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Die chronische Herzinsuffizienz stellt nach wie vor eine der häufigsten Todesursachen weltweit dar. Trotz intensiver Forschung ist es bisher nicht möglich die pathophysiologischen Prozesse aufzuhalten. Es wird nach neuen Strategien gesucht, hier therapeutisch eingreifen zu können. Kleine nicht-kodierende RNAs, sogenannte microRNAs (miRNAs), wurden als wichtige Faktoren bei verschiedenen Herzkrankheiten beschrieben. Die Mehrzahl der bisherigen Studien fokussierte sich dabei auf die am stärksten deregulierten miRNAs im erkrankten Herz. In einer automatisierten Analyse im 96 Well-Format untersuchten wir 230 miRNAs auf ihr Potential, in das Größenwachstum von primären Kardiomyozyten einzugreifen. Aus den miRNAs mit den größten Effekten selektierten wir diejenigen, die eine hohe endogene Expression aufwiesen, und unterzogen sie einem Validierungsprozess. Hier konnten wir die Effekte aller pro- (miR-22, miR-30c, miR-30d, miR-212, miR-365) und anti-hypertrophen (miR-27a, miR-27b, miR-133a) miRNAs bestätigen. Die Mehrzahl dieser miRNAs wurde hiermit erstmalig beschrieben, dass sie eine wichtige Rolle beim Größenwachstum von Kardiomyozyten spielen. Sie wären daher interessante Kandidaten für detaillierte funktionelle Studien mit dem Ziel ihr therapeutisches Potential zu evaluieren. In einem früheren genetischen Screen zur Identifizierung von kardialen, sezernierten Faktoren wurde der Protease Inhibitor 16 (PI16) entdeckt, der sich im insuffizienten Herz durch eine starke Akkumulation auszeichnet. Gegenstand des zweiten Teils dieser Arbeit war es, eine Mauslinie zu generieren, in der PI16 global oder konditionell mit Hilfe des Cre/LoxP-Systems ausgeschaltet werden kann. Nach Elektroporation des Pi16floxneo Targeting Vektors in embryonale Stammzellen und Blastozysteninjektion erhielten wir eine Mauslinie, die Träger der zielgerichteten Modifikation des Pi16 Allels war. Mit der globalen genetischen Deletion des LoxP-flankierten Abschnitts von Exon 3 bis 4 konnten wir die Expression des Pi16 Gens komplett unterbinden. Die PI16 Defizienz führte weder im Herz noch in anderen Organen per se zu pathologischen Veränderungen. Zudem war unbekannt, dass PI16 in der gesunden Maus in der kardialen Fibroblastenfraktion enthalten sowie in den Zilien der Epididymis und der Trachea und im Lumen der Schilddrüse lokalisiert ist. Im insuffizienten Herz bestätigten wir eine Akkumulation von PI16, die sich vor allem auf die fibrotischen Bereiche beschränkte. Das lässt Grund zur Annahme, dass die kardiale Funktion von PI16 erst dann offensichtlich wird, wenn man die defizienten Mäuse zukünftig entsprechenden Stressmodellen aussetzt. Das wird zu einem umfassenden Verständnis der kardialen Funktion von PI16 und dessen Potential als therapeutisches Zielmolekül führen.
Background
Blood-born miRNA signatures have recently been reported for various tumor diseases. Here, we compared the miRNA signature in Wilms tumor patients prior and after preoperative chemotherapy according to SIOP protocol 2001.
Results
We did not find a significant difference between miRNA signature of both groups. However both, Wilms tumor patients prior and after chemotherapy showed a miRNA signature different from healthy controls. The signature of Wilms tumor patients prior to chemotherapy showed an accuracy of 97.5% and of patients after chemotherapy an accuracy of 97.0%, each as compared to healthy controls.
Conclusion
Our results provide evidence for a blood-born Wilms tumor miRNA signature largely independent of four weeks preoperative chemotherapy treatment.
Background: miRNA profiles are promising biomarker candidates for a manifold of human pathologies, opening new avenues for diagnosis and prognosis. Beyond studies that describe miRNAs frequently as markers for specific traits, we asked whether a general pattern for miRNAs across many diseases exists.
