SUNScholar - Browsing by Author "Carr, Jonathan"

Browsing by Author "Carr, Jonathan"

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Altered mitochondrial respiration and other features of mitochondrial function in parkin-mutant fibroblasts from parkinson’s disease patients
(Hindawi Publishing Corporation, 2016) Haylett, William; Swart, Chrisna; Van der Westhuizen, Francois; Van Dyk, Hayley; Van der Merwe, Lize; Van der Merwe, Celia; Loos, Ben; Carr, Jonathan; Kinnear, Craig; Bardien, Soraya
Mutations in the parkin gene are the most common cause of early-onset Parkinson’s disease (PD). Parkin, an E3 ubiquitin ligase, is involved in respiratory chain function, mitophagy, and mitochondrial dynamics. Human cellular models with parkin null mutations are particularly valuable for investigating the mitochondrial functions of parkin. However, published results reporting on patient-derived parkin-mutant fibroblasts have been inconsistent. This study aimed to functionally compare parkin-mutant fibroblasts from PD patients with wild-type control fibroblasts using a variety of assays to gain a better understanding of the role of mitochondrial dysfunction in PD. To this end, dermal fibroblasts were obtained from three PD patients with homozygous whole exon deletions in parkin and three unaffected controls. Assays of mitochondrial respiration, mitochondrial network integrity, mitochondrial membrane potential, and cell growth were performed as informative markers of mitochondrial function. Surprisingly, it was found that mitochondrial respiratory rates were markedly higher in the parkin-mutant fibroblasts compared to control fibroblasts (p = 0.0093), while exhibiting more fragmented mitochondrial networks (). Moreover, cell growth of the parkin-mutant fibroblasts was significantly higher than that of controls (). These unanticipated findings are suggestive of a compensatory mechanism to preserve mitochondrial function and quality control in the absence of parkin in fibroblasts, which warrants further investigation.
Clinical findings and genetic screening for copy number variation mutations in a cohort of South African patients with Parkinson’s disease
(Health & Medical Publishing Group, 2016) Mahne, Anna Cecelia; Carr, Jonathan; Bardien, Soraya; Schutte, Clara Maria
ENGLISH ABSTRACT: Background. Parkinson’s disease (PD), with a prevalence of up to 4% in Western countries, appears to be less common in Africa, possibly in part because of genetic factors. African studies investigating the genetic causation of PD are limited. Objective. To describe the clinical and genetic findings in a group of black South African patients with PD. Methods. All black African patients with PD from a tertiary hospital neurology clinic were examined. Symptoms were scored according to the Unified Parkinson’s Disease Rating Scale (UPDRS), and patients were classified according to motor features. Genomic DNA was extracted and multiplex ligation-dependent probe amplification was used for detection of copy number variation (CNV) mutations in the known PD-causing genes. Results. Sixteen patients were identified (ages 56 - 82 years). Three had a family history of PD. Classification into motor subtypes showed 44% mixed, 31% akinetic-rigid, and 25% tremor-dominant subtypes. UPDRS scores ranged from 7 to 88, with dementia in 20%. No patient had G2019S LRRK2 and A30P SNCA mutations, and all except one had no CNV mutations in the known PD-causing genes. A female patient (age of onset 50 years, no family history) had a parkin gene heterozygous deletion of exon 4. She had hyperreflexia, bilateral Hoffmann’s reflexes, normal plantar responses and no dystonia. Conclusion. This group of black African patients showed similar characteristics to patients in Western studies, possibly with a higher proportion having tremor-dominant disease. Genetic analysis showed one parkin gene mutation. The limited knowledge on PD-causing genes and mutations in black populations warrants further studies involving next-generation sequencing approaches.
Emerging differences between Huntington's disease-like 2 and Huntington's disease : a comparison using MRI brain volumetry
(Elsevier, 2019) Anderson, David G.; Haagensen, Mark; Ferreira-Correia, Aline; Pierson, Ronald; Carr, Jonathan; Krause, Amanda; Margolis, Russell L.
