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Investigating mitochondrial DNA sequence variation and copy number in individuals of African ancestry living with Parkinson’s disease.
Muller-Nedebock, Amica Corda. 2022. Investigating mitochondrial DNA sequence variation and copy number in individuals of African ancestry living with Parkinson’s disease. Unpublished doctoral dissertation. Stellenbosch : Stellenbosch University [online]. Available at: https://scholar.sun.ac.za/items...
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Stellenbosch : Stellenbosch University
2022
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| access_status_str | Open Access |
| author | Muller-Nedebock, Amica Corda |
| author2 | Bardien, Soraya |
| author_browse | Bardien, Soraya Muller-Nedebock, Amica Corda |
| author_facet | Bardien, Soraya Muller-Nedebock, Amica Corda |
| author_sort | Muller-Nedebock, Amica Corda |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Muller-Nedebock, Amica Corda. 2022. Investigating mitochondrial DNA sequence variation and copy number in individuals of African ancestry living with Parkinson’s disease. Unpublished doctoral dissertation. Stellenbosch : Stellenbosch University [online]. Available at: https://scholar.sun.ac.za/items/1c95c728-94c2-48b3-9621-53561205707f |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/125168 |
| institution | Stellenbosch University (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:41:30.564Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
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| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/125168 Investigating mitochondrial DNA sequence variation and copy number in individuals of African ancestry living with Parkinson’s disease. Muller-Nedebock, Amica Corda Bardien, Soraya Van der Westhuizen, Francois Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Biomedical Sciences. Molecular Biology and Human Genetics. Parkinson's disease Mitochondrial DNA African ancestry Parkinson's disease -- Africa Genetic disorders -- Africa Mitochondrial DNA UCTD Muller-Nedebock, Amica Corda. 2022. Investigating mitochondrial DNA sequence variation and copy number in individuals of African ancestry living with Parkinson’s disease. Unpublished doctoral dissertation. Stellenbosch : Stellenbosch University [online]. Available at: https://scholar.sun.ac.za/items/1c95c728-94c2-48b3-9621-53561205707f Thesis (PhD)--Stellenbosch University, 2022. ENGLISH ABSTRACT: Parkinson’s disease (PD) is an incurable, neurodegenerative movement disorder, characterized by the predominant loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc). Mitochondrial dysfunction has long been implicated as a possible mechanism underlying this neurodegeneration in affected individuals with PD. Many proteins encoded by nuclear DNA (nDNA) genes are key for maintaining proper mitochondrial function. Consequently, pathogenic mutations, including copy number variations (CNVs), in such genes (e.g., PINK1, PRKN and LRRK2) impair mitochondrial function, and have been identified as monogenic causes of PD. However, these mutations have primarily been found in populations of Asian and European ancestry but have rarely been reported in individuals of African ancestry from sub-Saharan Africa (SSA), possibly due to the limited number of PD genetic studies in these populations. Apart from variation in nDNA, mitochondrial DNA (mtDNA) variation has also been implicated in PD. Mitochondria harbor several copies of their own DNA (i.e., mtDNA) that encode important components needed for cellular energy production via oxidative phosphorylation (OXPHOS). Thus, deleterious mtDNA sequence variation or reduced levels of intact mtDNA molecules can decrease the amount of energy produced in a cell and may contribute to mitochondrial dysfunction in highly energy-dependent SNpc neurons, and subsequent cell death. Despite over four decades of research and substantial evidence implicating mtDNA in PD, its precise role in this disease remains elusive and has never before been investigated in PD individuals of African ancestry. Therefore, this study aimed to firstly address the lack of genetic screening for some of the well-known nuclear genetic determinants of PD