Class of 2012 Abstract / OBJECTIVES: Therapeutic response to chemotherapeutic agents in vitro can be studied using immortalized lymphoblastoid cell lines (LCLs). While LCLs provide a valuable model to study heritable factors and anticancer drug reponse in large populations, the results may be confounded by properties inherent to the model. This study is used to explore possible confounders in Choy et al.’s publicially available dataset (Accession#: GSE11582). METHODS: This study utilized Affymetrics U133A array gene expression and phenotypic data for 162 unrelated LCLs. SPSS was used for two-tailed bivariate Pearson correlation analysis comparing relative 6-mercaptopurine (6-MP), 5-fluorouracil (5-FU), and methotrexate sensitivities, growth rate and ATP levels. GeneSpring was used to compare the top and bottom quartiles of relative ATP levels using the unpaired T-test with a significance threshold of 0.001 and Benjamin-Hochberg FDR (n=82). RESULTS: It was found that relative sensitivities of 5-FU and 6-MP are significantly correlated (r2= 0.627, p<0.0001). Furthermore, it was determined that 5-FU sensitivity and growth rate and ATP levels are also correlated; however, no significant correlation was found between growth rate and ATP levles (r2=0.127, p=0.107). Relative ATP level was found to be a more significant determinant of 5-FU sensitivity than growth rate. GeneSpring analysis showed that 1500 genes are differentially regulated based on ATP levels. The gene ontology related to nucleic acid metabolism was overrepresented (p=1.425E-15). CONCLUSIONS: The results above suggest that growth rate and, to a greater extent, baseline ATP levels influence genetic expression of LCLs and may confound in vitro studies of antineoplastic agents.

A micronucleus assay was developed using HSC-3TO, a human continuous lymphoblastoid cell line (LCL) and cytochalasin B (Cyt-B) to block cytokinesis. Mitomycin C (MMC), a chemotherapeutic agent and an inducer of micronuclei in various human cell types, was used as a positive control. MMC induced micronuclei in HSC-3TO at levels over six times that of control cells when cells were treated with the D₅₀ dose (i.e., the dose of MMC which was toxic to 50% of treated cells). It was found that harvest time was a very important variable and that a harvest time of 108 hours was optimal. 2-Nitrofluoranthene (2-NFA), a nitrated polycyclic aromatic hydrocarbon, the most abundant nitroarene found in the particulate organic matter fraction of ambient air and a potent direct-acting mutagen in the Ames Salmonella assay, was tested using the established CBMN assay protocol. Doses (20, 200 and 2000 ng/mL 2-NFA) were chosen based on the estimated yearly total body exposure and did not produce elevated levels of micronuclei at a dose of 100 times the estimated yearly total body exposure. / Thesis / Master of Science (MS)

Human clinical genome-wide association studies (GWAS) have helped identify disease trait and pharmacogenomic loci without the need for biological under- standing. Molecular GWAS - associating genetic variation with traits such as gene expression - have been slow to fill the mechanistic gaps. While tissue specificity, lack of DNA resolution, and the need for better data integration are no dou bt important bottlenecks in molecular GWAS, there is also a very poor general understanding of which molecular phenotypes are important and how best to model them. Added to this is the clear need for a greater understanding of the strengths and weaknesses facing in vitro (and ex vivo) models as hypoth- esis generating and GWAS validation tools. The studies in this work focus on RNA expression in a popular human model: lymphoblastoid cell lines (LCLs). Chapters 2 and 3 examine microRNA (miRNA) and messenger RNA (mRNA) expression in a total of 300 genotyped human LCLs. The expression of only one miRNA could be associated with a nearby genetic variant. This result was observed in both the African and European samples studied, in a separate val- idation data set, and was technically validated with quantitative PCR. While limited genotype resolution and small sample sizes are likely to be important contributors to this low hit rate, the results strongly suggest experimental con- founders. Highly expressed miRNAs reflected the transformed nature of the cells, highly correlated miRNAs enriched for EBV and malaria associated tar- get mRNA genes, and several miRNAs that were differentially expressed be- tween the European and African samples suggested differential EBV transfer- mation. Chapter 4 presents a study on single cells from some of the same samples, to test the hypothesis that the lack of tissue spatial resolution is an important limiting factor in human genetic epidemiology. Experimental con- founders were also considered: sample growth was found to associate with the expression of several genes. Cell-to-cell gene correlations and distributions made it possible to propose how genes change their expression, functionally differ from each other, and are able to alter their behaviours without altered whole-tissue expression. The results suggest which type of genes are more likely to be susceptible to genetic effects, and propose promoter behaviours altered by genetic variants located near to 13 genes. From these whole-tissue and single cell results the broad conclusion is that, while LCLs are likely to be inappropriate for the study of miRNA genetics, their functional genomics at higher spatial resolution shows promise as a more mechanistic approach for the study of germline genetics.