ENGLISH ABSTRACT: Huntington's Disease-Like 2 (HDL2), caused by a CTG/CAG expansion in JPH3 on chromosome 16q24, is the most common Huntington's Disease (HD) phenocopy in populations with African ancestry. Qualitatively, brain MRIs of HDL2 patients have been indistinguishable from HD. To determine brain regions most affected in HDL2 a cross-sectional study using MRI brain volumetry was undertaken to compare the brains of nine HDL2, 11 HD and nine age matched control participants. Participants were ascertained from the region in South Africa with the world's highest HDL2 incidence. The HDL2 and HD patient groups showed no significant differences with respect to mean age at MRI, disease duration, abnormal triplet repeat length, or age at disease onset. Overall, intracerebral volumes were smaller in both affected groups compared to the control group. Comparing the HDL2 and HD groups across multiple covariates, cortical and subcortical volumes were similar with the exception that the HDL2 thalamic volumes were smaller. Consistent with other similarities between the two diseases, these results indicate a pattern of neurodegeneration in HDL2 that is remarkably similar to HD. However smaller thalamic volumes in HDL2 raises intriguing questions into the pathogenesis of both disorders, and how these volumetric differences relate to their respective phenotypes.
Factors influencing the development of early- or late-onset Parkinson's disease in a cohort of South African patients
(Health & Medical Publishing Group, 2012-10-01) Van der Merwe, Celia; Haylett, William; Harvey, Justin; Lombard, Debbie; Bardien, Soraya; Carr, Jonathan
Background. Neurodegenerative disorders such as Parkinson’s disease (PD) contribute significantly to global disease burden. PD can be categorised into early-onset PD (EOPD) with an age at onset (AAO) of ≤50 years and late-onset PD (LOPD) with an AAO of 50 years. Aims. To identify factors influencing EOPD and LOPD development in a group of patients in South Africa (SA). Methods. A total of 397 unrelated PD patients were recruited from the Movement Disorders Clinic at Tygerberg Hospital and via the Parkinson’s Association of SA. Patient demographic and environmental data were recorded and associations with PD onset (EOPD v. LOPD) were analysed with a Pearson’s Chi-squared test. The English- and Afrikaans-speaking (Afrikaner) white patients were analysed separately. Results. Logistic regression analysis showed that ethnicity (p<0.001) and family history (p=0.004) were independently associated with AAO of PD. Average AAO was younger in black, coloured and Afrikaner patients than English-speaking white patients. A positive family history of PD, seen in 31.1% of LOPD patients, was associated with a younger AAO in the study population. Conclusions. These associations may be attributed to specific genetic and/or environmental risk factors that increase PD susceptibility and influence the clinical course of the disorder. More studies on PD in the unique SA populations are required to provide novel insights into mechanisms underlying this debilitating condition.
Familial adult myoclonus epilepsy : a clinical, neurophysiological and genetic study of a familial form of myoclonic epilepsy
(Stellenbosch : University of Stellenbosch, 2009-12) Carr, Jonathan; Brink, P. A.; University of Stellenbosch. Faculty of Health Sciences. Dept. of Medicine. Internal Medicine.
