Clinical and Genetic Analysis of Costa Rican Patients With Parkinson's Disease

Background: Most research in genomics of Parkinson’s disease (PD) has been done in subjects of European ancestry, leading to sampling bias and leaving Latin American populations underrepresented. We sought to clinically characterize PD patients of Costa Rican origin and to sequence familial PD and atypical parkinsonism-associated genes in cases and controls. Methods: We enrolled 118 PD patients with 97 unrelated controls. Collected information included demographics, exposure to risk and protective factors, and motor and cognitive assessments. We sequenced coding and untranslated regions in familial PD and atypical parkinsonism-associated genes including GBA, SNCA, VPS35, LRRK2, GCH1, PRKN, PINK1, DJ-1, VPS13C, and ATP13A2. Results: Mean age of PD probands was 62.12 ± 13.51 years; 57.6% were male. The frequency of risk and protective factors averaged ∼45%. Physical activity significantly correlated with better motor performance despite years of disease. Increased years of education were significantly associated with better cognitive function, whereas hallucinations, falls, mood disorders, and coffee consumption correlated with worse cognitive performance. We did not identify an association between tested genes and PD or any damaging homozygous or compound heterozygous variants. Rare variants in LRRK2 were nominally associated with PD; six were located between amino acids p.1620 and 1623 in the C-terminal-of-ROC (COR) domain of Lrrk2. Non-synonymous GBA variants (p.T369M, p.N370S, and p.L444P) were identified in three healthy individuals. One PD patient carried a pathogenic GCH1 variant, p.K224R. Discussion: This is the first study that describes sociodemographics, risk factors, clinical presentation, and genetics of Costa Rican patients with PD, adding information to genomics research in a Latino population.Antecedentes: la mayor parte de la investigación en genómica de la enfermedad de Parkinson (EP) se ha realizado en sujetos de ascendencia europea, lo que provoca un sesgo de muestreo y deja a las poblaciones latinoamericanas infrarrepresentadas. Buscamos caracterizar clínicamente a los pacientes con EP de origen costarricense y secuenciar la EP familiar y los genes asociados con el parkinsonismo atípico en casos y controles. Métodos: Inscribimos a 118 pacientes con EP con 97 controles no relacionados. La información recopilada incluyó datos demográficos, exposición a factores de riesgo y de protección, y evaluaciones motoras y cognitivas. Se secuenciaron las regiones codificantes y no traducidas en la EP familiar y los genes asociados con el parkinsonismo atípico, incluidos GBA, SNCA, VPS35, LRRK2, GCH1, PRKN, PINK1, DJ-1, VPS13C y ATP13A2. Resultados: La edad media de los probandos de EP fue de 62,12 ± 13,51 años; El 57,6% eran hombres. La frecuencia de los factores de riesgo y protección promedió ~ 45%. La actividad física se correlacionó significativamente con un mejor rendimiento motor a pesar de años de enfermedad. El aumento de años de educación se asoció significativamente con una mejor función cognitiva, mientras que las alucinaciones, las caídas, los trastornos del estado de ánimo y el consumo de café se correlacionaron con un peor rendimiento cognitivo. No identificamos una asociación entre los genes probados y la EP ni ninguna variante heterocigótica homocigótica o compuesta dañina. Las variantes raras en LRRK2 se asociaron nominalmente con la EP; seis estaban ubicados entre los aminoácidos p.1620 y 1623 en el dominio C-terminal-de-ROC (COR) de Lrrk2. Se identificaron variantes de GBA no sinónimas (p.T369M, p.N370S y p.L444P) en tres individuos sanos. Un paciente con EP portaba una variante patógena de GCH1, p.K224R.Universidad de Costa Rica/[837-B5-304]/UCR/Costa RicaCanadian Consortium on Neurodegeneration in Aging/[]/CCNA/CanadáCanada First Research Excellence Fund/[]/CFREF/CanadáHealthy Brains for Healthy Lives/[]/HBHL/CanadáUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias de la Salud::Centro de Investigación en Neurociencias (CIN)UCR::Vicerrectoría de Docencia::Salud::Facultad de Medicina::Escuela de Medicin

R1441G but not G2019S mutation enhances LRRK2 mediated Rab10 phosphorylation in human peripheral blood neutrophils