The immune system is a target of arsenic toxicity. Epidemiological data have shown that arsenic exposure is associated with characteristics of immunosuppression. Human B-lymphoblastoid cell lines (LCL) were used as an in vitro model of immune cell targeting by arsenic to investigate the mechanism of arsenic-induced cytotoxicity, which could provided insight into the mechanism underlying arsenic-induced immunotoxicity leading to the immunosuppression observed in humans. In LCL arsenite-induced cytotoxicity was not associated with apoptosis, but associated with hallmarks of autophagy, a cell stress-responsive process that facilitates the removal of cellular components through lysosome-mediated degradation. At environmentally relevant concentrations, arsenite-induced toxicity resulted in a decrease in cell proliferation that was correlated with hallmarks of autophagy including expansion of acidic vesicles, global induction of lysosomal gene expression, increased flux of the autophagosome marker LC3-II, and increased enzymatic activity of the lysosomal hydrolase cathepsin D. Investigation of the upstream cellular damage leading to the induction of autophagy revealed that arsenite induces proteotoxic damage leading to an accumulation of protein aggregates that may be targeted to the lysosome for degradation. In addition, global gene expression data showed an enrichment of ER stress responsive genes after arsenite exposure. Further evaluation of global gene expression data indicated that the global induction of lysosomal genes occurs before the activation of ER stress genes, suggesting that the induction of autophagy may occur before the generation of ER stress. To investigate the effect of arsenite-induced proteotoxicity and autophagy on normal immune function, the ability of LCL to process and present exogenous antigens onto MHC class II molecules was evaluated. Arsenite decreased antigen presentation of the exogenous antigen HSA. This decrease was associated with decreased lysosomal degradation of the model substrate DQ-Ova, suggesting that arsenite is disrupting lysosome-mediated degradation. In addition, arsenite exposure was associated with an increase in MHC class II protein aggregates, which could render them unavailable to bind peptide fragments. Through the identification that arsenite induces proteotoxicity and autophagy in LCL, it provides novel insight into the mechanisms of arsenic-induced immunotoxicity that could lead to a better understanding of the mechanisms underlying arsenic-induced immunosuppression observed in humans.