ENGLISH ABSTRACT: Progressive Myoclonic Epilepsies (PME) are characterized by progressive neurological impairment with myoclonus, seizures and dementia. In contradistinction, Familial Adult Myoclonic Epilepsy (FAME) is characterized by a benign course with rare seizures and cortical tremor. Both conditions have neurophysiological features suggestive of a cortical origin for their myoclonus. This dissertation reports on a novel form of PME. Many of those who were affected had no or minimal progression of their illness, low seizure frequency and were cognitively intact, suggestive of non-progressive disorders linked to the FAME loci. The majority of patients had features of cortical myoclonus, with generalized spike and wave discharges on electroencephalography, enlarged evoked potentials, enhanced C reflexes, and evidence of cortical excitability with magnetic stimulation. However, there was evidence of cerebellar dysfunction both pathologically and on imaging. With regard to similar conditions, dentatorubral pallidoluysian atrophy and Unverricht-Lundborg syndrome were excluded by linkage analysis. Similarly, linkage was not present for either the FAME 1 or FAME 2 loci. This syndrome is both clinically and genetically novel, and has a nosology which is difficult to characterize, in which the condition appears to lie on the spectrum between FAME and PME. The dissociation between the pathological and radiological findings which suggest subcortical dysfunction, and the neurophysiological findings of cortical myoclonus is striking. Review of the literature associated with the neurophysiology of related conditions associated with PME and FAME suggests that: 1. The assumption that generalized forms of myoclonic disorders represent multifocal forms of focal cortical discharges is an oversimplification. 2. The dissociation between initial and later components of the evoked potential is less robust than is generally supposed, and that subcortical inputs may affect later components of the evoked potential. 3. In a high proportion of cases the latency from cortical spike discharge to myoclonic jerk obtained with jerk locked averaging is incompatible with a cortical origin for the spike discharge. 4. The proposal that myoclonus is a form of long latency reflex and that myoclonus represents a reflex arising from subclinical sensory input, is unproven.
Identification of a common founder couple for 40 South African Afrikaner families with Parkinson’s disease
(Health & Medical Publishing Group, 2014-06) Geldenhuys, Gerhard; Glanzmann, Brigitte; Lombard, Debbie; Boolay, Sihaam; Carr, Jonathan; Bardien, Soraya
Background. Afrikaners are a unique ethnic group in South Africa (SA) with well-documented ancestral records spanning a period of over 350 years. They are mainly descended from Dutch, German and French settlers to SA in the 17th and 18th centuries. Today several disorders in this population occur at relatively high frequencies as a result of founder effects. Objective. To determine whether a founder effect for Parkinson’s disease (PD) is present in the Afrikaner population. Methods. Study participants were recruited from the Movement Disorders Clinic at Tygerberg Hospital in Cape Town, SA, and from support groups of the Parkinson’s Association of South Africa. Standard methods for genealogical research in SA on hereditary diseases were used including interviews and searches in sources such as state archives, the Huguenot Museum in Franschhoek, marriage and baptismal records, and tombstone inscriptions. Results. For 40 of the PD families, there was only a single most recent ancestral couple common to all of the families. On average there are between three and four ancestral lines to the founder couple per proband (range 1 -14). Conclusion. If genetic studies confirm the presence of a founder effect for PD in Afrikaners, this would imply that there is a large number of individuals from this ethnic group who may potentially be at risk of developing this debilitating condition. This study illustrates and reinforces the concept that genealogical analysis is a powerful tool for identification of founder effects for various disorders in the Afrikaner population.
Identification of a novel functional deletion variant in the 5'-UTR of the DJ-1 gene
(BioMed Central, 2009-10) Keyser, Rowena J.; Van der Merwe, Lize; Venter, Mauritz; Kinnear, Craig; Warnich, Louise; Carr, Jonathan; Bardien, Soraya
Background: DJ-1 forms part of the neuronal cellular defence mechanism against oxidative insults, due to its ability to undergo self-oxidation. Oxidative stress has been implicated in the pathogenesis of central nervous system damage in different neurodegenerative disorders including Alzheimer's disease and Parkinson's disease (PD). Various mutations in the DJ-1 (PARK7) gene have been shown to cause the autosomal recessive form of PD. In the present study South African PD patients were screened for mutations in DJ-1 and we aimed to investigate the functional significance of a novel 16 bp deletion variant identified in one patient. Methods: The possible effect of the deletion on promoter activity was investigated using a Dual- Luciferase Reporter assay. The DJ-1 5'-UTR region containing the sequence flanking the 16 bp deletion was cloned into a pGL4.10-Basic luciferase-reporter vector and transfected into HEK293 and BE(2)-M17 neuroblastoma cells. Promoter activity under hydrogen peroxide-induced oxidative stress conditions was also investigated. Computational (in silico) cis-regulatory analysis of DJ-1 promoter sequence was performed using the transcription factor-binding site database, TRANSFAC via the PATCH™ and rVISTA platforms. Results: A novel 16 bp deletion variant (g.-6_+10del) was identified in DJ-1 which spans the transcription start site and is situated 93 bp 3' from a Sp1 site. The deletion caused a reduction in luciferase activity of approximately 47% in HEK293 cells and 60% in BE(2)-M17 cells compared to the wild-type (P < 0.0001), indicating the importance of the 16 bp sequence in transcription regulation. The activity of both constructs was up-regulated during oxidative stress. Bioinformatic analysis revealed putative binding sites for three transcription factors AhR, ARNT, HIF-1 within the 16 bp sequence. The frequency of the g.-6_+10del variant was determined to be 0.7% in South African PD patients (2 heterozygotes in 148 individuals). Conclusion: This is the first report of a functional DJ-1 promoter variant, which has the potential to influence transcript stability or translation efficiency. Further work is necessary to determine the extent to which the g.-6_+10del variant affects the normal function of the DJ-1 promoter and whether this variant confers a risk for PD.