in SSA, and to subsequently investigate mtDNA sequence variation and mtDNA copy number (mtDNA-CN) within a unique collection of African ancestry PD cases and controls. To do so, this study undertook the largest genetic screening of SSA African ancestry PD cases to date (N = 131), using the Multiplex Ligation-dependent Probe Amplification (MLPA) and High-Resolution Melt (HRM) techniques, but did not detect known PD-associated CNV mutations, or the common LRRK2 p.Gly2019Ser mutation, in any of the cases. This supported the notion that the genetic causes of PD in SSA may differ from those previously identified and underscored the need to investigate mtDNA as a possible genetic contributor to PD in populations from this region. A review of the literature revealed that discrepant reports due to limitations and challenges of past mtDNA studies have likely contributed to the unresolved role of mtDNA in PD, highlighting that alternative hypotheses and reproducible study designs could ultimately aid in elucidating its role in PD. Applying the lessons learned, we investigated homoplasmic (i.e., inherited or de novo) mtDNA variation in PD using the so-called ‘out-of-place’ variant hypothesis in African ancestry late-onset PD cases and controls, as well as a second African ancestry control group and a European ancestry replication cohort. This hypothesis tested whether carrying a haplogroup-defining variant in mtDNA-encoded OXPHOS genes, could be associated with increased PD risk when occurring ‘out-of-place’ on a different maternal lineage. After sequencing whole mitochondrial genomes on an Ion S5 System and analyzing the data using the mtDNA-Server pipeline and in-house Python scripts, no significant differences between the number of cases and the number of controls, with out-of-place OXPHOS variants, were noted in either the African ancestry discovery group or the European ancestry replication group. However, significantly more discovery cases harbored out-of-place OXPHOS variants when compared to the second control group, possibly due to population stratification. Overall, the findings from this exploratory study warrant additional research to further assess a potential contribution of out-of-place mtDNA variation to PD risk and to determine whether the hypothesis put forward here is indeed affected by population substructure. In addition to investigating mtDNA variation in the African ancestry study group, we evaluated mtDNA-CN in these individuals using droplet digital PCR. Intriguingly, we detected a significant increase in blood-derived mtDNA-CN in the PD cases that could be indicative of systemic mitochondrial dysfunction. Although these findings support the possible utility of mtDNA-CN as a potential marker of mitochondrial dysfunction in PD, replicating these results using an independent African ancestry cohort that is well-matched for age, will be necessary. Moreover, additional research is needed regarding whether altered levels of mtDNA-CN truly reflect mitochondrial impairment in PD. Importantly, variation in nDNA encoding factors involved in mtDNA-related processes (e.g., replication, transcription, and translation) could underlie the mtDNA-CN changes observed in this study (and in previous studies) and could contribute to mitochondrial impairment. In support of this notion, we compiled compelling evidence in a review that highlighted perturbed mtDNA-related processes (caused by nDNA changes) as an alternative avenue of mitochondrial dysfunction in PD and as a possible contributor to disease risk. avenue of mitochondrial dysfunction in PD and as a possible contributor to disease risk. As the first to explore mtDNA variation and mtDNA-CN in an SSA PD context, this study has made a considerable contribution to the PD genetics field. While we were unable to reproducibly implicate homoplasmic out-of-place mtDNA variation in PD risk of African ancestry individuals, our findings of significantly increased mtDNA-CN in PD cases are intriguing and highlight the possible utility of altered, blood-derived mtDNA-CN as a minimally invasive marker of mitochondrial dysfunction and/or a biomarker for PD across different populations. Collectively, the research presented in this dissertation alludes to a secondary role of