Pooled-DNA target sequencing of Parkinson genes reveals novel phenotypic associations in Spanish population

PTEN: a new dawn in Parkinson's disease treatment

In recent years, the study of phosphatase and tension homolog (PTEN) has gradually become a research hotspot. As an important oncogene, the role of PTEN in cancer has long been widely recognized and intensively studied, but it has been relatively less studied in other diseases. Parkinson's disease (PD) is a neurodegenerative refractory disease commonly observed in middle-aged and elderly individuals. The etiology and pathogenesis of PD are numerous, complex, and incompletely understood. With the continuous deepening of research, numerous studies have proven that PTEN is related to the occurrence of PD. In this review, we discuss the relationship between PTEN and PD through the phosphorylation and ubiquitination of PTEN and other possible regulatory mechanisms, including the role of RNA molecules, exosomes, transcriptional regulation, chemical modification, and subtype variation, with the aim of clarifying the regulatory role of PTEN in PD and better elucidating its pathogenesis. Finally, we summarize the shortcomings of PTEN in PD research and highlight the great potential of its future application in PD clinical treatment. These findings provide research ideas and new perspectives for the possible use of PTEN as a PD therapeutic target for targeted drug development and clinical application in the future.

Rethinking 'rare' PINK1 Parkinson's disease: A meta-analysis of geographical prevalence, phenotypic diversity, and α-synuclein pathology

PTEN-induced kinase 1 (PINK1)-related Parkinson's disease (PD) is traditionally considered a rare autosomal recessive form of early-onset PD (EOPD), lacking classical Lewy body pathology. However, this characterization underestimates and oversimplifies PINK1-PD, largely due to a lack of extensive studies in diverse ethnic populations. This review and meta-analysis explores considerable variations in PINK1 variant rates and the wide heterogeneity influenced by patient- and variant-specific factors, delineating a more precise disease profile. Our findings reveal that PINK1-PD is more common than previously thought, with geographic 'hotspots' where up to 9% of EOPD cases are linked to PINK1 variants, including the pathogenic p.Leu347Pro variant affecting 1 in 1300 West Polynesians. Homozygous PINK1-PD typically manifests around age 35, predominantly affecting the lower limbs, with an excellent response to levodopa. Heterozygous PINK1-PD presents an 'intermediate' phenotype, with a later onset age (around 43 years) than homozygous PINK1-PD but earlier than idiopathic PD (typically after age 65). The severity of the phenotype is influenced by variant zygosity and pathogenicity, interacting with genetic and environmental factors to push some individuals beyond the disease threshold. Notably, females with PINK1-PD have earlier onset age than males, particularly in homozygous cases and when variants occur in the first half of PINK1's kinase domain. Contrary to traditional views, α-synuclein pathology is present in 87.5% of PINK1-PD postmortem cases across ages and variants. We challenge conventional views on PINK1-PD, highlighting distinct phenotypes influenced by zygosity, sex, and a role for α-synuclein pathology, urging for increased recognition and research of this not-so-rare disease.

Glucocerebrosidase (GBA) gene variants in a multi-ethnic Asian cohort with Parkinson's disease: mutational spectrum and clinical features

GBA variants are associated with increased risk and earlier onset of Parkinson's disease (PD), and more rapid disease progression especially with "severe" variants typified by p.L483P. GBA mutation screening studies from South-East Asia, with > 650 million inhabitants of diverse ancestries, are very limited. We investigated the spectrum of GBA variants, and associated clinico-demographic features, in a multi-ethnic PD cohort in Malaysia. Patients (n = 496) were recruited from seven centres, primarily of Chinese (45%), Malay (37%), and Indian (13%) ethnicities. All GBA coding exons were screened using a next-generation sequencing-based PD gene panel and verified with Sanger sequencing. We identified 14 heterozygous GBA alleles consisting of altogether 17 missense variants (8 classified as pathogenic or likely pathogenic for PD) in 25 (5.0%) patients, with a substantially higher yield among early (< 50 years) vs. late-onset patients across all three ethnicities (9.1-13.2% vs. 1.0-3.2%). The most common variant was p.L483P (including RecNciI, n = 11, 2.2%), detected in all three ethnicities. Three novel variants/recombinant alleles of uncertain significance were found; p.P71L, p.L411P, and p.L15S(;)S16G(;)I20V. The common European risk variants, p.E365K, p.T408M, and p.N409S, were not detected. A severe disease course was noted in the majority of GBA-variant carriers, across a range of detected variants. We report a potentially novel observation of spine posture abnormalities in GBA-variant carriers. This represents the largest study on GBA variation from South-East Asia, and highlights that these populations, especially those with EOPD, would be relevant for studies including clinical trials targeting GBA pathways.

Mutation Analysis of the Genes Associated with Parkinson's Disease in a Finnish Cohort of Early-Onset Dementia

BACKGROUND

Alzheimer's disease, frontotemporal lobar degeneration, dementia with Lewy bodies, and Parkinson's disease (PD) overlap in clinical characteristics, neuropathology, and genetics.