Listerial brainstem encephalitis – treatable, but easily missed
(Health & Medical Publishing Group, 2015) Fredericks, Pearl; Britz, Marcell; Eastman, Roland; Carr, Jonathan; Bateman, Kathleen Jane
ENGLISH ABSTRACT: Listerial brainstem encephalitis (LBE) is an uncommon form of listerial central nervous system infection that progresses rapidly and is invariably fatal unless detected and treated early. We report on six adult patients with LBE, of whom five were managed or co-managed by our unit during the period January - June 2012. All presented with a short prodromal illness followed by a combination of brainstem signs, including multiple cranial nerve palsies with emphasis on the lower cranial nerves, ataxia, motor and sensory long-tract signs, a depressed level of consciousness and apnoea. In two cases the diagnosis was delayed with adverse outcomes. LBE may be difficult to diagnose: clinicians may not be aware of this condition, the brainstem location may not be recognised readily, general markers of inflammation such as the erythrocyte sedimentation rate, C-reactive protein level or white cell count may be normal, and the cerebrospinal fluid is typically normal or there are only mild and nonspecific findings. Serological tests are unreliable, and diagnosis is achieved through blood cultures, magnetic resonance imaging and clinical recognition.
Parkinson’s disease : a systemic inflammatory disease accompanied by bacterial inflammagens
(Frontiers Media, 2019-08-27) Adams, Buin; Nunes, J. Massimo; Page, Martin J.; Roberts, Timothy; Carr, Jonathan; Nell, Theo A.; Kell, Douglas B.; Pretorius, Etheresia
Parkinson’s disease (PD) is a well-known neurodegenerative disease with a strong association established with systemic inflammation. Recently, the role of the gingipain protease group from Porphyromonas gingivalis was implicated in Alzheimer’s disease and here we present evidence, using a fluorescent antibody to detect gingipain R1 (RgpA), of its presence in a PD population. To further elucidate the action of this gingipain, as well as the action of the lipopolysaccharide (LPS) from P. gingivalis, low concentrations of recombinant RgpA and LPS were added to purified fluorescent fibrinogen. We also substantiate previous findings regarding PD by emphasizing the presence of systemic inflammation via multiplex cytokine analysis, and demonstrate hypercoagulation using thromboelastography (TEG), confocal and electron microscopy. Biomarker analysis confirmed significantly increased levels of circulating proinflammatory cytokines. In our PD and control blood analysis, our results show increased hypercoagulation, the presence of amyloid formation in plasma, and profound ultrastructural changes to platelets. Our laboratory analysis of purified fibrinogen with added RgpA, and/or LPS, showed preliminary data with regards to the actions of the protease and the bacterial membrane inflammagen on plasma proteins, to better understand the nature of established PD.