Epstein-Barr Virus (EBV), a ubiquitous herpesvirus that infects over 95&percnt; of the adult human population, has been implicated in the aetiology of a range of autoimmune diseases and tumours. In some of these disorders such as post-transplant B-cell lymphomas, EBV acts as a direct causal factor, in others, like Hodgkin's disease and nasopharyngeal carcinoma, it is an important co-factor. Additionally, EBV infection has been linked to several other diseases, most notably Multiple Sclerosis through positive correlation with the occurrence of Infectious Mononucleosis – a benign lymphoproliferative disease caused by primary EBV infection. The key feature of most EBV-disease associations is the ability of the virus to infect and transform human B- T- NK- and epithelial cells using a set of transcripts and proteins, some of which act as oncogenes. While it is evident that EBV viral load and gene expression may be correlated with the course of disease or even directly contributing to its pathology, the genetic determinants of EBV uptake, expression and its proliferative capacity remain unresolved. This project aimed to investigate the genetic determinants of EBV copy number and EBV latency gene expression for human B-cells immortalised by EBV in vitro and transformed into permanently growing lymphoblastoid cell lines (LCLs), as a model for early-stage EBV infection in naïve B-cells. LCL samples studied have been sourced from several different populations, the HapMap Project, the 1000 Genomes Project as well as British MRC-A family cohort. Methods used encompass quantification of viral expression and copy number using TaqMan and SybrGreen PCR techniques, followed by statistical association tests conducted using Plink, Merlin and MatrixEQTL. EBV QTLs identified by the assays were next subjected to a meta-analysis in GWAMA. Two most significant eQTLs were also selected for a replication experiment in an independent panel of newly generated LCLs and validated in peripheral blood B-cells sourced from the same donors. Multiple significant and suggestive expression and copy number QTLs were identified. However, most of these associations have not been replicated in more than a single cohort. The relatively small sample size of most cohorts tested as well as population structure posed a limitation. Some findings merit attention, particularly the presence of statistically significant viral eQTLs within or close to CSMD1 locus in two different cohorts, and finding of a significant EBV eQTL in a SNP associated with type 1 diabetes risk and located close to IL2RA, an immune-response gene harbouring multiple autoimmune disease risk loci. Suggestive associations were also identified in the 1000 Genomes Project samples by the copy number assay which resulted in the most robust test conducted. These encompassed an association to the PRDM9 locus as well as to a gene involved in TGF-&beta; secretion. This is particularly interesting since TGF-&beta; signal promotes lytic replication in EBV-infected B-cells and a consistent significant correlation between EBV lytic expression and increased viral copy number has been identified. In conclusion, although no significant association has been consistently replicated, the project provided several suggestive EBV QTL candidates with plausible biological links to EBV infection and replication, which could be studied further in independent experiments.

No description available.

We have studied the effect of interferon α (IFN-α) on MHC class II expression by human buccal epithelial cells (BEC), and mRNA expression by BEC and mucosal-associated mononuclear cells (MAMC). In 6 experiments, freshly collected BEC were suspended at a concentration of 1.0 x 105/ml in RPMI 1640 and incubated in the presence of 0-10000 IU/ml of human lymphoblastoid IFN-α (HuIFN-α). Zero and six hour samples were analyzed by single color flow cytometry using FITC-labeled murine IgG1 monoclonal antibody to HLA-DR. Preparations were also analyzed for expression of cytokine transcripts (IL-2 IL-4, IL-5, IL-6, IL-8, IFN-γ, GM-CSF) by reverse transcriptase polymerase chain reaction (RT-PCR). Increasing concentrations of IFN-α resulted in proportionate increases in the percentage of HLA-DR + BEC (r = 0.7897, p = 0.0627) and in the percentage of HLA-DR + staining at higher intensities (101 to 102 log fluorescence intensity) (LFI) (r = 0.40l0, p = 0.0424). The percentage of HLA-DR + BEC rose from a mean of 1.5% with no IFN-α to 7% with 10000 IU/ml IFN-α (p < 0.05). The percentage of HLA-DR + BEC staining at 101 to 102 LFI rose from a mean of 8.3% with no added IFN-α to 19.2% with 10000 IU/ml IFN-α (p <0.05). Unstimulated BEC constitutively expressed IL-8 and GM-CSF. IFN-α stimulated preparations also expressed IFN-γ, possibly due to the presence of MAMC, which comprised 2-9% of the total cell population. These data indicated that HuIFN-α upregulates MHC class II expression by human BEC, possibly by enhancing IFN-γ production by MAMC present in the culture preparations.

No description available.