Methods: We evaluated genome-wide circulating profiles of 1,049 patients suffering from 19 different cancer and non-cancer diseases as well as unaffected controls. The results were validated on 319 individuals using qRT-PCR.
Results: We discovered 34 miRNAs with strong disease association. Among those, we found substantially decreased levels of hsa-miR-144* and hsa-miR-20b with AUC of 0.751 ( 95% CI: 0.703-0.799), respectively. We also discovered a set of miRNAs, including hsa-miR-155*, as rather stable markers, offering reasonable control miRNAs for future studies. The strong downregulation of hsa-miR-144* and the less variable pattern of hsa-miR-155* has been validated in a cohort of 319 samples in three different centers. Here, breast cancer as an additional disease phenotype not included in the screening phase has been included as the 20th trait.
Conclusions: Our study on 1,368 patients including 1,049 genome-wide miRNA profiles and 319 qRT-PCR validations further underscores the high potential of specific blood-borne miRNA patterns as molecular biomarkers. Importantly, we highlight 34 miRNAs that are generally dysregulated in human pathologies. Although these markers are not specific to certain diseases they may add to the diagnosis in combination with other markers, building a specific signature. Besides these dysregulated miRNAs, we propose a set of constant miRNAs that may be used as control markers.
Background
Renal cell carcinoma (RCC) is marked by high mortality rate. To date, no robust risk stratification by clinical or molecular prognosticators of cancer-specific survival (CSS) has been established for early stages. Transcriptional profiling of small non-coding RNA gene products (miRNAs) seems promising for prognostic stratification. The expression of miR-21 and miR-126 was analysed in a large cohort of RCC patients; a combined risk score (CRS)-model was constructed based on expression levels of both miRNAs.
Methods
Expression of miR-21 and miR-126 was evaluated by qRT-PCR in tumour and adjacent non-neoplastic tissue in n = 139 clear cell RCC patients. Relation of miR-21 and miR-126 expression with various clinical parameters was assessed. Parameters were analysed by uni- and multivariate COX regression. A factor derived from the z-score resulting from the COX model was determined for both miRs separately and a combined risk score (CRS) was calculated multiplying the relative expression of miR-21 and miR-126 by this factor. The best fitting COX model was selected by relative goodness-of-fit with the Akaike information criterion (AIC).
Results
RCC with and without miR-21 up- and miR-126 downregulation differed significantly in synchronous metastatic status and CSS. Upregulation of miR-21 and downregulation of miR-126 were independently prognostic. A combined risk score (CRS) based on the expression of both miRs showed high sensitivity and specificity in predicting CSS and prediction was independent from any other clinico-pathological parameter. Association of CRS with CSS was successfully validated in a testing cohort containing patients with high and low risk for progressive disease.
Conclusions
A combined expression level of miR-21 and miR-126 accurately predicted CSS in two independent RCC cohorts and seems feasible for clinical application in assessing prognosis.
Dynamic interactions and their changes are at the forefront of current research in bioinformatics and systems biology. This thesis focusses on two particular dynamic aspects of cellular adaptation: miRNA and metabolites.
miRNAs have an established role in hematopoiesis and megakaryocytopoiesis, and platelet miRNAs have potential as tools for understanding basic mechanisms of platelet function. The thesis highlights the possible role of miRNAs in regulating protein translation in platelet lifespan with relevance to platelet apoptosis and identifying involved pathways and potential key regulatory molecules. Furthermore, corresponding miRNA/target mRNAs in murine platelets are identified. Moreover, key miRNAs involved in aortic aneurysm are predicted by similar techniques. The clinical relevance of miRNAs as biomarkers, targets, resulting later translational therapeutics, and tissue specific restrictors of genes expression in cardiovascular diseases is also discussed.