Heterozygous gain-of-kinase function variants in LRRK2 (leucine-rich repeat kinase 2) cause 1–2% of all cases of Parkinson’s disease (PD) albeit with incomplete and age-dependent penetrance. All pathogenic LRRK2 mutations reside within the two catalytic domains of LRRK2—either in its kinase domain (e.g. G2019S) with modest effect or its ROC-COR GTPase domain (e.g. R1441G/H) with large effect on LRRK2 kinase activity. We have previously reported assays to interrogate LRRK2 kinase pathway activity in human bio-samples measuring phosphorylation of its endogenous substrate Rab10, that mirrors LRRK2 kinase activation status. Here, we isolated neutrophils from fresh peripheral blood from 101 participants including 42 LRRK2 mutation carriers (21 with the G2019S and 21 with the R1441G mutations), 27 patients with idiopathic PD, and 32 controls. Using a dual approach, LRRK2 dependent Rab10 phosphorylation at Threonine 73 (pRab10(Thr73)) was measured by quantitative multiplexed immunoblotting for pRab10(Thr73)/total Rab10 as well as targeted mass-spectrometry for absolute pRab10(Thr73) occupancy. We found a significant over fourfold increase in pRab10(Thr73) phosphorylation in carriers of the LRRK2 R1441G mutation irrespective of clinical disease status. The effect of the LRRK2 G2019S mutation did not reach statistical significance. Furthermore, we show that LRRK2 phosphorylation at Serine 935 is not a marker for LRRK2 kinase activity in human neutrophils. When analysing pRab10(Thr73) phosphorylation in post-mortem brain samples, we observed overall high variability irrespective of clinical and LRRK2 mutation status and attributed this mainly to the adverse effect of the peri- and post-mortem period on the stability of posttranslational modifications such as protein phosphorylation. Overall, in vivo LRRK2 dependent pRab10(Thr73) phosphorylation in human peripheral blood neutrophils is a specific, robust and promising biomarker for significant LRRK2 kinase hyperactivation, as with the LRRK2 R1441G mutation. Additional readouts and/or assays may be needed to increase sensitivity to detect modest LRRK2 kinase activation, as with the LRRK2 G2019S mutation. Our assays could be useful for patient stratification and target engagement studies for LRRK2 kinase inhibitors. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00401-021-02325-z

Regulatory sites for splicing in human basal ganglia are enriched for disease-relevant information

Genome-wide association studies have generated an increasing number of common genetic variants associated with neurological and psychiatric disease risk. An improved understanding of the genetic control of gene expression in human brain is vital considering this is the likely modus operandum for many causal variants. However, human brain sampling complexities limit the explanatory power of brain-related expression quantitative trait loci (eQTL) and allele-specific expression (ASE) signals. We address this, using paired genomic and transcriptomic data from putamen and substantia nigra from 117 human brains, interrogating regulation at different RNA processing stages and uncovering novel transcripts. We identify disease-relevant regulatory loci, find that splicing eQTLs are enriched for regulatory information of neuron-specific genes, that ASEs provide cell-specific regulatory information with evidence for cellular specificity, and that incomplete annotation of the brain transcriptome limits interpretation of risk loci for neuropsychiatric disease. This resource of regulatory data is accessible through our web server, http://braineacv2.inf.um.es/

Identification of novel risk loci, causal insights, and heritable risk for Parkinson's disease: a meta-analysis of genome-wide association studies

Background Genome-wide association studies (GWAS) in Parkinson's disease have increased the scope of biological knowledge about the disease over the past decade. We aimed to use the largest aggregate of GWAS data to identify novel risk loci and gain further insight into the causes of Parkinson's disease. Methods We did a meta-analysis of 17 datasets from Parkinson's disease GWAS available from European ancestry samples to nominate novel loci for disease risk. These datasets incorporated all available data. We then used these data to estimate heritable risk and develop predictive models of this heritability. We also used large gene expression and methylation resources to examine possible functional consequences as well as tissue, cell type, and biological pathway enrichments for the identified risk factors. Additionally, we examined shared genetic risk between Parkinson's disease and other phenotypes of interest via genetic correlations followed by Mendelian randomisation. Findings Between Oct 1, 2017, and Aug 9, 2018, we analysed 7·8 million single nucleotide polymorphisms in 37 688 cases, 18 618 UK Biobank proxy-cases (ie, individuals who do not have Parkinson's disease but have a first degree relative that does), and 1·4 million controls. We identified 90 independent genome-wide significant risk signals across 78 genomic regions, including 38 novel independent risk signals in 37 loci. These 90 variants explained 16–36% of the heritable risk of Parkinson's disease depending on prevalence. Integrating methylation and expression data within a Mendelian randomisation framework identified putatively associated genes at 70 risk signals underlying GWAS loci for follow-up functional studies. Tissue-specific expression enrichment analyses suggested Parkinson's disease loci were heavily brain-enriched, with specific neuronal cell types being implicated from single cell data. We found significant genetic correlations with brain volumes (false discovery rate-adjusted p=0·0035 for intracranial volume, p=0·024 for putamen volume), smoking status (p=0·024), and educational attainment (p=0·038). Mendelian randomisation between cognitive performance and Parkinson's disease risk showed a robust association (p=8·00 × 10−7). Interpretation These data provide the most comprehensive survey of genetic risk within Parkinson's disease to date, to the best of our knowledge, by revealing many additional Parkinson's disease risk loci, providing a biological context for these risk factors, and showing that a considerable genetic component of this disease remains unidentified. These associations derived from European ancestry datasets will need to be followed-up with more diverse data. Funding The National Institute on Aging at the National Institutes of Health (USA), The Michael J Fox Foundation, and The Parkinson's Foundation (see appendix for full list of funding sources)

Caracterización funcional del gen responsable de la epilepsia autosómica dominante lateral temporal, LG11, en modelos animales vertebrados

