Soraya Bardien

Association of LRRK2 exonic variants with susceptibility to Parkinson's disease: A case-control study

BACKGROUNDnBackground The leucine-rich repeat kinase 2 gene (LRRK2) harbours highly penetrant mutations that are linked to familial parkinsonism. However, the extent of its polymorphic variability in relation to risk of Parkinsons disease (PD) has not been assessed systematically. We therefore assessed the frequency of LRRK2 exonic variants in individuals with and without PD, to investigate the role of the variants in PD susceptibility.nnnMETHODSnLRRK2 was genotyped in patients with PD and controls from three series (white, Asian, and Arab-Berber) from sites participating in the Genetic Epidemiology of Parkinsons Disease Consortium. Genotyping was done for exonic variants of LRRK2 that were identified through searches of literature and the personal communications of consortium members. Associations with PD were assessed by use of logistic regression models. For variants that had a minor allele frequency of 0·5% or greater, single variant associations were assessed, whereas for rarer variants information was collapsed across variants.nnnFINDINGSn121 exonic LRRK2 variants were assessed in 15u2008540 individuals: 6995 white patients with PD and 5595 controls, 1376 Asian patients and 962 controls, and 240 Arab-Berber patients and 372 controls. After exclusion of carriers of known pathogenic mutations, new independent risk associations were identified for polymorphic variants in white individuals (M1646T, odds ratio 1·43, 95% CI 1·15-1·78; p=0·0012) and Asian individuals (A419V, 2·27, 1·35-3·83; p=0·0011). A protective haplotype (N551K-R1398H-K1423K) was noted at a frequency greater than 5% in the white and Asian series, with a similar finding in the Arab-Berber series (combined odds ratio 0·82, 0·72-0·94; p=0·0043). Of the two previously reported Asian risk variants, G2385R was associated with disease (1·73, 1·20-2·49; p=0·0026), but no association was noted for R1628P (0·62, 0·36-1·07; p=0·087). In the Arab-Berber series, Y2189C showed potential evidence of risk association with PD (4·48, 1·33-15·09; p=0·012).nnnINTERPRETATIONnThe results for LRRK2 show that several rare and common genetic variants in the same gene can have independent effects on disease risk. LRRK2, and the pathway in which it functions, is important in the cause and pathogenesis of PD in a greater proportion of patients with this disease than previously believed. These results will help discriminate those patients who will benefit most from therapies targeted at LRRK2 pathogenic activity.nnnFUNDINGnMichael J Fox Foundation and National Institutes of Health.

Genetic characteristics of leucine-rich repeat kinase 2 (LRRK2) associated Parkinson’s disease

Parkinsons disease (PD) is a common neurodegenerative disorder characterized by the progressive and selective degeneration of nigrostriatal dopaminergic neurons. The discovery of at least six PD-causing genes in predominantly early-onset forms of the disorder has cemented a genetic component to the etiology. Notably, the discovery of mutations in the LRRK2 gene in patients presenting with typical sporadic PD with ages at onset in their sixties and seventies has shifted paradigms in the field of PD research. The G2019S mutation in LRRK2 has been found in diverse populations worldwide and usually resides on a common haplotype revealing that many of these individuals share a common ancestor, probably of Middle Eastern origin. The only validated coding susceptibility alleles for PD, G2385R and R1628P, are both in this gene but to date have been found exclusively in Asian populations. Concomitant with genetic testing for PD is the need for appropriate and informed genetic counseling. Families of patients with LRRK2 mutations and susceptibility alleles need to be informed about the current lack of disease preventative strategies and the implications surrounding incomplete penetrance. In summary, single-handedly LRRK2 has had a major impact on the field of PD research and the findings have been of interest to both clinicians and scientists. We anticipate that other genes of such major impact exist for PD and look forward to their discovery.

A rapid method for detection of five known mutations associated with aminoglycoside-induced deafness

BackgroundSouth Africa has one of the highest incidences of multidrug-resistant tuberculosis (MDR-TB) in the world. Concomitantly, aminoglycosides are commonly used in this country as a treatment against MDR-TB. To date, at least five mutations are known to confer susceptibility to aminoglycoside-induced hearing loss. The aim of the present study was to develop a rapid screening method to determine whether these mutations are present in the South African population.MethodsA multiplex method using the SNaPshot technique was used to screen for five mutations in the MT-RNR1 gene: A1555G, C1494T, T1095C, 961delT+C(n) and A827G. A total of 204 South African control samples, comprising 98 Mixed ancestry and 106 Black individuals were screened for the presence of the five mutations.ResultsA robust, cost-effective method was developed that detected the presence of all five sequence variants simultaneously. In this pilot study, the A1555G mutation was identified at a frequency of 0.9% in the Black control samples. The 961delT+C(n) variant was present in 6.6% of the Black controls and 2% of the Mixed ancestry controls. The T1095C, C1494T and A827G variants were not identified in any of the study participants.ConclusionThe frequency of 0.9% for the A1555G mutation in the Black population in South Africa is of concern given the high incidence of MDR-TB in this particular ethnic group. Future larger studies are warranted to determine the true frequencies of the aminoglycoside deafness mutations in the general South African population. The high frequencies of the 961delT+C(n) variant observed in the controls suggest that this change is a common non-pathogenic polymorphism. This genetic method facilitates the identification of individuals at high risk of developing hearing loss prior to the start of aminoglycoside therapy. This is important in a low-resource country like South Africa where, despite their adverse side-effects, aminoglycosides will continue to be used routinely and are accompanied with very limited or no audiological monitoring.