mtDNA in PD, with to-date unknown nDNA variation being the primary genetic causal agent of disease, and somatic mtDNA changes being a possibly detrimental consequence thereof. However, much larger studies leveraging multi-omics approaches, together with a more extensive understanding of the mitochondrial genome itself, will be key to fully assess the magnitude of its contribution to disease and to ultimately define its role in PD. AFRIKAANSE OPSOMMING: Parkinson se siekte (PS) is 'n ongeneeslike, neurodegeneratiewe bewegingsversteuring, wat deur die verlies van dopamien-neurone in die substantia nigra pars compacta (SNpc) gekenmerk word. Mitochondriale disfunksie is lank reeds as 'n moontlike meganisme van neurodegenerasie in mense met PS geïmpliseer. Baie proteïene wat deur gene in die kern-DNA gekodeer word, is belangrik vir mitochondriale funksie. Gevolglik kan patogeniese mutasies, insluitend kopienommervariasie (CNV's) in sulke gene (bv. PINK1, PRKN en LRRK2), mitochondriale funksie ontwrig en is as monogeniese oorsake van PS geïdentifiseer. Hierdie mutasies is hoofsaaklik in bevolkings van Asiatiese en Europese afkoms gerapporteer, maar is nog selde in Afrika-populasies suid van die Sahara (SSA) gevind - moontlik as gevolg van die beperkte genetiese sifting wat vir PSgeassosieerde mutasies in hierdie bevolkings gedoen word. Afgesien van genetiese variasie in kern-DNA, is mitochondriale DNA (mtDNA) variasie ook by PS betrokke. Mitochondria het verskeie kopieë van hul eie DNA (d.w.s. mtDNA), wat vir belangrike oksidatiewe fosforilasie (OXPHOS) komponente kodeer en wat derhalwe nodig is vir sellulêre energieproduksie. mtDNA variasie wat tot verandering in transkripsie lei, of verlaagde mtDNA kopieë kan dus bydra tot mitochondriale disfunksie in SNpc neurone. Ten spyte van meer as vier dekades van navorsing en aansienlike bewyse wat mtDNA in PS impliseer, bly die presiese rol daarvan in hierdie siekte ontwykend, met geen gerapporteerde ondersoeke in mense met PS van Afrika-afkoms nie. Daarom was die doel van hierdie studie om eers die gebrek aan genetiese sifting vir sommige van die bekende kern-DNA-determinante van PS in SSA te ondersoek, en daarna die mtDNA variasie en mtDNA-kopienommer (mtDNA-CN) binne 'n unieke versameling van PS pasiënte van SSA Afrikaafkoms, asook kontroles, te ondersoek. Om dit te doen, het hierdie studie die grootste genetiese sifting van SSA PS pasiënte van Afrika-afkoms onderneem (N = 131), met behulp van die multipleks ligeringsafhanklike peileramplifisering (Eng.: multiplex ligation-dependent probe amplification, MLPA) en hoë-resolusie smelt (Eng.: High-resolution melt, HRM) tegnieke. Hierdie studie het egter nié bekende PS-geassosieerde CNV-mutasies, of die mees algemene LRRK2-mutasie (p.Gly2019Ser) in enige van die PS pasiënte ontdek nie. Dit het die idee ondersteun dat die genetiese oorsake van PS in SSA-individue van dié wat voorheen geïdentifiseer is verskil, en beklemtoon die behoefte om mtDNA as 'n moontlike genetiese bydraer tot PD in SSA te ondersoek. 'n Oorsig van die literatuur het aan die lig gebring dat botsende verslae, as gevolg van beperkings en uitdagings van vorige mtDNA-studies, waarskynlik bygedra het tot ʼn onvoldoende evaluering van die rol van mtDNA in PS. Dit versterk die moontlikheid dat alternatiewe hipoteses en reproduseerbare studieontwerpe uiteindelik kan help om ʼn beter begrip van mtDNA se rol in PS te vorm. Gevolglik het ons mtDNA-variasie in PS met behulp van die sogenaamde 'buite-plek‘ variant (Eng.: out-of-place variant) hipotese in PS-pasiënte en -kontroles van Afrika-herkoms, sowel as 'n tweede Afrikavoorvaderbeheergroep en 'n Europese-afkoms repliseringskohort, ondersoek. Hierdie hipotese het getoets of haplogroepbepalende variante in mtDNA- gekodeerde OXPHOS-gene met verhoogde PSrisiko geassosieer kan word, wanneer hulle op 'n ander moederlyn voorkom. Nadat die volledige mtDNA-genome se volgorde op ʼn Ion S5-sisteem bepaal is, is die data met behulp van die aanlyn mtDNA-Server-, asook ʼn in-huis Python-pyplyn geanaliseer. Geen statisties-betekenisvolle verskille is tussen die aantal pasiënte en aantal kontroles met buite-plek OXPHOS variante in enige van die kohorte waargeneem nie. Aansienlik meer gevalle in die Afrika-voorvaderbeheergroep