT SUMMARY ProstaTrend provides molecular patient risk stratification after radical prostatectomy.
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Affiliation(s)
- Markus Kreuz
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany; Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Dominik J Otto
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany; Institute of Clinical Immunology, Faculty of Medicine, University of Leipzig, Leipzig, Germany
| | - Susanne Fuessel
- Department of Urology, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Conny Blumert
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany; Institute of Clinical Immunology, Faculty of Medicine, University of Leipzig, Leipzig, Germany
| | - Catharina Bertram
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Sophie Bartsch
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Dennis Loeffler
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany; Institute of Clinical Immunology, Faculty of Medicine, University of Leipzig, Leipzig, Germany
| | - Sven-Holger Puppel
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Michael Rade
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Tilo Buschmann
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Sabina Christ
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Kati Erdmann
- Department of Urology, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany; National Center for Tumor Diseases (NCT), Dresden, Germany
| | - Maik Friedrich
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany; Institute of Clinical Immunology, Faculty of Medicine, University of Leipzig, Leipzig, Germany
| | - Michael Froehner
- Department of Urology, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany; Department of Urology, Zeisigwaldkliniken Bethanien, Chemnitz, Germany
| | - Michael H Muders
- Institute of Pathology, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany; Rudolf-Becker-Laboratory for Prostate Cancer Research, Institute of Pathology, University of Bonn Medical Center, Bonn, Germany
| | | | - Michael Specht
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Marieta I Toma
- Institute of Pathology, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Fabio Benigni
- Department of Urology and Division of Experimental Oncology, URI, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Massimo Freschi
- Pathology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giorgio Gandaglia
- Department of Urology and Division of Experimental Oncology, URI, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alberto Briganti
- Department of Urology and Division of Experimental Oncology, URI, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Gustavo B Baretton
- Institute of Pathology, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | | | - Kristin Reiche
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany; Institute of Clinical Immunology, Faculty of Medicine, University of Leipzig, Leipzig, Germany.
| | - Manfred Wirth
- Department of Urology, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Friedemann Horn
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany; Institute of Clinical Immunology, Faculty of Medicine, University of Leipzig, Leipzig, Germany
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10
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Oberbach A, Schlichting N, Feder S, Lehmann S, Kullnick Y, Buschmann T, Blumert C, Horn F, Neuhaus J, Neujahr R, Bagaev E, Hagl C, Pichlmaier M, Rodloff AC, Gräber S, Kirsch K, Sandri M, Kumbhari V, Behzadi A, Behzadi A, Correia JC, Mohr FW, Friedrich M. New insights into valve-related intramural and intracellular bacterial diversity in infective endocarditis. PLoS One 2017; 12:e0175569. [PMID: 28410379 PMCID: PMC5391965 DOI: 10.1371/journal.pone.0175569] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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: 09/06/2016] [Accepted: 03/28/2017] [Indexed: 12/17/2022] Open
Abstract
Aims In infective endocarditis (IE), a severe inflammatory disease of the endocardium with an unchanged incidence and mortality rate over the past decades, only 1% of the cases have been described as polymicrobial infections based on microbiological approaches. The aim of this study was to identify potential biodiversity of bacterial species from infected native and prosthetic valves. Furthermore, we compared the ultrastructural micro-environments to detect the localization and distribution patterns of pathogens in IE. Material and methods Using next-generation sequencing (NGS) of 16S rDNA, which allows analysis of the entire bacterial community within a single sample, we investigated the biodiversity of infectious bacterial species from resected native and prosthetic valves in a clinical cohort of 8 IE patients. Furthermore, we investigated the ultrastructural infected valve micro-environment by focused ion beam scanning electron microscopy (FIB-SEM). Results Biodiversity was detected in 7 of 8 resected heart valves. This comprised 13 bacterial genera and 16 species. In addition to 11 pathogens already described as being IE related, 5 bacterial species were identified as having a novel association. In contrast, valve and blood culture-based diagnosis revealed only 4 species from 3 bacterial genera and did not show any relevant antibiotic resistance. The antibiotics chosen on this basis for treatment, however, did not cover the bacterial spectra identified by our amplicon sequencing analysis in 4 of 8 cases. In addition to intramural distribution patterns of infective bacteria, intracellular localization with evidence of bacterial immune escape mechanisms was identified. Conclusion The high frequency of polymicrobial infections, pathogen diversity, and intracellular persistence of common IE-causing bacteria may provide clues to help explain the persistent and devastating mortality rate observed for IE. Improved bacterial diagnosis by 16S rDNA NGS that increases the ability to tailor antibiotic therapy may result in improved outcomes.