In a second part of thesis we highlight the importance of scientific software solution development in metabolic modelling and how it can be helpful in bioinformatics tool development along with software feature analysis such as performed on metabolic flux analysis applications. We proposed the “Butterfly” approach to implement efficiently scientific software programming. Using this approach, software applications were developed for quantitative Metabolic Flux Analysis and efficient Mass Isotopomer Distribution Analysis (MIDA) in metabolic modelling as well as for data management. “LS-MIDA” allows easy and efficient MIDA analysis and, with a more powerful algorithm and database, the software “Isotopo” allows efficient analysis of metabolic flows, for instance in pathogenic bacteria (Salmonella, Listeria). All three approaches have been published (see Appendices).
Wilms tumor (WT) is the most common childhood renal cancer. Recent findings of mutations in microRNA (miRNA) processing proteins suggest a pivotal role of miRNAs in WT genesis. We performed miRNA expression profiling of 36 WTs of different subtypes and four normal kidney tissues using microarrays. Additionally, we determined the gene expression profile of 28 of these tumors to identify potentially correlated target genes and affected pathways. We identified 85 miRNAs and 2107 messenger RNAs (mRNA) differentially expressed in blastemal WT, and 266 miRNAs and 1267 mRNAs differentially expressed in regressive subtype. The hierarchical clustering of the samples, using either the miRNA or mRNA profile, showed the clear separation of WT from normal kidney samples, but the miRNA pattern yielded better separation of WT subtypes. A correlation analysis of the deregulated miRNA and mRNAs identified 13,026 miRNA/mRNA pairs with inversely correlated expression, of which 2844 are potential interactions of miRNA and their predicted mRNA targets. We found significant upregulation of miRNAs-183, -301a/b and -335 for the blastemal subtype, and miRNAs-181b, -223 and -630 for the regressive subtype. We found marked deregulation of miRNAs regulating epithelial to mesenchymal transition, especially in the blastemal subtype, and miRNAs influencing chemosensitivity, especially in regressive subtypes. Further research is needed to assess the influence of preoperative chemotherapy and tumor infiltrating lymphocytes on the miRNA and mRNA patterns in WT
The role of miR-21 in the pathophysiology of neuropathic pain using the model of B7-H1 knockout mice
(2017)
The impact of microRNA (miRNA) as key players in the regulation of immune and neuronal gene expression and their role as master switches in the pathophysiology of neuropathic pain is increasingly recognized. miR-21 is a promising candidate that could be linked to the immune and the nociceptive system. To further investigate the pathophysiological role of miR-21 in neuropathic pain, we assesed mice deficient of B7 homolog 1 (B7-H1 ko), a protein with suppressive effect on inflammatory responses.
B7-H1 ko mice and wildtype littermates (WT) of three different age-groups, young (8 weeks), middle-aged (6 months), and old (12 months) received a spared nerve injury (SNI). Thermal withdrawal latencies and mechanical withdrawal thresholds were determined. Further, we investigated anxiety-, depression-like and cognitive behavior. Quantitative real time PCR was used to determine miR-21 relative expression in peripheral nerves, dorsal root ganglia and white blood cells (WBC) at distinct time points after SNI.
Naïve B7-H1 ko mice showed mechanical hyposensitivity with increasing age. Young and middle-aged B7-H1 ko mice displayed lower mechanical withdrawal thresholds compared to WT mice. From day three after SNI both genotypes developed mechanical and heat hypersensitivity, without intergroup differences. As supported by the results of three behavioral tests, no relevant differences were found for anxiety-like behavior after SNI in B7-H1 ko and WT mice. Also, there was no indication of depression-like behavior after SNI or any effect of SNI on cognition in both genotypes. The injured nerves of B7-H1 ko and WT mice showed higher miR-21 expression and invasion of macrophages and T cells 7 days after SNI without intergroup differences. Perineurial miR-21 inhibitor injection reversed SNI-induced mechanical and heat hypersensitivity in old B7-H1 ko and WT mice.
This study reveals that reduced mechanical thresholds and heat withdrawal latencies are associated with miR-21 induction in the tibial and common peroneal nerve after SNI, which can be reversed by perineurial injection of a miR-21 inhibitor. Contrary to expectations, miR-21 expression levels were not higher in B7-H1 ko compared to WT mice. Thus, the B7-H1 ko mouse may be of minor importance for the study of miR-21 related pain. However, these results spot the contribution of miR-21 in the pathophysiology of neuropathic pain and emphasize the crucial role of miRNA in the regulation of neuronal and immune circuits that contribute to neuropathic pain.
