Cell-type specific roles of long non-coding RNAs in Neurodegenerative diseases
by Ranjit Pradhan
Date of Examination:2025-04-29
Date of issue:2025-07-14
Advisor:Prof. Dr. André Fischer
Referee:Prof. Dr. Tiago Fleming Outeiro
Referee:Prof. Dr. Alexander Flügel
Referee:Prof. Dr. Christine Stadelmann-Nessler
Referee:Prof. Dr. Oliver Wirths
Referee:Prof. Dr. Ralf Heinrich
Persistent Address:
http://dx.doi.org/10.53846/goediss-11268
Files in this item
Name:PhD Dissertation RP.pdf
Size:10.6Mb
Format:PDF
The following license files are associated with this item:
Abstract
English
Long non-coding RNAs (lncRNAs) are a heterogeneous group of RNAs that occupy a substantial proportion of the genome and are intricately involved in the regulation of various cellular processes. A notable feature of lncRNAs is their high cell- and tissue- specificity, and emerging evidence suggests that lncRNAs can play unique roles in individual cell-types. The specificity of lncRNAs is particularly noteworthy in the brain tissue as approximately 40% of the lncRNAs are predicted to be brain specific in expression. In the ageing brain, there are drastic changes at the cellular and molecular level that contribute to the age-related cognitive decline. Consequently, ageing is the primary risk factor for neurodegenerative diseases (NDDs) including Alzheimer’s disease (AD). Despite several studies describing the cell-type specific roles of lncRNAs in the brain, there is currently, limited information on the role of lncRNAs in the ageing- and AD- brain. lncRNAs provide a largely unexplored window into cellular functions in the healthy and diseased brains and offers a novel opportunity for the discovery of biomarkers and therapeutic targets for age-related NDDs like AD. My doctoral work was aimed at evaluating the roles of lncRNAs in a cell-type specific manner in the ageing- and AD- brain. To accomplish this, I identified and characterized two lncRNAs during my doctorate that are presented as two manuscripts in this dissertation. In the first manuscript, I describe a novel neuron-specific lncRNA that we named as “NeuID” (abbreviation for Neuronal Identity). NeuID was observed to be a neuron-specific and brain enriched lncRNA that is decreased in the brains of AD patients. NeuID possessed a human homolog and played a role in the regulation of gene-expression in neurons. Specifically, NeuID knockdown (KD) decreased the levels of synaptic genes in neurons and upregulated non-neuronal genes. The decrease in synaptic genes upon NeuID KD was consistent with the reduced neuronal activity and decreased dendritic spines and synapse density of primary hippocampal neurons. The changes in synaptic plasticity elicited by NeuID KD further resulted in impairment of memory consolidation in mice. These findings suggest that NeuID regulates synaptic plasticity through transcriptomic control of synaptic genes, and this in turn regulates memory formation in mice. I found NeuID to be decreased in the brains of AD patients and further observed that NeuID expression is negatively correlated with progressive Braak & Braak stages of AD pathology. Based on these observations, I studied the roles of NeuID in neuronal cells in the context of amyloid beta (Aβ) based AD-pathology. Aβ-exposure resulted in the reduction of NeuID levels in neurons and decrease in neuronal activity comparable to the findings in NeuID KD neurons. Overexpression of NeuID using CRISPRa resulted in the rescue of Aβ-mediated neuronal activity changes. Mechanistically, NeuID binds to the PRC2 complex subunit EZH2 to regulate h3k27me3-levels of non-neuronal genes. Decrease in h3k27me3 levels at the non-neuronal gene loci leads to the upregulation of non-neuronal genes. The upregulation of non-neuronal genes in neurons due to NeuID KD is contributing to the observed neuronal function impairment. Overall, this study identifies, to the best of my knowledge, the first neuron-specific lncRNA that is involved in the regulation of neuronal function in the context of AD. Additionally, NeuID provides an opportunity for the development of a lncRNA mediated therapy against neuronal pathology in AD. The second manuscript in this dissertation is focused on an ageing-related lncRNA named “3222401L13Rik”, and here I describe the functions of this lncRNA in microglia cells in the context of ageing and AD. 3222401L13Rik was observed to be increased in the glial cells of the aged mice brain. It was further increased in expression in aged microglia cells based on the single-cell ageing mouse brain database. 3222401L13Rik also has a human homolog named “ENSG00000272070” which shows decreased levels in the brains of AD patients. Both 3222401L13Rik and ENSG00000272070, upon KD, increased the expression of proinflammatory cytokine “TNF𝛼” in microglia cells of mice and human origin respectively. The elevated expression of TNF𝛼 was consistent with the observed increase in the phagocytic activity of microglia. The transcriptomic changes elicited in primary microglia and human derived iPSC microglia like cells (iMGLs) were comparable to the transcriptomic changes in the AD brain. Consequently, the KD of the lncRNA in primary microglia and iMGLs increased the engulfment of pathologic Aβ due to the increased phagocytic activity of microglia. Mechanistically, the lncRNA binds to the AD-associated TF PU.1, and the transcriptomic changes in microglia induced by PU.1 activity are similar, at least in part, to the transcriptomic changes elicited by 3222401L13Rik. In conclusion, these findings identify an ageing-related lncRNA that regulates microglia function through interaction with AD-associated TF PU.1. This lncRNA reveals a novel molecular mechanism behind PU.1 function in microglia, and lncRNA mediated regulation of PU.1 function could be a potential means to target microglia pathology in AD. In the context of ageing, I speculate that the increased levels of 3222401L13Rik in the ageing brain and microglia might play a protective role in healthy ageing by attenuating the levels of proinflammatory cytokines and microglia activity. In summary, this dissertation demonstartes the roles that lncRNAs play in specific cell-types in the brain, and adds to the growing literature of lncRNA involved in brain function. Moreover, these findings demonstrate a link between lncRNAs and AD-related cellular impairments, therefore, providing a yet unexplored avenue for therepautic intervention in AD.
Keywords: Neuroscience; RNA; lncRNA; Neuron; Microglia; Neurodegeneration; Alzheimer's Disease; RNA Therapeutics
