In Parkinson's disease, cholinergic neurons of the pedunculopontine nucleus, located in the upper pons, undergo extensive degeneration, contributing to severe hypokinetic-motor and non-motor symptoms. We previously demonstrated that loss of these neurons is associated with mitochondrial dysfunction, driven by high mitochondrial DNA deletion burden. Increased mitochondrial DNA replication was also observed in these neurons, contrasting with reduced mitochondrial DNA copy number previously reported in Parkinson's-affected surviving nigral-dopaminergic neurons. Here, ultra-deep whole-genome sequencing combined with stringent quality control was used to characterise mitochondrial DNA alterations within single-cell pedunculopontine-cholinergic neurons isolated from Parkinson's-affected and neurologically-normal post-mortem specimens. Analyses included mitochondrial DNA deletion spectrum, -size distribution, genomic location, heteroplasmy levels, breakpoint classification, and point-mutation frequency. Thermodynamic modelling was used to investigate whether the stability of mitochondrial DNA secondary structures surrounding deletion breakpoints could provide insight into the mechanisms underlying mitochondrial DNA deletion formation in Parkinson's disease. In parallel, nuclear-encoded mitochondrial pathway responses were assessed using a customised single-cell multiplexed multi-target gene expression assay, comparing Parkinson's and control post-mortem neurons. Parkinson's-affected neurons exhibited substantial mitochondrial DNA damage, characterised by large-scale mitochondrial DNA deletions predominantly locating within mitochondrial DNA's major arc. Mitochondrial DNA deletions ranged ∼50-5,500 base-pairs, with most exceeding 1,000 base-pairs. Clonal expansion of large-scale mitochondrial DNA deletions, likely arising from replication-associated errors, represented the dominant mutant species. Small mitochondrial DNA deletions (<50bp) were rare, suggesting that free radical-induced strand breakage was not the primary driver of somatic mitochondrial DNA damage. Point-mutation frequency was similar between Parkinson's and control neurons but showed greater functional impact on electron transport chain complex-I subunits in Parkinsonian neurons. Thermodynamic modelling revealed reduced stability of mitochondrial DNA secondary structures flanking mitochondrial DNA deletion breakpoints in Parkinsonian post-mortem neurons, with an average decrease of ∼2 kJ/mol across two major mitochondrial DNA deletions formation models. The increased mitochondrial DNA damage was accompanied by marked upregulation of the nuclear-encoded mitophagy regulator PINK1, specifically in PD patients with extended survival, suggesting activation of a compensatory cytoprotective response. Together, these findings provide comprehensive single-cell resolution profiling of mitochondrial genomic alterations in pedunculopontine-cholinergic neurons in Parkinson's, displaying extensive mitochondrial DNA structural disruption dominated by large-scale mitochondrial DNA deletions. Our results further suggest that upregulation of mitophagy-related pathways may represent an adaptive mechanism to mitigate progressive mitochondrial genomic instability and preserve neuronal energy homeostasis.