MicroRNAs (miRNAs) are increasingly recognized as regulators of immune and neuronal gene expression and are potential master switches in neuropathic pain pathophysiology. miR-21 is a promising candidate that may link the immune and the pain system. To investigate the pathophysiological role of miR-21 in neuropathic pain, we assessed mice deficient of B7 homolog 1 (B7-H1), a major inhibitor of inflammatory responses. In previous studies, an upregulation of miR-21 had been shown in mouse lymphocytes. Young (8 weeks), middle-aged (6 months), and old (12 months) B7-H1 ko mice and wildtype littermates (WT) received a spared nerve injury (SNI). We assessed thermal withdrawal latencies and mechanical withdrawal thresholds. Further, we performed tests for anxiety-like and cognitive behavior. Quantitative real time PCR was used to determine miR-21 relative expression in peripheral nerves, and dorsal root ganglia (DRG) at distinct time points after SNI. We found mechanical hyposensitivity with increasing age of naïve B7-H1 ko mice. Young and middle-aged B7-H1 ko mice were more sensitive to mechanical stimuli compared to WT mice (young: p < 0.01, middle-aged: p < 0.05). Both genotypes developed mechanical and heat hypersensitivity (p < 0.05) after SNI, without intergroup differences. No relevant differences were found after SNI in three tests for anxiety like behavior in B7-H1 ko and WT mice. Also, SNI had no effect on cognition. B7-H1 ko and WT mice showed a higher miR-21 expression (p < 0.05) and invasion of macrophages and T cells in the injured nerve 7 days after SNI without intergroup differences. Our study reveals that increased miR-21 expression in peripheral nerves after SNI is associated with reduced mechanical and heat withdrawal thresholds. These results point to a role of miR-21 in the pathophysiology of neuropathic pain, while affective behavior and cognition seem to be spared. Contrary to expectations, B7-H1 ko mice did not show higher miR-21 expression than WT mice, thus, a B7-H1 knockout may be of limited relevance for the study of miR-21 related pain.
Merkel cell carcinoma (MCC) is a deadly skin cancer, and about 80% of its cases have been shown to harbor integrated Merkel polyomavirus in the tumor cell genome. Viral oncoproteins expressed in the tumor cells are considered as the oncogenic factors of these virus-positive Merkel cell carcinoma (VP-MCC). In contrast, the molecular pathogenesis of virus-negative MCC (VN-MCC) is less well understood. Using gene expression analysis of MCC cell lines, we found histone methyltransferase PRDM8 to be elevated in VN-MCC. This finding was confirmed by immunohistochemical analysis of MCC tumors, revealing that increased PRDM8 expression in VN-MCC is also associated with increased H3K9 methylation. CRISPR-mediated silencing of PRDM8 in MCC cells further supported the histone methylating role of this protein in VN-MCC. We also identified miR-20a-5p as a negative regulator of PRDM8. Taken together, our findings provide insights into the role of PRDM8 as a histone methyltransferase in VN-MCC tumorigenesis.
Das Prostatakarzinom (PCa) stellt die zweithäufigste krebsbedingte Todesursache bei Männern in Deutschland dar. Seine heterogenen Verlaufsformen erschweren es, eine optimale Therapieentscheidung zu treffen, denn die derzeit bekannten klinischen und molekularen Prognosemarker sind trotz intensiver Forschungsbemühungen nicht ausreichend in der Lage den Krankheitsverlauf vorherzusagen. Große Hoffnungen auf brauchbare prognostische Marker werden seit ihrer Entdeckung in miRNAs gesetzt, kleine genregulatorische, nicht-kodierende RNAs. MiRNAs regulieren im Rahmen einer posttranskriptionellen Inhibierung die Expression einer Vielzahl relevanter Zielgene. Für einige miRNAs ist bereits belegt, dass ihre differentielle Expression in verschiedenen Tumorentitäten mit der Genese und in einzelnen Fällen auch mit der Prognose assoziiert ist.