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MESH Headings
- Aged
- Aged, 80 and over
- Bacteria/genetics
- Bacteria/isolation & purification
- Endocarditis/diagnosis
- Endocarditis/microbiology
- Female
- Heart Valves/microbiology
- High-Throughput Nucleotide Sequencing
- Humans
- Male
- Metagenome
- Microscopy, Electron, Scanning
- Middle Aged
- Phenotype
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Sequence Analysis, DNA
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Affiliation(s)
- Andreas Oberbach
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
- University of Leipzig/Heart Center Leipzig, Department of Cardiac Surgery, Leipzig, Germany
- Department of Medicine and Division of Gastroenterology and Hepatology. The Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Nadine Schlichting
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Stefan Feder
- University of Leipzig/Heart Center Leipzig, Department of Cardiac Surgery, Leipzig, Germany
| | - Stefanie Lehmann
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Yvonne Kullnick
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Tilo Buschmann
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Conny Blumert
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Friedemann Horn
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
- Institute of Clinical Immunology, University of Leipzig, Leipzig, Germany
| | - Jochen Neuhaus
- Department of Urology, University of Leipzig, Leipzig, Germany
| | - Ralph Neujahr
- Carl Zeiss Microscopy GmbH, Global Sales Support Life Sciences Microscopy Labs Munich, Munich, Germany
| | - Erik Bagaev
- Department of Cardiac Surgery, Ludwig-Maximilians-University, Munich, Germany
| | - Christian Hagl
- Department of Cardiac Surgery, Ludwig-Maximilians-University, Munich, Germany
| | | | - Arne Christian Rodloff
- Institute for Medical Microbiology and Epidemiology of Infectious Diseases, Leipzig University Hospital, Leipzig, Germany
| | - Sandra Gräber
- Institute for Medical Microbiology and Epidemiology of Infectious Diseases, Leipzig University Hospital, Leipzig, Germany
| | - Katharina Kirsch
- University of Leipzig, Heart Centre, Department of Internal Medicine/Cardiology, Leipzig, Germany
| | - Marcus Sandri
- University of Leipzig, Heart Centre, Department of Internal Medicine/Cardiology, Leipzig, Germany
| | - Vivek Kumbhari
- Department of Medicine and Division of Gastroenterology and Hepatology. The Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Armirhossein Behzadi
- University of Leipzig/Heart Center Leipzig, Department of Cardiac Surgery, Leipzig, Germany
| | - Amirali Behzadi
- University of Leipzig/Heart Center Leipzig, Department of Cardiac Surgery, Leipzig, Germany
| | - Joao Carlos Correia
- University of Leipzig/Heart Center Leipzig, Department of Cardiac Surgery, Leipzig, Germany
| | - Friedrich Wilhelm Mohr
- University of Leipzig/Heart Center Leipzig, Department of Cardiac Surgery, Leipzig, Germany
| | - Maik Friedrich
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
- * E-mail:
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11
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Horn F, Christ-Breulmann S, Puppel SH, Buschmann T, Reiche K, Specht M, Bertram C, Friedrich M, Binder S, Blumert C, Hackermüller J, Kreuz M, Löffler M, Toma MI, Muders M, Baretton GB, Fröhner M, Füssel S, Wirth M. MP02-03 NEXT-GENERATION SEQUENCING REVEALS TRANSCRIPT CLUSTERS WITH PROGNOSTIC POTENTIAL FOR PROSTATE CANCER. J Urol 2016. [DOI: 10.1016/j.juro.2016.02.1875] [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]
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12
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Hackermüller J, Reiche K, Otto C, Hösler N, Blumert C, Brocke-Heidrich K, Böhlig L, Nitsche A, Kasack K, Ahnert P, Krupp W, Engeland K, Stadler PF, Horn F. Cell cycle, oncogenic and tumor suppressor pathways regulate numerous long and macro non-protein-coding RNAs. Genome Biol 2014; 15:R48. [PMID: 24594072 PMCID: PMC4054595 DOI: 10.1186/gb-2014-15-3-r48] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 03/04/2014] [Indexed: 12/16/2022] Open
Abstract
