Amyloid-beta driven changes in transcriptome plasticity: From OMICS to Therapy

Alzheimer’s disease is characterized by a progressive cognitive decline coinciding with the formation of amyloid plaques and tau ﬁbrils in the human brain. It is the most common form of dementia and the number of people suffering from dementia worldwide was recently estimated to 46.8 million people, our knowledge on the molecular basics of AD and its development is rather little. Even though many different therapeutic drugs were tested in pre-clinical trials and some drugs are commonly used for treating AD patients, no cure is available yet. Unfortunately, the possibilities to study the disease in human patients is limited and mainly rely on post-mortem tissue. Thus, mouse models speciﬁcally reﬂecting different aspects of the disease were generated during the recent years. In this study, I used an APP/PS1 transgenic mouse line to study the speciﬁc effect of amyloid pathology on gene expression, DNA methylation and histone methylation, thereby identifying core modulators of disease progression and new potential therapeutic strategies for counteracting AD. I was able to show that amyloid deposits on gene expression are independent from the respective brain region, though the transcription proﬁles of these brain regions are strikingly diverse. This global deregulation of gene expression can be linked to a small set of TFs that might serve as target proteins for therapeutic drugs. Gene expression is mainly driven by immune response related processes while deregulation of genes that function in neuronal processes is rather mild. Interestingly though, the identiﬁed signiﬁcant TFs bridge the induction of immune response upon amyloid deposition with a loss of neuronal function leading to cognitive decline. The deregulation of genes and corresponding functional pathways becomes more severe with increasing age and thus follows the progressive cognitive decline observed in APP/PS1 mice. The wildtype-like cognitive performance of young transgenic mice can be explained by compensatory mechanisms counteracting the effect of neurotoxic Aβ. These compensatory mechanisms become overwhelmed while Aβ plaques spread, leading to pathological aging. In contrast to the strong effect of the immune response on gene expression, splicing does almost exclusively affect neuronal functioning and is rather affected by aging than amyloidosis. Nonetheless, I was able to detect differentially spliced genes with splice variants previously shown to promote the disease and identiﬁed two genes where alternative splicing was not yet related to neurodegenerative diseases, namely Thy1 and Ctsd. The deregulation of gene expres- sion observed in APP/PS1 mice might partially be driven my a global disruption of the epigenetic landscape concerning DNA methylation. This disruption, is likely to cause a deterioration in higher order chromatin structures and might thereby impact gene expression rather indirectly. In contrast, I claim that gene-directed effects of DNA methylation leading to the silencing of genes is primarily involved in encoding cell-fate. By using the DrugPairSeeker on RNAseq data, I identiﬁed a number of drugs potentially able to reinstate healthy gene expression in APP/PS1 transgenic mice through diverse mechanisms. Some of these drugs were already successfully tested in animal models for AD and our group recently conﬁrmed a beneﬁcial effect of the HDAC-inhibitor SAHA on cognition and neuro- inﬂammation in regard to AD. Here, I studied the therapeutic potential of a combinatory treat- ment of SAHA along with the NMDA-receptor antagonist memantine, a commonly used drug for AD patients. I hypothesized, that a combinatory treatment might broaden the medications’ eﬃcacy and enables the use of mild dosages of the individual drugs thereby limiting adverse side effects. Unfortunately, a beneﬁcial effect on memory functioning of either drug individually or in combination was not conﬁrmed for APP/PS1 mice, presumably due to the reduced dosages and mild cognitive impairment observed in mice of the chosen age. Altogether, I identiﬁed a set of core-modulators of differential gene expression and novel alternative splicing in the Thy1 and Ctsd genes that might drive disease progression. Furthermore, I hypothesize that the severe disruptions of gene expression are at least partially driven by deterioration of the chromatin architecture resulting from deregulated epigenetic mechanisms. Further experiments on DNA-DNA interactions via ”chromosome conﬁrmation capture” approaches and DNA-protein interactions, i.e. regarding CTCF, are necessary to test this hypothesis. Based on RNAseq data, I predicted a set of therapeutic drugs able to counteract amyloidosis in AD patients and illustrated the need for further studies concerning the combinatory usage of these drugs for enhancing the treatment of human patients. Based on previous studies regarding the identiﬁed drugs, I conclude that the applied procedure in this work is a suitable and valid approach for discovering novel therapeutic drugs for counteracting AD and other human diseases.