Neben chemotherapeutischen und chirurgischen Maßnahmen ist die Bestrahlung integraler Bestandteil multimodaler Therapiekonzepte bei malignen Tumorerkrankungen. In diesem Zusammenhang spielt der Einblick in physiologische und pathophysiologische Abläufe in menschlichen Zellen und auf molekularer Ebene  eine zunehmende Rolle. Auf diese Weise werden komplexe Stoffwechselwege mit ihren unterschiedlichen Funktionen und ihren aus einzelnen Proteinen bestehenden Komponenten immer besser verstanden. Allerdings entstehen durch die Kenntnis dieser Stoffwechselwege neue Fragen, die Gegenstand medizinischer Forschung sind.  Der TGFβ-Signalweg ist ein wesentlicher intrazellulärer Signalweg, der neben zahlreichen anderen Funktionen einen Einfluss auf die Entstehung bestimmter Tumorerkrankungen hat. Eine Vielzahl an Einzelnukleotid-Polymorphismen (single nucleotide polymorphisms, SNP) ist bekannt sowie die Erkenntnis darüber, dass die Anwesenheit von verschiedenen Varianten eines SNP einen Einfluss auf die Zellvitalität hat je nach Behandlungsbedingung. Ziel dieser Arbeit war es den Einfluss von Keimbahn-Polymorphismen in Genen des TGFβ-Signalwegs und der DNA-Reparatur auf die Strahlenempfindlichkeit lymphoblastoider Zellen zu untersuchen. Hierzu wurden 54 käuflich erworbene lymphoblastoide Zellen angezüchtet. Jede dieser Zelllinien wurde sechs parallelen Behandlungsbedingungen unterworfen. Neben der unbehandelten Kontrolle und einer mit anti-TGFβ behandelten Kontrolle wurden Zellen einer alleinigen Bestrahlung mit 3 Gy ausgesetzt. Darüber hinaus wurden Zellen 16 Stunden vor der Bestrahlung mit TGFβ1 oder anti-TGFβ vorinkubiert oder unmittelbar nach der Bestrahlung mit TGFβ1 behandelt.  Nach Ablauf einer 24-stündigen Inkubationszeit erfolgte die Zellvitalitätsmessung mittels FACS (fluorescence activated cell sorting)–Analyse. Die Ergebnisse wurden mit Daten von insgesamt 1656 polymorphen Positionen (aus HapMap Datenbank) aus 21 Kandidatengenen korreliert. Auf diese Weise sollte der Einfluss dieser Polymorphismen auf die Zellvitalität ermittelt werden. Sowohl bei SMAD3 als auch bei SMAD7 fanden sich jeweils 2 SNP, die ein perfektes bzw hohes Kopplungsungleichgewicht (linkage disequilibrium) aufwiesen. Insgesamt waren zwölf Polymorphismen aus acht Genen (TGFBR1, SMAD2, SMAD3, SMAD7, BRCA2, MSH2, MSH6 und XRCC1) mit signifikanten Veränderungen der Zellvitalität assoziiert. Das Variantenallel scheint bis auf wenige Ausnahmen einen zytoprotektiven Effekt zu haben. Ausnahmen sind 3 SNP der Gene BRCA2, SMAD3 und SMAD 7, bei denen der Wildtyp mit höherer Zellvitalität einhergeht. Bei alleiniger Bestrahlung wirkten sich SNP aus SMAD3, SMAD7, MSH2 und MSH6 modulierend auf die Zytotoxizität aus, wenn auch statistisch nicht signifikant. Interessanterweise zeigten sich bei Betrachtung der Auswirkung einer Stimulation mit TGFβ1 vor und nach Bestrahlung mit 3 Gy dieselben SNP als statistisch signifikante Modellprädiktoren wie auch bei alleiniger Bestrahlung mit Ausnahme eines SNP aus SMAD3.  Bei Vorinkubation mit TGFβ1 wirkte sich die MSH2-Variante stärker aus. Hier entstand beim Wildtyp ein zusätzlich zytotoxischer Einfluss im Vergleich zur Stimulation nach Bestrahlung. Bei Inhibition durch anti-TGFβ vor der Bestrahlung zeigte noch ein SNP aus MSH6 und ein SNP aus SMAD7 einen zytoprotektiven Effekt.  Einige Ergebnisse dieser Arbeit könnten, sofern sie im Verlauf durch nachfolgende Studien bestätigt bzw. erweitert werden helfen Therapiekonzepte maligner Tumoren zu optimieren und eine individuelle Radiotherapie zu ermöglichen.