Background The genome is pervasively transcribed but most transcripts do not code for proteins, constituting non-protein-coding RNAs. Despite increasing numbers of functional reports of individual long non-coding RNAs (lncRNAs), assessing the extent of functionality among the non-coding transcriptional output of mammalian cells remains intricate. In the protein-coding world, transcripts differentially expressed in the context of processes essential for the survival of multicellular organisms have been instrumental in the discovery of functionally relevant proteins and their deregulation is frequently associated with diseases. We therefore systematically identified lncRNAs expressed differentially in response to oncologically relevant processes and cell-cycle, p53 and STAT3 pathways, using tiling arrays. Results We found that up to 80% of the pathway-triggered transcriptional responses are non-coding. Among these we identified very large macroRNAs with pathway-specific expression patterns and demonstrated that these are likely continuous transcripts. MacroRNAs contain elements conserved in mammals and sauropsids, which in part exhibit conserved RNA secondary structure. Comparing evolutionary rates of a macroRNA to adjacent protein-coding genes suggests a local action of the transcript. Finally, in different grades of astrocytoma, a tumor disease unrelated to the initially used cell lines, macroRNAs are differentially expressed. Conclusions It has been shown previously that the majority of expressed non-ribosomal transcripts are non-coding. We now conclude that differential expression triggered by signaling pathways gives rise to a similar abundance of non-coding content. It is thus unlikely that the prevalence of non-coding transcripts in the cell is a trivial consequence of leaky or random transcription events.
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13
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Blumert C, Kalkhof S, Brocke-Heidrich K, Kohajda T, von Bergen M, Horn F. Analysis of the STAT3 interactome using in-situ biotinylation and SILAC. J Proteomics 2013; 94:370-86. [PMID: 24013128 DOI: 10.1016/j.jprot.2013.08.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 08/01/2013] [Accepted: 08/26/2013] [Indexed: 12/28/2022]
Abstract
UNLABELLED Signal transducer and activator of transcription 3 (STAT3) is activated by a variety of cytokines and growth factors. To generate a comprehensive data set of proteins interacting specifically with STAT3, we applied stable isotope labeling with amino acids in cell culture (SILAC). For high-affinity pull-down using streptavidin, we fused STAT3 with a short peptide tag allowing biotinylation in situ (bio-tag), which did not affect STAT3 functions. By this approach, 3642 coprecipitated proteins were detected in human embryonic kidney-293 cells. Filtering using statistical and functional criteria finally extracted 136 proteins as putative interaction partners of STAT3. Both, a physical interaction network analysis and the enrichment of known and predicted interaction partners suggested that our filtering criteria successfully enriched true STAT3 interactors. Our approach identified numerous novel interactors, including ones previously predicted to associate with STAT3. By reciprocal coprecipitation, we were able to verify the physical association between STAT3 and selected interactors, including the novel interaction with TOX4, a member of the TOX high mobility group box family. Applying the same method, we next investigated the activation-dependency of the STAT3 interactome. Again, we identified both known and novel interactions. Thus, our approach allows to study protein-protein interaction effectively and comprehensively. BIOLOGICAL SIGNIFICANCE The location, activity, function, degradation, and synthesis of proteins are significantly regulated by interactions of proteins with other proteins, biopolymers and small molecules. Thus, the comprehensive characterization of interactions of proteins in a given proteome is the next milestone on the path to understanding the biochemistry of the cell. In order to generate a comprehensive interactome dataset of proteins specifically interacting with a selected bait protein, we fused our bait protein STAT3 with a short peptide tag allowing biotinylation in situ (bio-tag). This bio-tag allows an affinity pull-down using streptavidin but affected neither the activation of STAT3 by tyrosine phosphorylation nor its transactivating potential. We combined SILAC for accurate relative protein quantification, subcellular fractionation to increase the coverage of interacting proteins, high-affinity pull-down and a stringent filtering method to successfully analyze the interactome of STAT3. With our approach we confirmed several already known and identified numerous novel STAT3 interactors. The approach applied provides a rapid and effective method, which is broadly applicable for studying protein-protein interactions and their dependency on post-translational modifications.