PET-CT in brain disorders : the South African context
(AOSIS, 2021-11) Doruyter, Alexander G. G.; Parkes, Jeannette; Carr, Jonathan; Warwick, James M.
Positron emission tomography combined with X-ray computed tomography (PET-CT) has an established role in the management of brain disorders, but may be underutilised in South Africa. Possible barriers to access include the limited number of PET-CT facilities and the lack of contemporary guidelines for the use of brain PET-CT in South Africa. The current review aims to highlight the evidence-based usage of brain Positron emission tomography (PET) in dementia, movement disorders, brain tumours, epilepsy, neuropsychiatric lupus, immunemediated encephalitides, and brain infections. While being areas of research, there is currently no clinical role for the use of PET-CT in traumatic brain injury or in psychiatric or neurodevelopmental disorders. Strategies to expand the appropriate use of PET-CT in brain disorders are discussed in this article.
Prioritization of candidate genes for a South African family with Parkinson’s disease using in-silico tools
(Public Library of Science, 2021) Sebate, Boiketlo; Cuttler, Katelyn; Cloete, Ruben; Britz, Marcell; Christoffels, Alan; Williams, Monique; Carr, Jonathan; Bardien, Soraya
Parkinson’s disease (PD) is a neurodegenerative disorder exhibiting Mendelian inheritance in some families. Next-generation sequencing approaches, including whole exome sequencing (WES), have revolutionized the field of Mendelian disorders and have identified a number of PD genes. We recruited a South African family with autosomal dominant PD and used WES to identify a possible pathogenic mutation. After filtration and prioritization, we found five potential causative variants in CFAP65, RTF1, NRXN2, TEP1 and CCNF. The variant in NRXN2 was selected for further analysis based on consistent prediction of deleteriousness across computational tools, not being present in unaffected family members, ethnic-matched controls or public databases, and its expression in the substantia nigra. A protein model for NRNX2 was created which provided a three-dimensional (3D) structure that satisfied qualitative mean and global model quality assessment scores. Trajectory analysis showed destabilizing effects of the variant on protein structure, indicated by high flexibility of the LNS-6 domain adopting an extended conformation. We also found that the known substrate N-acetyl-D-glucosamine (NAG) contributed to restoration of the structural stability of mutant NRXN2. If NRXN2 is indeed found to be the causal gene, this could reveal a new mechanism for the pathobiology of PD.
A putative founder effect for Parkinson’s disease in South African Afrikaners
(Health & Medical Publishing Group, 2014-06) Carr, Jonathan; Van Coller, Riaan
There is evidence for a founder effect for Parkinson’s disease in South African Afrikaners. This finding is of importance for two reasons. Firstly, given that established genetic causes of PD have not been identified in the Afrikaner population, it appears likely that this population carries unique mutations that remain to be identified by genome-wide screening. Secondly, in the event that effective treatments are developed, particularly for presymptomatic patients, the Afrikaner population may be considered to be at risk and requiring careful assessment with accurate biomarkers.
Reliability and diagnostic performance of CT imaging criteria in the diagnosis of Tuberculous Meningitis
(PLOS One, 2012-06) Botha, Hugo; Ackerman, Christelle; Candy, Sally; Carr, Jonathan; Griffith-Richards, Stephanie; Bateman, Kathleen J.
