Single nuclear RNA sequencing shows altered microglial and astrocytic functions in post-mortem Parkinson’s disease tissue

ABSTRACT Background Parkinson’s disease (PD) is a neurodegenerative disease marked by a progressive loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc) and formation of misfolded protein aggregates. A growing body of research has implicated glial cell dysfunction in PD etiology, including the concentration of activated glial cells around protein aggregates in post-mortem tissue. Disruptions in the balance of pro– and anti-inflammatory immune response functions of the microglia and astrocytes is believed to contribute towards neurons being lost as the disease progresses. However, the molecular mechanisms remain unclear. To shed light on the role of inflammation in PD, this study analyses two public single nuclear RNA sequencing datasets of the SNpc from patient and control postmortem brain to identify altered molecular pathways in PD-associated microglia and astrocytes. Results The results show that both cell types have a significant upregulation in heat shock binding and misfolded protein response pathways, likely in response to the accumulation of protein aggregates. Microglia annotated with the MKI67 marker gene show a decreased expression in PD patient derived tissue. Markers associated with activated/reactive states in astrocytes and microglia are upregulated in PD samples. Notably, expression of genes associated with resting state microglia and non-inflammatory reactive state microglia are downregulated in PD microglia, including P2RY12, CSF1R, CSF2RA, CSF3R, and TGFBR1. Concurrently, genes associated with activated microglial states such as HSP90AB1 and GPNMB are upregulated. Among the top downregulated functions, genes associated with ion channel functions are downregulated in both astrocytes and microglia. Conclusions Taken together, the findings imply that astrocytes and microglia respond to protein misfolding pathology in PD by upregulating chaperone protein folding functions. Additionally, the profile of upregulated genes implies that pathways responding to oxidative stress are also activated. The downregulation of inflammation-associated genes in PD microglia paired with the upregulation of misfolding protein response pathways, suggests a switch from immune receptor functions to protein aggregate clearance by the end of disease stages. Finally, GPNMB emerged as a potential target for therapeutic intervention, as the one primary non-HSP gene that is significantly increased in PD-associated microglia. Abbreviations Parkinson’s disease (PD); neurodegenerative diseases (NDD); dopaminergic neurons (DNs); substantia nigra pars compacta (SNpc); microglia (Mg); Lewy body dementia (LBD); single nuclear RNA sequencing (snRNA-seq), single cell RNA sequencing (scRNA-seq); Gene Ontology (GO)

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