Single‐cell expression profiling of dopaminergic neurons combined with association analysis identifies pyridoxal kinase as Parkinson's disease gene

Abstract

Objective-The etiology of Parkinson disease (PD) is complex and multifactorial, with hereditary and environmental factors contributing. Monogenic forms have provided molecular clues to disease mechanisms but genetic modifiers of idiopathic PD are still to be determined.Methods-We carried out whole-genome expression profiling of isolated human substantia nigra (SN) neurons from patients with PD vs. controls followed by association analysis of tagging single-nucleotide polymorphisms (SNPs) in differentially regulated genes. Association was investigated in a German PD sample and confirmed in Italian and British cohorts.Results-We identified four differentially expressed genes located in PD candidate pathways, ie, MTND2 (mitochondrial, p = 7.14 × 10 −7 ), PDXK (vitamin B6/dopamine metabolism, p = 3.27 × 10 −6 ), SRGAP3 (axon guidance, p = 5.65 × 10 −6 ), and TRAPPC4 (vesicle transport, p = 5.81 × 10 −6 ). We identified a DNA variant (rs2010795) in PDXK associated with an increased risk of PD in the German cohort (p = 0.00032). This association was confirmed in the British (p = 0.028) and Italian (p = 0.0025) cohorts individually and reached a combined value of p = 1.2 × 10 −7 (odds ratio [OR], 1.3; 95% confidence interval [CI], 1.18-1.44).Interpretation-We provide an example of how microgenomic genome-wide expression studies in combination with association analysis can aid to identify genetic modifiers in neurodegenerative disorders. The detection of a genetic variant in PDXK, together with evidence accumulating from clinical studies, emphasize the impact of vitamin B6 status and metabolism on disease risk and therapy in PD.Parkinson's disease (PD) is a neurodegenerative disorder, characterized by age-related dysfunction and loss of dopaminergic neurons in the substantia nigra (SN) pars compacta (SNc). Hereditary forms of PD have provided evidence for linkage to 13 loci and nine causative genes, and their functional study has greatly helped to elucidate molecular disease mechanisms. 1 For idiopathic PD, both genetic and environmental factors are believed to modulate disease risk, but the impact of genetic variants remains unclear. 2 Genome-wide association (GWA) studies offer an unbiased approach for detecting effects in common variants, but large studies with sufficient power are still lacking. Restriction to candidate genes increases the a priori odds for phenotypic involvement and thus the chance of detecting significant associations. Here, we applied a functional genomic approach for the discovery of candidate genes and key regulatory pathways. We focused directly on the In order to isolate high-quality RNA from frozen human brain tissues, tissue pH and RNA integrity numbers (RIN) were measured in homogenates of frontal cortex and mid-brain sections from 41 suitable cases and 39 controls. This provided eight cases and nine agematched controls of good RNA quality for laser microdissection (LMD). Postmortem data for matched cases/controls were as follows: age at death 78.6 ± 6.5/76.8 ± 9.8 years; postmorte...

High Dimensional Endophenotype Ranking in the Search for Major Depression Risk Genes

“…Other members of the ubiquitin-proteosome system were previously implicated in anxiety, depression and vulnerability to seizures (47, 48). PDXK , an essential cofactor in the intermediate metabolism of amino acids and neurotransmitters, including serotonin and dopamine (49), confers risk for Parkinson disease (50) and epilepsy (49). Additionally, MARK2 and ABHD12 have previously been implicated in neuronal migration (51), degeneration (52) and regulation of endocannabinoid signaling pathways (53), respectively.…”

Exploiting the potential of molecular profiling in Parkinson’s disease: current practice and future probabilities

“…In another whole-genome expression profiling study, the genomic conversion approach was used to identify gene candidates based on whether they were differentially expressed in SN neurons from PD patients and controls and associated with disease at a tagging SNP level [127]. Four possible biomarker candidates were identified: a NADH dehydrogenase (MTND2), a pyridoxal kinase (PDXK, vitamin B6/dopamine metabolism,), SRGAP3 (axon guidance) and TRAPPC4 (vesicle transport).…”

Genetics of Parkinson disease and essential tremor

“…Recently, Elstner and colleagues [30 • ] reported an association between genetic variation in the pyridoxal kinase gene ( PDXK ) and risk for Parkinson disease. They used an innovative approach by examining the whole-genome expression profile in isolated cells from the substantia nigra in patients with Parkinson disease and controls, followed by an association study.…”