Aminoglycoside: induced hearing loss in HIV-positive and HIV-negative multidrug-resistant tuberculosis patients

Background. Ototoxicity following aminoglycoside treatment for multidrug-resistant tuberculosis (MDR-TB) is a significant problem. This study documents the incidence of ototoxicity in HIV-positive and HIV-negative patients with MDR-TB and presents clinical guidelines relating to ototoxicity. Methods. A prospective cohort study of 153 MDR-TB patients with normal hearing and middle ear status at baseline controlling for 6 mitochondrial mutations associated with aminoglycoside-related ototoxicity, at Brooklyn Chest Hospital in Cape Town. Pure tone audiometry was performed monthly for 3 months to determine hearing loss. HIV status was recorded, as was the presence of 6 mutations in the MT-RNR1 gene. Results. Fifty-seven per cent developed high-frequency hearing loss. HIV-positive patients (70%) were more likely to develop hearing loss than HIV-negative patients (42%). Of 115 patients who were genetically screened, none had MT-RNR1 mutations. Conclusion. Ototoxic hearing loss is common in MDR-TB patients treated with aminoglycosides. HIV-positive patients are at increased risk of ototoxicity. Auditory monitoring and auditory rehabilitation should be an integral part of the package of care of MDR-TB patients.

Molecular analysis of the parkin gene in South African patients diagnosed with Parkinson's disease

Parkinsons disease (PD) is a common movement disorder which may arise from mutations in the parkin gene. To date, more than 100 different parkin mutations have been reported. The aim of the present study was to determine the frequency of point mutations and homozygous exon deletions in the parkin gene in a group of 91 South African patients diagnosed with PD. Mutation screening of the 12 exons of parkin was performed using single strand conformation polymorphism analysis and the high-resolution melt technique. Six different mutations were identified: four putative disease-causing missense heterozygous changes (H200Q, D280N, E310D and R402C) and two homozygous exon deletions (exons 3 and 4, and exon 4). The D280N and R402C variants have both previously been described but their pathogenic status has been equivocal. In the present study, the D280N variant was observed in three early onset PD-affected siblings and was not present in a 63-year-old unaffected sibling. This data provide further support for the pathogenicity of this variant which is situated within the first RING finger of the RING-box. None of the four missense variants were detected in over 100 ethnic-matched control chromosomes. We conclude that point mutations and homozygous exon deletions in the parkin gene are not a major cause of PD in the South African population. Further studies on this group of patients are needed to determine the contribution of heterozygous exon deletions and insertions in parkin. The present study is the first report on the molecular etiology of PD in South African patients.

Evidence for a common biological pathway linking three Parkinson's disease-causing genes: parkin, PINK1 and DJ-1.

Parkinsons disease (PD) is characterised by the loss of dopaminergic neurons in the midbrain. Autosomal recessive, early‐onset cases of PD are predominantly caused by mutations in the parkin, PINK1 and DJ‐1 genes. Animal and cellular models have verified a direct link between parkin and PINK1, whereby PINK1 phosphorylates and activates parkin at the outer mitochondrial membrane, resulting in removal of dysfunctional mitochondria via mitophagy. Despite the overwhelming evidence for this interaction, few studies have been able to identify a link for DJ‐1 with parkin or PINK1. The aim of this review is to summarise the functions of these three proteins, and to analyse the existing evidence for direct and indirect interactions between them. DJ‐1 is able to rescue the phenotype of PINK1‐knockout Drosophila models, but not of parkin‐knockouts, suggesting that DJ‐1 may act in a parallel pathway to that of the PINK1/parkin pathway. To further elucidate a commonality between these three proteins, bioinformatics analysis established that Miro (RHOT1) interacts with parkin and PINK1, and HSPA4 interacts with all three proteins. Furthermore, 30 transcription factors were found to be common amongst all three proteins, with many of them being involved in transcriptional regulation. Interestingly, expression of these proteins and their associated transcription factors are found to be significantly down‐regulated in PD patients compared to healthy controls. In summary, this review provides insight into common pathways linking three PD‐causing genes and highlights some key questions, the answers to which may provide critical insight into the disease process.

