Protein misfolding has a major implication in the development of neurodegenerative diseases like Alzheimer’s, Parkinson’s, Prions, Huntington’s and dementia. Elucidation of misfolded protein neurotoxicity for such chronic diseases has been challenging to model in the lab. Using cell cultures, the biology of misfolded proteins can be studied in short term, but the biologically integrated models remain to be established for long-term modeling. Therefore, in chapter I, we established an organotypic brain slice culture model that maintains the 3-dimensional environment and functionally relevance for chronic studies. Further, we have experimentally demonstrated the applications such as viability assessment, response to toxicants, cytokine release, modeling traumatic brain injury, targeted gene delivery. In chapter II, we report a novel organotypic slice culture assay coupled with seeding assays such as real-time quaking-induced conversion (OSCAR) assay. We hypothesized that the brain slice cultures coupled with sensitive readouts would provide fast and efficient alternative to modeling prions ex-vivo. OSCAR model was characterized for seeding activity at various time points and the titers are quantified. OSCAR supports investigating the biological mechanisms of prions and supports screening of anti-prion therapeutics. chronic wasting disease (CWD) is a prion disease of cervids that has been rapidly expanding in several states in USA including Iowa and Canada. Therefore, in chapter III, I developed a CWD brain slice culture model to characterize the CWD prions. Using traditional prion detection and ultra-sensitive detection such as Real-Time Quaking-Induced Conversion (RT-QuIC) and Protein Misfolding Cyclic Amplification (PMCA), we characterize the seeding ability of CWD prions. Further, we demonstrate infectious ability of the CWD prions from slices to infect the mice. We also demonstrate the diagnostic ability of this model to detect CWD prions from a biological sample. Environmental factors such as Manganese can induce neuroimmune transformations that possibly alter the course of neurodegenerative processes. Therefore, in chapter IV, we systemically characterized the transcriptome of microglia in response to the neurotoxicant Manganese, misfolded α-syn, and the influence of their interaction. Our findings provide novel insights into global transcriptome of microglia. α-syn predominately activated innate immune genes particularly, cytokine and chemokines, TNF, NF-kB, and TLR signaling. In contrast, Mn caused distinct changes to pathways related to cellular senescence, NOD-like receptor signaling, HIF-1 signaling, and pyrimidine metabolism. Mn and α-syn co-treatment caused major perturbations in Rho GTPase signaling and inflammasome activation. Co-treatment also caused profound changes in transcripts that triggered microglia to switch to their more cytotoxic, M1 phenotype. Collectively, we report the brain slice cultures to model the in-vivo like propagation of amyloids in environmentally linked neurodegenerative disorders. The reliability of this quantitative model for protein misfolding diseases could help us in understanding the mechanisms of diseases and to identify potential therapeutic targets. Additionally, we identified novel microglial genes and pathways that are perturbated in response to Mn and α-syn that allow us to discover therapeutic targets for treatment of synucleinopathies such as Parkinson’s disease.