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An overexpression of the E3 ubiquitin ligase TRIM25 is implicated in several human cancers and frequently correlates with a poor prognosis and occurrence of therapy resistance in patients. Previous studies of our group have identified the mRNA encoding the pro-apoptotic caspase-2 as a direct target of the ubiquitous RNA binding protein human antigen R (HuR). The constitutive HuR binding observed in colon carcinoma cells negatively interferes with the translation of caspase-2 mainly through binding to the 5' untranslated region (UTR) of caspase-2 and thereby confers an increased survival of tumor cells. The main objective of this thesis was to unravel novel regulatory proteins critically involved in the control of caspase-2 translation and their impact on therapeutic drug resistance of human colon carcinoma cells. By employing RNA affinity chromatography in combination with mass-spectrometry, among several putative caspase-2 mRNA binding proteins, we have identified the tripartite motif-containing protein 25 (TRIM25) as novel caspase-2 translation regulatory protein in colon carcinoma cells. The constitutive TRIM25 binding to caspase-2 mRNA in two different human colorectal carcinoma cell lines was validated by ribonucleoprotein (RNP)-immunoprecipitation (RIP)-RT-PCR assay and by means of biotin-labeled RNA-pull-down assay. Since caspase-2 is a caspase which is particularly involved in the DNA-damage-induced apoptosis, I tested the functional relevance of negative caspase-2 regulation by TRIM25 for chemotherapeutic drug-induced cell death of different adenocarcinoma cells by RNA interference (RNAi)- mediated loss-of-function and gain-of-function approaches. In the first part of the thesis, I could demonstrate that transient silencing of TRIM25 caused a significant increase in caspase-2 protein levels without affecting the amount of corresponding mRNAs. Mechanistically, the TRIM25 silencing-triggered increase in caspase-2 was totally impaired by cycloheximide, indicating that the stimulatory effects on caspase-2 levels depend on protein synthesis. This finding was corroborated by RNP/polysomal fractionation, which revealed that the transient knockdown of TRIM25 caused a significant redistribution of caspase-2 transcripts from the fraction of RNP particles to that from translationally active polyribosomes.
The second part of my thesis aimed at the elucidation of the functional consequences of the negative caspase-2 regulation by TRIM25 for enhanced tumor cell survival. Thereby, I found that the siRNA-mediated knockdown of TRIM25 caused a significant increase in the chemotherapeutic drug-induced cleavage of caspase-3 and to elevations in cytoplasmic cytochrome c levels implicating that TRIM25 depletion did mainly affect the intrinsic apoptotic pathway. Concordantly, the ectopic expression of TRIM25 caused a reduction in caspase-2 protein levels, concomitant with an attenuated sensitivity of tumor cells to doxorubicin.
To test the functional impact of caspase-2 in the TRIM25 depletion-dependent sensitization to drug-induced apoptosis, I employed a siRNA-mediated knockdown of caspase-2. Interestingly, the strong induction of caspase-3 and -7 cleavage after doxorubicin treatment was fully impaired after the additional knockdown of caspase-2, indicating the sensitizing effects by TRIM25 knockdown depend on caspase-2.
Data from this thesis identified the TRIM25 as a novel RNA-binding protein of caspase-2 mRNA, which negatively interferes with the translation of caspase-2 and which functionally contributes to chemotherapeutic drug resistance of colon carcinoma cells. Interfering with the negative TRIM25-caspase-2 axis may represent a promising therapeutic avenue for sensitizing colorectal cancers to conventional anti-tumor therapies.
Natural science is only just beginning to understand the complex processes surrounding transcription. Epitranscriptional regulation is in large parts conveyed by transcription factors (TFs) and two recently discovered small RNA (smRNA) species: microRNAs (miRNAs) and transfer RNA fragments (tRFs). As opposed to the fairly well-characterised function of TFs in shaping the phenotype of the cell, the effects and mechanism of action of smRNA species is less well understood. In particular, the multi-levelled combinatorial interaction (many-to-many) of smRNAs presents new challenges to molecular biology. This dissertation contributes to the study of smRNA dynamics in mammalian cells in several ways, which are presented in three main chapters.
I) The exhaustive analysis of the many-to-many network of smRNA regulation is reliant on bioinformatic support. Here, I describe the development of an integrative database capable of fast and efficient computation of complex multi-levelled transcriptional interactions, named miRNeo. This infrastructure is then applied to two use cases. II) To elucidate smRNA dynamics of cholinergic systems and their relevance to psychiatric disease, an integrative transcriptomics analysis is performed on patient brain sample data, single-cell sequencing data, and two closely related in vitro human cholinergic cellular models reflecting male and female phenotypes. III) The dynamics between small and large RNA transcripts in the blood of stroke victims are analysed via a combination of sequencing, analysis of sorted blood cell populations, and bioinformatic methods based on the miRNeo infrastructure. Particularly, importance and practicality of smRNA:TF:gene feedforward loops are assessed.