Analysis of exon dosage using MLPA in South African Parkinson's disease patients

Genomic rearrangements (exon dosage) are common mutations reported in Parkinsons disease (PD) patients. In the present study, we aimed to investigate the prevalence of genomic rearrangements in 88 South African patients with predominantly early-onset PD (age-at-onset ≤50xa0years). The multiplex ligation-dependent probe amplification method was used to detect exon dosage changes. Two commercially available probe kits, SALSA P051 and P052, were used and together the kits consisted of probes for exons of α-synuclein, parkin, PINK1, DJ-1, LRRK2, UCH-L1, ATP13A2, LPA, TNFRSF9, CAV2, CAV1, GCH1, and two-point mutations. We identified exonic rearrangements in parkin and α-synuclein in 8% of South African patients from different ethnic groups. One patient had a whole-gene triplication of α-synuclein; representing only the fourth family with this mutation reported to date. We found six patients with parkin mutations who had either heterozygous duplications and deletions, or homozygous deletions. A false positive result of an exonic deletion detected in one patient turned out to be homozygous point mutation (Y258X) in PINK1. No exonic rearrangements were found in four of the PD genes; LRRK2, PINK1, DJ-1, and ATP13A2. Mutations in parkin were the predominant genetic cause; however, the frequency of exon dosage in our study group is low compared with previous studies. This indicates the possible involvement of other as yet unidentified PD genes in the development of the disease in the South African population.

Parkinson's disease-related LRRK2 G2019S mutation results from independent mutational events in humans

Mutations in the leucine-rich-repeat kinase 2 (LRRK2) gene have been identified in families with autosomal dominant Parkinsons disease (PD) and in sporadic cases; the G2019S mutation is the single most frequent. Intriguingly, the frequency of this mutation in PD patients varies greatly among ethnic groups and geographic origins: it is present at <0.1% in East Asia, approximately 2% in European-descent patients and can reach frequencies of up to 15-40% in PD Ashkenazi Jews and North African Arabs. To ascertain the evolutionary dynamics of the G2019S mutation in different populations, we genotyped 74 markers spanning a 16 Mb genomic region around G2019S, in 191 individuals carrying the mutation from 126 families of different origins. Sixty-seven families were of North-African Arab origin, 18 were of North/Western European descent, 37 were of Jewish origin, mostly from Eastern Europe, one was from Japan, one from Turkey and two were of mixed origins. We found the G2019S mutation on three different haplotypes. Network analyses of the three carrier haplotypes showed that G2019S arose independently at least twice in humans. In addition, the population distribution of the intra-allelic diversity of the most widespread carrier haplotype, together with estimations of the age of G2019S determined by two different methods, suggests that one of the founding G2019S mutational events occurred in the Near East at least 4000 years ago.

An investigation into LOXL1 variants in black South African individuals with exfoliation syndrome

OBJECTIVEnTo investigate the association between 2 lysyl oxidase-like 1 (LOXL1) polymorphisms, rs1048661 (R141L) and rs3825942 (G153D), and exfoliation syndrome (XFS) in black South African individuals.nnnMETHODSnA total of 43 black patients with XFS and 47 ethnically matched controls were recruited for genetic analysis. Samples were analyzed for presence of the LOXL1-R141L and G153D variants using restriction fragment length polymorphism analysis. A case-control association study was performed.nnnRESULTSnThe R141L and G153D single-nucleotide polymorphisms (SNPs) were both significantly associated with XFS (P = .00582 and P < .00001, respectively). Consistent with findings in white populations but not in Asian cohorts, the GG genotype of the R141L SNP was present in significantly more XFS cases than controls (P = .00582). However, in this black South African study population, the AA genotype of G153D was present in an overwhelming majority of cases with XFS (P < .00001; odds ratio, 17.10; 95% confidence interval, 4.91-59.56), contrary to all previous articles in which the GG genotype was strongly associated with the disease phenotype.nnnCONCLUSIONnThe LOXL1 SNPs R141L and G153D are significantly associated with XFS in this black South African population. The AA genotype of G153D confers XFS risk in this population, as opposed to the GG genotype described in all other populations, suggesting that unidentified genetic or environmental factors independent of these LOXL1 SNPs may influence phenotypic expression of the syndrome.nnnCLINICAL RELEVANCEnElucidation of the role of genetic factors, including the LOXL1 gene, in XFS will facilitate identification of individuals predisposed to developing this condition.

A South African mixed ancestry family with Huntington disease-like 2: Clinical and genetic features

Huntington disease‐like 2 (HDL2) is a neurodegenerative disorder caused by an expansion of a CTG repeat in the junctophilin‐3 gene (JPH3). A limited number of HDL2 families have been reported, all of apparently Black African ancestry. We report on a South African family that presented with progressive dementia and a movement disorder affecting numerous family members. Genotyping of the JPH3 CTG repeat revealed pathogenic expansions in three affected individuals. Whereas HDL2 is thought to be clinically indistinguishable from Huntington disease (HD), 2 of the patients in this study presented with clinical symptoms that differed substantially from HD; one had myoclonus and the other had Parkinsonism. Moreover, brain magnetic resonance imaging scans of these patients showed imaging features atypical for HD. Mitochondrial DNA and Y‐chromosome DNA analysis on a family member showed that his maternal and paternal ancestries are typical of that found among the South African mixed ancestry or colored population. A difference in the distribution of CTG repeats between Caucasian and Black individuals was detected. We conclude that the phenotype of HDL2 is broad and can differ from that of typical HD. The diagnosis therefore should be considered in a wide spectrum of neuropsychiatric and abnormal movement presentations.