Finding Common Patterns In Heterogeneous Perturbation Data

This work investigates and proposes statistical analysis methods for pattern detection in high-throughput data from perturbation experiments in biology and medicine. This is demonstrated in three examples. The first part of this thesis investigates the transcriptional responses of TGF-beta stimulation in different human and mouse cell types based on time-course microarray data from extensive experiments. The used statistical and bioinformatics methods enabled to identify commonly affected biological subsystems across different cell types. In particular the analysis suggests an important role of transcription factors, which appear to have a conserved influence across cell-types and species. Validation via an independent dataset confirms the findings and network analyses suggest explanations, how TGF-beta perturbation could lead to the observed effects. The second part investigates pro epileptic markers in microRNA expression profiling data from perturbation-induced pathogenic animal models. Experimental implica-tions resulting in incomplete and censored high-throughput qPCR data impairs the performance of analysis methods. A designated test procedure, which showed higher detection power at lower false positive rates base on simulated data, is proposed to resolve this issue. The method enabled the identification of novel pathogenic relevant miRNAs in epilepsy models. In the last part of this work a new method for drug-drug similarity assessment based on drug-proteins interaction network and drug pharmacological effects on disease related targets is proposed. The similarity measure, which does not require chemical structure information, is applied within a consensus clustering algorithm to detect useful patterns in a large compound dataset from different diseases. The method produced separated and stable clusters that could not be found using chemical structure-based approaches. Target proteins of compounds falling into one cluster suggested several new compound-target combinations, which could in several cases be confirmed by independent data. Altogether this thesis demonstrates that advanced analysis methods could help to extract common patterns from complex and seemingly heterogeneous data

Co-Inflammatory Roles of TGFβ1 in the Presence of TNFα Drive a Pro-inflammatory Fate in Mesenchymal Stem Cells

High plasticity is a hallmark of mesenchymal stem cells (MSCs), and as such, their differentiation and activities may be shaped by factors of their microenvironment. Bones, tumors, and cardiomyopathy are examples of niches and conditions that contain MSCs and are enriched with tumor necrosis factor α (TNFα) and transforming growth factor β1 (TGFβ1). These two cytokines are generally considered as having opposing roles in regulating immunity and inflammation (pro- and anti-inflammatory, respectively). Here, we performed global gene expression analysis of human bone marrow-derived MSCs and identified overlap in half of the transcriptional programs that were modified by TNFα and TGFβ1. The two cytokines elevated the mRNA expression of soluble factors, including mRNAs of pro-inflammatory mediators. Accordingly, the typical pro-inflammatory factor TNFα prominently induced the protein expression levels of the pro-inflammatory mediators CCL2, CXCL8 (IL-8), and cyclooxygenase-2 (Cox-2) in MSCs, through the NF-κB/p65 pathway. In parallel, TGFβ1 did not elevate CXCL8 protein levels and induced the protein expression of CCL2 at much lower levels than TNFα; yet, TGFβ1 readily induced Cox-2 and acted predominantly via the Smad3 pathway. Interestingly, combined stimulation of MSCs by TNFα + TGFβ1 led to a cooperative induction of all three inflammatory mediators, indicating that TGFβ1 functioned as a co-inflammatory cytokine in the presence of TNFα. The cooperative activities of TNFα + TGFβ1 that have led to CCL2 and CXCL8 induction were almost exclusively dependent on p65 activation and were not regulated by Smad3 or by the upstream regulator TGFβ-activated kinase 1 (TAK1). In contrast, the TNFα + TGFβ1-induced cooperative elevation in Cox-2 was mostly dependent on Smad3 (demonstrating cooperativity with activated NF-κB) and was partly regulated by TAK1. Studies with MSCs activated by TNFα + TGFβ1 revealed that they release factors that can affect other cells in their microenvironment and induce breast tumor cell elongation, migration, and scattering out of spheroid tumor masses. Thus, our findings demonstrate a TNFα + TGFβ1-driven pro-inflammatory fate in MSCs, identify specific molecular mechanisms involved, and propose that TNFα + TGFβ1-stimulated MSCs influence the tumor niche. These observations suggest key roles for the microenvironment in regulating MSC functions, which in turn may affect different health-related conditions