In both analytic scenarios, I identify the most pertinent regulators of disease-relevant processes and biological pathways implicated in either pathogenesis or responses to the disease. While the examples described in chapters three and four of this dissertation are disease-specific applications of miRNeo, the database and methods described have been developed to be applicable to the whole genome and all known smRNAs.
Alzheimer’s disease (AD) is the major cause of dementia. It is characterized by the accumulation of abnormal proteins (amyloid-β plaque and neurofibrillary tangles) leading to loss of synapses, dendrites, neurons, memory and cognition. Sporadic late-onset AD is the major type of AD characterized by unclear etiology and a lack of disease-modifying therapy. To understand this disease, an alternative AD hypothesis has been proposed: AD may resemble diabetes in the brain or “diabetes type 3”. This hypothesis is supported by the fact that (1) brain glucose hypometabolism precedes AD clinical symptoms and (2) diabetes increases the risk of AD. To test this hypothesis, wild-type rats receiving intracerebroventricular administration of streptozotocin (icv-STZ) were used as a model. Streptozotocin (STZ) is a glucosamine-nitrosourea compound commonly used to induce experimental diabetes by peripheral administration. A similar pathological mechanism to peripheral STZ is then proposed to explain icv-STZ toxicity: insulin receptor signaling impairment results in glucose hypometabolism leading to cognitive deficits.
Objective: Icv-STZ model seems promising as a toxin-induced, non-transgenic AD model with the possibility to connect AD and diabetes mellitus (DM), one of the risk factors for AD. However, the mechanisms of how icv-STZ induced AD-like symptoms are unclear. Therefore, using microdialysis as the main technique, we tested 2 AD hypotheses in this model: (1) the glucose hypometabolism as an alternative AD hypothesis and (2) the cholinergic deficit as an important characteristic of AD pathology. Hippocampus was chosen because cholinergic function in this region is severely affected in AD. In comparison, the striatum was chosen because it contains cholinergic interneurons and is less affected in AD.
Methods: In this study, we used male Wistar rats of 190-220 g body weight (5 weeks of age). The rats were injected intracerebrally with STZ at a dose of 3 mg/kg (2x1.5 mg/kg; „high dose“) and 0.6 mg/kg („low dose“) with saline as control. After 21 days, samples were collected to investigate cholinergic and metabolic changes using histology, biochemistry, and neurochemistry. Brain injury was confirmed using GFAP staining and Fluoro jade staining in the hippocampus. Mitochondrial toxicity was investigated by measurement of mitochondrial
respiratory function in both hippocampus and striatum. Cholinergic markers such as acetylcholinesterase (AChE) activity, choline acetyltransferase (ChAT) activity, and choline transporter (CHT-1) activity, commonly known as high-affinity choline uptake (HACU), were measured in both hippocampus and striatum using a spectrophotometer and a scintillator.
Microdialysis is the main technique in our study. It was done in awake animals under behavioral or pharmacological stimulation. We used a self-built probe with a semi-permeable membrane (pore size of 30 kDa) that was implanted in either hippocampus or striatum. The probes were then perfused with artificial cerebrospinal fluid (aCSF) supplemented with 0.1 μM neostigmine for extracellular acetylcholine level measurement. During the perfusion, small hydrophilic compounds from brain extracellular space diffuse into the dialysates. Dialysates of 15 minutes intervals were collected for 90 minutes and used for analysis. After collection of dialysates for the first 90 minutes (basal data), rats were moved to an open field box (35x32x20 cm) for behavioral stimulation. After collection of the second 90 minute dialysates, the rats were transferred back to the microdialysis cage and dialysates were collected for another 90 minutes. On day 2, after collection of dialysates under basal conditions, 1 μM scopolamine was added to the perfusion solution for stimulation of acetylcholine release. The dialysates were also collected for 90 min followed by another 90 min of dialysis without scopolamine. The microdialysate samples were then analyzed as follows. ACh level was measured by HPLC-ECD. Glucose metabolites (glucose, lactate, pyruvate) were measured by a CMA-600 microanalyzer. An alternative energy metabolite (beta-hydroxybutyrate/BHB) was measured by GC-MS. Choline and glycerol as membrane breakdown markers were also measured by HPLC-ECD and CMA-600 microanalyzer, respectively. Markers of oxidative stress (isoprostanes) were measured using a commercially available ELISA kit.
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