OBJECTIVE

The aim of this study was to evaluate the role of pathogenic mutations and rare variants in genes associated with PD among early-onset dementia (EOD) patients.

METHODS

Rare non-synonymous variants (MAF < 0.01) in ten genes (SNCA, PARK2, PARK7, LRRK2, PINK1, ATP13A2, UCHL1, HTRA2, GBA, and SNCAIP) and low-frequency (MAF < 0.05) GBA variants were screened using a targeted next-generation sequencing panel in a strictly defined cohort of 37 early-onset (age at onset (AAO) <65 years) dementia patients presenting with atypical features (e.g., myoclonia or spasticity), rapidly progressive course of the disease or with a family history of dementia. The identified variations were further screened in a larger cohort of EOD (n = 279, mean AAO 57, range 36-65) patients.

RESULTS

No pathogenic mutations were found, but we identified seven possible risk variants for neurodegeneration (LRRK2 p.Arg793Met, PARK2 p.Ala82Glu, SNCAIP p.Arg240Gln, SNCAIP p.Phe369Leu, GBA p.Asn409Ser, GBA p.Glu365Lys, GBA p.Thr408Met).

DISCUSSION

Altogether, the frequency of these variants was two times higher in the first selected cohort compared to the whole cohort. This suggests that specific rare variants in the genes associated with PD might play a role also especially in familial EOD.

Functional genomic analyses uncover APOE-mediated regulation of brain and cerebrospinal fluid beta-amyloid levels in Parkinson disease

Alpha-synuclein is the main protein component of Lewy bodies, the pathological hallmark of Parkinson's disease. However, genetic modifiers of cerebrospinal fluid (CSF) alpha-synuclein levels remain unknown. The use of CSF levels of amyloid beta1-42, total tau, and phosphorylated tau181 as quantitative traits in genetic studies have provided novel insights into Alzheimer's disease pathophysiology. A systematic study of the genomic architecture of CSF biomarkers in Parkinson's disease has not yet been conducted. Here, genome-wide association studies of CSF biomarker levels in a cohort of individuals with Parkinson's disease and controls (N = 1960) were performed. PD cases exhibited significantly lower CSF biomarker levels compared to controls. A SNP, proxy for APOE ε4, was associated with CSF amyloid beta1-42 levels (effect = - 0.5, p = 9.2 × 10-19). No genome-wide loci associated with CSF alpha-synuclein, total tau, or phosphorylated tau181 levels were identified in PD cohorts. Polygenic risk score constructed using the latest Parkinson's disease risk meta-analysis were associated with Parkinson's disease status (p = 0.035) and the genomic architecture of CSF amyloid beta1-42 (R2 = 2.29%; p = 2.5 × 10-11). Individuals with higher polygenic risk scores for PD risk presented with lower CSF amyloid beta1-42 levels (p = 7.3 × 10-04). Two-sample Mendelian Randomization revealed that CSF amyloid beta1-42 plays a role in Parkinson's disease (p = 1.4 × 10-05) and age at onset (p = 7.6 × 10-06), an effect mainly mediated by variants in the APOE locus. In a subset of PD samples, the APOE ε4 allele was associated with significantly lower levels of CSF amyloid beta1-42 (p = 3.8 × 10-06), higher mean cortical binding potentials (p = 5.8 × 10-08), and higher Braak amyloid beta score (p = 4.4 × 10-04). Together these results from high-throughput and hypothesis-free approaches converge on a genetic link between Parkinson's disease, CSF amyloid beta1-42, and APOE.

The Genetic Architecture of Parkinson Disease in Spain: Characterizing Population-Specific Risk, Differential Haplotype Structures, and Providing Etiologic Insight

BACKGROUND

The Iberian Peninsula stands out as having variable levels of population admixture and isolation, making Spain an interesting setting for studying the genetic architecture of neurodegenerative diseases.

OBJECTIVES

To perform the largest PD genome-wide association study restricted to a single country.

METHODS

We performed a GWAS for both risk of PD and age at onset in 7,849 Spanish individuals. Further analyses included population-specific risk haplotype assessments, polygenic risk scoring through machine learning, Mendelian randomization of expression, and methylation data to gain insight into disease-associated loci, heritability estimates, genetic correlations, and burden analyses.

RESULTS

We identified a novel population-specific genome-wide association study signal at PARK2 associated with age at onset, which was likely dependent on the c.155delA mutation. We replicated four genome-wide independent signals associated with PD risk, including SNCA, LRRK2, KANSL1/MAPT, and HLA-DQB1. A significant trend for smaller risk haplotypes at known loci was found compared to similar studies of non-Spanish origin. Seventeen PD-related genes showed functional consequence by two-sample Mendelian randomization in expression and methylation data sets. Long runs of homozygosity at 28 known genes/loci were found to be enriched in cases versus controls.

CONCLUSIONS

Our data demonstrate the utility of the Spanish risk haplotype substructure for future fine-mapping efforts, showing how leveraging unique and diverse population histories can benefit genetic studies of complex diseases. The present study points to PARK2 as a major hallmark of PD etiology in Spain. © 2019 International Parkinson and Movement Disorder Society.