Diese Arbeit sollte untersuchen, welches globale miRNA-Expressionsprofil in einem Kollektiv von Hochrisiko-Prostatakarzinomen (HR-PCa) vorliegt und welche miRNAs im HR-PCa aberrant exprimiert sind. Zudem sollte sie klären, ob Assoziationen der so identifizierten miRNAs mit Prognosegruppen des PCa vorliegen. Somit sollten erste Hinweise auf prognostisch relevante miRNAs und deren mögliche Bedeutung für die Tumorgenese aber auch für die Progression des PCa erbracht werden. Hierzu wurde die Expression von 640 miRNAs mittels Microarray-Analysen in Proben eines HR-PCa-Kollektivs (n=14) bestimmt und anschließend die Expression von acht tumorassoziierten miRNAs mittels qRT-PCR in einem erweiterten HR-PCa-Kollektiv (n=23) evaluiert. Um eine Grundlage für weitere molekulare Analysen vorzubereiten, wurde eine Zielgensuche in drei verschiedenen Datenbanken für elf potentielle Onkomirs durchgeführt.
Im Vergleich zum nicht-tumorös veränderten Referenzgewebe wurden mittels Microarray-Analyse im HR-PCa 52 miRNAs als signifikant unterschiedlich exprimiert detektiert und es zeigte sich eine ausgeprägte Herunterregulation der globalen miRNA-Expression im HR-PCa. Mit diesen 52 miRNAs konnte in einer Clusteranalyse das Referenzgewebe von HR-PCa unterschieden werden. Bei 21 tumorspezifischen miRNAs zeigte sich eine Überlappung mit Daten bereits publizierter Studien. Hierunter fanden sich die als Onkomirs beschriebenen miRNAs miR-let-7a, miR-126 und miR-16 mit jeweils möglichen Zielgenen wie z.B. MAP4K3, EGFR und ESSRA. 15 miRNAs waren – im Gegensatz zur Expression in Kollektiven mit konventionellem Risikoprofil – im HR-PCa gegenüber nicht-malignem Referenzgewebe signifikant unterschiedlich exprimiert, darunter miR-515-5p mit den vorhergesagten Zielgenen C13orf34 und CDCA7. Die vorliegenden qRT-PCR-Analysen zeigten eine deutliche und häufige Herunterregulation von miR-221, -125b und -29a im HR-PCa. Als mögliche Zielgene wurden z.B. FOS und IRF2 für miR-221, EIF2C2 für miR-125b sowie MYBL2 und TRAF4 für miR-29a vorhergesagt. Mit den genannten drei miRNAs konnte das HR-PCa vom nicht-malignen Referenzgewebe unterschieden werden.
Anhand eines Expressionsprofiles von 24 miRNAs war eine partielle Trennung der Kollektive nach Gleason-Score möglich. Die miRNAs miR-147 und miR-515-3p waren in den Microarray-Analysen in Prognosegruppen nach dem Gleason-Score signifikant unterschiedlich exprimiert. Eine mittels qRT-PCR determinierte niedrige Expression von miR-221 konnte mit hohem Gleason-Score assoziiert werden. Die signifikant unterschiedliche Expression von miR-422a in Prognosegruppen des PCa konnte in den Validierungsexperimenten nicht bestätigt werden.
Die miRNAs miR-147, miR-515-3p bzw. miR-221 sind mit Blick auf ihr Potential als Prognosefaktoren Kandidaten für weitere Untersuchungen. Als potentielle Zielgene wurden z.B. RGS3, CDKN1B bzw. FOS/IRF2 vorhergesagt.
Die Bedeutung einzelner miRNAs als mögliche prognostische Marker sollte in größeren Kollektiven und anhand von funktionellen Untersuchungen weiter geklärt werden. Die vorliegende Arbeit stellt eine Grundlage dar, um in weiterführenden Untersuchungen die hier im HR-PCa aberrant exprimierten miRNAs als brauchbare prognostische Marker für das PCa zu bestätigen und deren molekulare Funktionen im Rahmen der Genese des HR-PCa zu definieren.