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Affiliation(s)
- Conny Blumert
- Institute of Clinical Immunology, Medical Faculty, University of Leipzig, Johannisallee 30, 04103 Leipzig, Germany; Fraunhofer Institute for Cell Therapy and Immunology, Perlickstrasse 1, 04103 Leipzig, Germany
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14
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Blumert C, Mörbt N, von Bergen M, Horn F. Combination of SILAC and in situ biotinylation to detect specific protein interacions. Cell Commun Signal 2009. [PMCID: PMC4291592 DOI: 10.1186/1478-811x-7-s1-a11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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15
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Bauer K, Kretzschmar AK, Cvijic H, Blumert C, Löffler D, Brocke-Heidrich K, Schiene-Fischer C, Fischer G, Sinz A, Clevenger CV, Horn F. Cyclophilins contribute to Stat3 signaling and survival of multiple myeloma cells. Oncogene 2009; 28:2784-95. [PMID: 19503092 DOI: 10.1038/onc.2009.142] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Signal transducer and activator of transcription 3 (Stat3) is the major mediator of interleukin-6 (IL-6) family cytokines. In addition, Stat3 is known to be involved in the pathophysiology of many malignancies. Here, we show that the cis-trans peptidyl-prolyl isomerase cyclophilin (Cyp) B specifically interacts with Stat3, whereas the highly related CypA does not. CypB knockdown inhibited the IL-6-induced transactivation potential but not the tyrosine phosphorylation of Stat3. Binding of CypB to Stat3 target promoters and alteration of the intranuclear localization of Stat3 on CypB depletion suggested a nuclear function of Stat3/CypB interaction. By contrast, CypA knockdown inhibited Stat3 IL-6-induced tyrosine phosphorylation and nuclear translocation. The Cyp inhibitor cyclosporine A (CsA) caused similar effects. However, Stat1 activation in response to IL-6 or interferon-gamma was not affected by Cyp silencing or CsA treatment. As a result, Cyp knockdown shifted IL-6 signaling to a Stat1-dominated pathway. Furthermore, Cyp depletion or treatment with CsA induced apoptosis in IL-6-dependent multiple myeloma cells, whereas an IL-6-independent line was not affected. Thus, Cyps support the anti-apoptotic action of Stat3. Taken together, CypA and CypB both play pivotal roles, yet at different signaling levels, for Stat3 activation and function. These data also suggest a novel mechanism of CsA action.
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Affiliation(s)
- K Bauer
- Institute of Clinical Immunology and Transfusion Medicine, University of Leipzig, Germany
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Löffler D, Brocke-Heidrich K, Pfeifer G, Stocsits C, Hackermüller J, Kretzschmar AK, Burger R, Gramatzki M, Blumert C, Bauer K, Cvijic H, Ullmann AK, Stadler PF, Horn F. Interleukin-6 dependent survival of multiple myeloma cells involves the Stat3-mediated induction of microRNA-21 through a highly conserved enhancer. Blood 2007; 110:1330-3. [PMID: 17496199 DOI: 10.1182/blood-2007-03-081133] [Citation(s) in RCA: 500] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Signal transducer and activator of transcription 3 (Stat3) is implicated in the pathogenesis of many malignancies and essential for IL-6-dependent survival and growth of multiple myeloma cells. Here, we demonstrate that the gene encoding oncogenic microRNA-21 (miR-21) is controlled by an upstream enhancer containing 2 Stat3 binding sites strictly conserved since the first observed evolutionary appearance of miR-21 and Stat3. MiR-21 induction by IL-6 was strictly Stat3 dependent. Ectopically raising miR-21 expression in myeloma cells in the absence of IL-6 significantly reduced their apoptosis levels. These data provide strong evidence that miR-21 induction contributes to the oncogenic potential of Stat3.
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Affiliation(s)
- Dennis Löffler
- Institute of Clinical Immunology and Transfusion Medicine, Medical Faculty, University of Leipzig, Leipzig, Germany
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