Das Nijmegen-Breakage-Syndrom (NBS) ist ein autosomal-rezessiv vererbtes Chromosomenbruchsyndrom, dem in > 90% der Patienten eine 5bp-Deletion im Nbs1-Gen zugrundeliegt. Klinisches Hauptmerkmal ist ein stark erhöhtes Krebsrisiko, insbesondere für B-Zell-Lymphome. Bereits bekannt ist die Funktion des entsprechenden Genprodukts, Nibrin, bei den für die Krebsprävention wichtigen Mechanismen der DNA-Reparatur und der Zellzykluskontrolle. Daneben spielt die Apoptose eine essentielle Rolle bei der Krebsentstehung. Zu untersuchen ob Nibrin auch hier Funktionen übernimmt war Gegenstand dieser Arbeit. Eine Störung der Apoptose könnte dabei mitverantwortlich für das hohe Krebsrisiko der NBS-Patienten sein. Kern der Arbeit war die Untersuchung von NBS-B-Lymphozyten hinsichtlich ihrer Fähigkeit, nach einer DNA-Schädigung die Apoptose zu induzieren. Hierzu wurde in den entsprechenden Zellen mittels Bleomycin der Apoptoseprozess ausgelöst und die prozentualen Apoptoseraten durchflusszytometrisch bestimmt. Die Mehrheit der NBS-Zelllinien zeigte eine Störung in der Apoptoseinduktion im Sinne signifikant verminderter Apoptoseraten. Dies weist auf eine Funktion des Nibrins bei der Induktion der Apoptose hin. Andere NBS-Zelllinien zeigten normale Apoptoseindices. Dies könnte auf dem individuellen genetischen Hintergrund der Zellen beruhen, der auch für die erhebliche klinische Variabilität des Krankheitsbildes verantwortlich ist. Eine Korrelation der Apoptoseraten mit der Krebsinzidenz zeigte, dass alle Patienten mit reduzierten Apoptoseraten bereits Lymphome entwickelt hatten, während Patienten mit normalen Apoptoseindices bisher keine Lymphome aufwiesen. Möglicherweise gibt es also generell zwei Gruppen von NBS-Patienten - Patienten mit höherem und mit niedrigerem Entartungsrisiko, wobei eine verminderte Apoptoseinduktion als Risikofaktor für Krebs angesehen werden könnte. / The human genetic disorder, Nijmegen-Breakage-Syndrome (NBS), is characterised by an in increased risk for cancer, particularly B-cell-lymphoma. The Nbs1-gene codes for a protein, Nibrin, involved in the processing/repair of DNA double strand breaks and in cell cycle checkpoints - mechanisms relevant for cancer-prevention. As a third mechanism, apoptosis is important in preventing cancer. To evaluate whether Nibrin plays a role in this process was the aim of this study. Failure of apoptosis-induction could be another factor responsible for the high cancer risk in NBS. For this purpose we examined a set of NBS-B-cell-lines for their capacitiy to enter into apoptosis after a DNA-damaging treatment with Bleomycin. The majority of NBS-cell-lines showed a deficiency in apoptosis-induction. This may indicate a function of Nibrin in mechanisms of apoptosis-regulation. Some NBS-cell-lines showed a proficient apoptotic response, though. The reason may be found in the variable genetic background of the cell lines, also responsible for the high clinical variability of the disease. Correlation of apoptosis rates with cancer incidence showed that all patients deficient in apoptosis had already developed B-cell-lymphoma, whereas patients with normal rates had not developed lymphoma so far. Possibly there are two groups of NBS-patients- patients with higher and with lower risk of malignancy, with reduced apoptotic rates being a risk-factor for the development of cancer in NBS.