Tesis doctoral del Dpto. de Genética, Antropología Física y Fisiología Animal. Univ. del País VascoEste trabajo se ha enmarcado dentro del proyecto “Caracterización funcional de Epitempina, el gen responsable de la Epilepsia lateral temporal” financiado por el Ministerio de Ciencia y Tecnología (número de referencia SAF2002-0060). Para la realización de esta tesis, la autora ha sido beneficiaria de una “beca Ilundain de investigación neurogenética” concedida por la Fundación Ilundain (Convocatoria 2000) y de una beca para la formación de investigadores, modalidad predoctoral (AE), del Gobierno Vasco (convocatoria 2001).Peer reviewe

Mutazioak progranulina genean: eragiten duten klinika, patologia eta RNA mailako adierazpena

La degeneración del lóbulo frontotemporal (FTLD) es un complejo grupo de enfermedades que se clasifican dentro de las demencias. En este trabajo presentamos los análisis clínicos, moleculares y patológicos de una serie de enfermos que padecen FTLD. Entre los 72 enfermos hemos encontrado 4 mutaciones diferentes y 14 enfermos portadores de mutación. Además, hemos medido el nivelde expresión del gen PGRN que se encuentra en las células de la sangre y demostramos que se puede utilizar como marcador biológico de la enfermedad.Garuneko lobulu fronto-tenporalaren degenerazioa (FTLD) dementzien barruan sailkatzen den gaixotasun talde konplexu bat da. Lan honetan FTLD duten gaixo serie baten analisi kliniko, molekular eta patologikoak aurkezten ditugu. 72 gaixoen artean 4 mutazio desberdin aurkitu ditugu eta 14 mutaziodun gaixo. Gainera, odoleko zeluletan aurkitzen den PGRN genearen adierazpen maila neurtudugu eta gaixotasunaren markatzaile biologiko bezela erabil litekela erakusten dugu.La dégénération du lobe fronto-temporel (FTLD) fait partie d'un complexe groupe de maladies qualifiées de démences. Ce travail présente les résultats des prélèvements cliniques, moléculaires et pathologiques effectués chez toute une série de malades atteints de FTLD. Parmi les 72 malades analysés, nous avons trouvé 4 mutations différentes et 14 malades porteurs de mutatión. Nous avons, par ailleurs, mesuré le niveau de expression du gène PGRN qui se trouve dans les cellules du sang, pour démontrer qu'il peut être utilisé comme marqueur biologique de la maladie.The degeneration of the frontotemporal lobe (FTLD) is a complex group ofillnesses which are classified within those of dementia. In this work we present the clinical analysis, molecular and pathologic, of a series of patients who suffer from FLD. Among the 72 patients we found 4 different mutations and 14 mutated patients. In addition we have measured the level of representation of the PGRN gene which is found in the blood cells and we have demonstrated that it can be used as a biological indicator of the illness

Identification of sixteen novel candidate genes for late onset Parkinson's disease

Altres ajuts: Italian Ministry of Health grant (RF 2019-12370224, GR2016-02362247); Italian Ministry of Economic Development (F/0009/00X26); Fondazione Umberto Veronesi.Background: Parkinson's disease (PD) is a neurodegenerative movement disorder affecting 1-5% of the general population for which neither effective cure nor early diagnostic tools are available that could tackle the pathology in the early phase. Here we report a multi-stage procedure to identify candidate genes likely involved in the etiopathogenesis of PD. Methods: The study includes a discovery stage based on the analysis of whole exome data from 26 dominant late onset PD families, a validation analysis performed on 1542 independent PD patients and 706 controls from different cohorts and the assessment of polygenic variants load in the Italian cohort (394 unrelated patients and 203 controls). Results: Family-based approach identified 28 disrupting variants in 26 candidate genes for PD including PARK2, PINK1, DJ-1(PARK7), LRRK2, HTRA2, FBXO7, EIF4G1, DNAJC6, DNAJC13, SNCAIP, AIMP2, CHMP1A, GIPC1, HMOX2, HSPA8, IMMT, KIF21B, KIF24, MAN2C1, RHOT2, SLC25A39, SPTBN1, TMEM175, TOMM22, TVP23A and ZSCAN21. Sixteen of them have not been associated to PD before, were expressed in mesencephalon and were involved in pathways potentially deregulated in PD. Mutation analysis in independent cohorts disclosed a significant excess of highly deleterious variants in cases (p = 0.0001), supporting their role in PD. Moreover, we demonstrated that the co-inheritance of multiple rare variants (≥ 2) in the 26 genes may predict PD occurrence in about 20% of patients, both familial and sporadic cases, with high specificity (> 93%; p = 4.4 × 10). Moreover, our data highlight the fact that the genetic landmarks of late onset PD does not systematically differ between sporadic and familial forms, especially in the case of small nuclear families and underline the importance of rare variants in the genetics of sporadic PD. Furthermore, patients carrying multiple rare variants showed higher risk of manifesting dyskinesia induced by levodopa treatment. Conclusions: Besides confirming the extreme genetic heterogeneity of PD, these data provide novel insights into the genetic of the disease and may be relevant for its prediction, diagnosis and treatment