Die IgG4-assoziierte Orbitopathie

IgG4-assoziierte Erkrankungen sind seltene, progredient verlaufende Krankheitsbilder. Diese fibrosierenden Entzündungen mit tumoröser Schwellung können sich in jedem Organ manifestieren. Ihre Ätiologie und Pathomorphologie sind bisher kaum verstanden. Die Abgrenzung von IgG4-assoziierter Erkrankungen von entzündlichen, malignen und rheumatischen Prozessen ist häufig schwierig. Als Hauptkriterien gelten erhöhte IgG4-Serumkonzentrationen, Nachweis erhöhter IgG4-Plasmazellinfiltration sowie eine storiforme Fibrose im Präparat. Es handelt sich dabei um eine Ausschlussdiagnose.Wir behandeln eine 66-jährige, kaukasische Patientin, welche uns notfallmäßig mit einer chronischen exazerbierten Rhinosinusitis mit orbitaler Beteiligung und multiplen Voroperationen zugewiesen wurde. Es wurden rechtsseitige supraorbitale Cephalgien, Ptosis, Lidödem sowie Visusminderung beschrieben. Bei initialer bildmorphologischer Verdachtsdiagnose eines Retrobulbärabszesses erfolgte die notfallmäßige operative Intervention. In der histopathologischen Auswertung wurde eine erhöhte IgG4-Plasmazellinfiltration als Hinweis für eine IgG4-assoziierte Grunderkrankung festgestellt. Ein systemischer Befall der Krankheit wurde ausgeschlossen. Neben den wiederholten operativen Interventionen wurden parallel Glucocorticoide verabreicht. Im Verlauf zeigten sich neben der Orbita auch die gleichseitige Nasenhaupthöhle, der Sinus maxillaris und der Sinus frontalis betroffen.Im europäischen Raum wurden bisher kaum Fälle berichtet. In der Literatur werden weltweit ca. 240 Fälle im HNO-Bereich diskutiert, wobei mehr als 85% der Fälle vor allem aus der asiatischen Population stammen. Eine IgG4-assoziierte Orbitopathie stellt damit eine seltene Differentialdiagnose entzündlicher Veränderungen im HNO-Bereich dar.Der Erstautor gibt keinen Interessenkonflikt an

TGF-β stimulation in human and murine cells reveals commonly affected biological processes and pathways at transcription level

BACKGROUND: The TGF-β signaling pathway is a fundamental pathway in the living cell, which plays a key role in many central cellular processes. The complex and sometimes contradicting mechanisms by which TGF-β yields phenotypic effects are not yet completely understood. In this study we investigated and compared the transcriptional response profile of TGF-β1 stimulation in different cell types. For this purpose, extensive experiments are performed and time-course microarray data are generated in human and mouse parenchymal liver cells, human mesenchymal stromal cells and mouse hematopoietic progenitor cells at different time points. We applied a panel of bioinformatics methods on our data to uncover common patterns in the dynamic gene expression response in respective cells. RESULTS: Our analysis revealed a quite variable and multifaceted transcriptional response profile of TGF-β1 stimulation, which goes far beyond the well-characterized classical TGF-β1 signaling pathway. Nonetheless, we could identify several commonly affected processes and signaling pathways across cell types and species. In addition our analysis suggested an important role of the transcription factor EGR1, which appeared to have a conserved influence across cell-types and species. Validation via an independent dataset on A549 lung adenocarcinoma cells largely confirmed our findings. Network analysis suggested explanations, how TGF-β1 stimulation could lead to the observed effects. CONCLUSIONS: The analysis of dynamical transcriptional response to TGF-β treatment experiments in different human and murine cell systems revealed commonly affected biological processes and pathways, which could be linked to TGF-β1 via network analysis. This helps to gain insights about TGF-β pathway activities in these cell systems and its conserved interactions between the species and tissue types