Introduction: Abnormalities on CT imaging may contribute to the diagnosis of tuberculous meningitis (TBM). Recently, an expert consensus case definition (CCD) and set of imaging criteria for diagnosing basal meningeal enhancement (BME) have been proposed. This study aimed to evaluate the sensitivity, specificity and reliability of these in a prospective cohort of adult meningitis patients. Methods: Initial diagnoses were based on the CCD, classifying patients into: ‘Definite TBM’ (microbiological confirmation), ‘Probable TBM’ (diagnostic score $10), ‘Possible TBM’ (diagnostic score 6–9), ‘Not TBM’ (confirmation of an alternative diagnosis) or ‘Uncertain’ (diagnostic score of ,6). CT images were evaluated independently on two occasions by four experienced reviewers. Intra-rater and inter-rater agreement were calculated using the kappa statistic. Sensitivities and specificities were calculated using both ‘Definite TBM’ and either ‘Definite TBM’ or ‘Probable TBM’ as gold standards. Results: CT scan criteria for BME had good intra-rater agreement (k range 0.35–0.78) and fair to moderate inter-rater agreement (k range 0.20–0.52). Intra- and inter-rater agreement on the CCD components were good to fair (k = ranges 0.47–0.81 and 0.21–0.63). Using ‘Definite TBM’ as a gold standard, the criteria for BME were very specific (61.5%–100%), but insensitive (5.9%–29.4%). Similarly, the imaging components of the CCD were highly specific (69.2–100%) but lacked sensitivity (0–56.7%). Similar values were found when using ‘Definite TBM’ or ‘Probable TBM’ as a gold standard. Discussion: The fair to moderate inter-rater agreement and poor sensitivities of the criteria for BME suggest that little reliance should be placed in these features in isolation. While the presence of the CCD criteria of acute infarction or tuberculoma(s) appears useful as rule-in criteria, their absence is of little help in excluding TBM. The CCD and criteria for BME, as well as any new criteria, need to be standardized and validated in prospective cohort studies.
Stem cell therapy and amyotrophic lateral sclerosis
(Health and Medical Publishing Group (HMPG), 2012-06) Henning, Franclo; Carr, Jonathan
We have been made aware of several patients with neurological diseases attending stem cell therapy centres, and in particular individuals with amyotrophic lateral sclerosis (ALS). The opening of stem cell clinics in South Africa has led to an increased number of patients pursuing this therapy at great financial cost and with high expectations.
Targeted next-generation sequencing identifies novel variants in candidate genes for Parkinson’s disease in Black South African and Nigerian patients
(BioMed Central, 2020-02-04) Oluwole, Oluwafemi G.; Kuivaniemi, Helena; Abrahams, Shameemah; Haylett, William L.; Vorster, Alvera A.; Van Heerden, Carel J.; Kenyon, Colin P.; Tabb, David L.; Fawale, Michael B.; Sunmonu, Taofiki A.; Ajose, Abiodun; Olaogun, Matthew O.; Rossouw, Anastasia C.; Van Hillegondsberg, Ludo S.; Carr, Jonathan; Ross, Owen A.; Komolafe, Morenikeji A.; Tromp, Gerard; Bardien, Soraya
Background: The prevalence of Parkinson’s disease (PD) is increasing in sub-Saharan Africa, but little is known about the genetics of PD in these populations. Due to their unique ancestry and diversity, sub-Saharan African populations have the potential to reveal novel insights into the pathobiology of PD. In this study, we aimed to characterise the genetic variation in known and novel PD genes in a group of Black South African and Nigerian patients. Methods: We recruited 33 Black South African and 14 Nigerian PD patients, and screened them for sequence variants in 751 genes using an Ion AmpliSeq™ Neurological Research panel. We used bcftools to filter variants and annovar software for the annotation. Rare variants were prioritised using MetaLR and MetaSVM prediction scores. The effect of a variant on ATP13A2’s protein structure was investigated by molecular modelling. Results: We identified 14,655 rare variants with a minor allele frequency ≤ 0.01, which included 2448 missense variants. Notably, no common pathogenic mutations were identified in these patients. Also, none of the known PD-associated mutations were found highlighting the need for more studies in African populations. Altogether, 54 rare variants in 42 genes were considered deleterious and were prioritized, based on MetaLR and MetaSVM scores, for follow-up studies. Protein modelling showed that the S1004R variant in ATP13A2 possibly alters the conformation of the protein. Conclusions: We identified several rare variants predicted to be deleterious in sub-Saharan Africa PD patients; however, further studies are required to determine the biological effects of these variants and their possible role in PD. Studies such as these are important to elucidate the genetic aetiology of this disorder in patients of African ancestry.

Browsing by Author "Carr, Jonathan"

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