het buite-plek OXPHOS variante gehad in vergelyking met die tweede kontrolegroep. Dit was moontlik as gevolg van populasiestratifikasie. Bykomende navorsing is dus nodig om 'n potensiële bydrae van buite-plek mtDNA variasie op PS risiko verder te evalueer. Ons het ook mtDNA-CN in individue van Afrika-afkoms geëvalueer met behulp van druppel digitale PCR. Ons het 'n beduidende toename in bloed-afgeleide mtDNA-CN in die PS-pasiënte waargeneem. Dit kan 'n aanduiding van sistemiese mitochondriale-disfunksie wees. Alhoewel hierdie bevindings die moontlike nut van bloed-afgeleide mtDNA-CN as 'n merker van mitochondriale disfunksie in PS ondersteun, sal die herhaling van hierdie resultate met behulp van 'n onafhanklike Afrika-afkoms kohort nodig wees. Daarbenewens is bykomende navorsing nodig oor die vraag of veranderde vlakke van mtDNA-CN werklik mitochondriale disfunksie in PD weerspieël. Variasie in kern-DNA wat by mtDNA-verwante prosesse (bv. replikasie, transkripsie en vertaling) betrokke is, kan die mtDNA-CN-veranderinge, wat in hierdie studie waargeneem is, onderlê, en kan tot mitochondriale disfunksie bydrae. Ter ondersteuning van hierdie idee, het ons ondersteunende data wat die mtDNA-verwante prosesse as 'n alternatiewe weg van mitochondriale disfunksie in PD – en gevolglik as 'n moontlike bydraer tot siekterisiko – in ʼn oorsigartikel saamgevat. As die eerste studie om mtDNA variasie en mtDNA-CN in 'n SSA PS konteks te ondersoek, het hierdie studie 'n aansienlike bydrae tot die PS genetikaveld gemaak. Terwyl ons nie homoplasmiese mtDNA variasie in PS risiko van Afrika-afkoms individue kon reproduseer nie, is ons bevindings van beteknisvolle verhoogde mtDNA-CN in PS pasiënte treffend en beklemtoon die moontlike nut van veranderde, bloed-afgeleide mtDNA-CN as 'n minimaal-indringende merker van mitochondriale disfunksie en / of biomerker vir PS, vir verskillende populasies. Gesamentlik verwys hierdie navorsing na 'n sekondêre rol van mtDNA in PS, met nog ongerapporteerde kern-DNA-variasie wat die primêre genetiese oorsaak van PS, en somatiese mtDNA-veranderinge, asook gedisreguleerde mtDNAprosesse, wat potensieel nadelige gevolg daarvan kan wees. Dus stel ons voor dat, bykomend tot meer omvattende studies na homoplasmiese mtDNA-variasie as ʼn moontlike oorsaak van mitochondriale disfunksie, toekomstige grootskaalse studies genetiese variasie in kern-gekodeerde gene, wat met mDNA funksie geassosieer word, ondersoek. Doctoral 2022-01-19T07:04:28Z 2022-04-29T12:57:03Z 2022-01-19T07:04:28Z 2022-04 Thesis http://hdl.handle.net/10019.1/125168 en Stellenbosch University xxii, 135 pages : illustrations application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Parkinson's disease Mitochondrial DNA African ancestry Parkinson's disease -- Africa Genetic disorders -- Africa Mitochondrial DNA UCTD Muller-Nedebock, Amica Corda Investigating mitochondrial DNA sequence variation and copy number in individuals of African ancestry living with Parkinson’s disease. |
| title | Investigating mitochondrial DNA sequence variation and copy number in individuals of African ancestry living with Parkinson’s disease. |
| title_full | Investigating mitochondrial DNA sequence variation and copy number in individuals of African ancestry living with Parkinson’s disease. |
| title_fullStr | Investigating mitochondrial DNA sequence variation and copy number in individuals of African ancestry living with Parkinson’s disease. |
| title_full_unstemmed | Investigating mitochondrial DNA sequence variation and copy number in individuals of African ancestry living with Parkinson’s disease. |
| title_short | Investigating mitochondrial DNA sequence variation and copy number in individuals of African ancestry living with Parkinson’s disease. |
| title_sort | investigating mitochondrial dna sequence variation and copy number in individuals of african ancestry living with parkinson s disease |
| topic | Parkinson's disease Mitochondrial DNA African ancestry Parkinson's disease -- Africa Genetic disorders -- Africa Mitochondrial DNA UCTD |
| url | http://hdl.handle.net/10019.1/125168 |
| work_keys_str_mv | AT mullernedebockamicacorda investigatingmitochondrialdnasequencevariationandcopynumberinindividualsofafricanancestrylivingwithparkinsonsdisease |