[en] Biallelic mutations in PINK1/PRKN cause recessive Parkinson’s disease. Given the established role of PINK1/Parkin in regulating mitochondrial dynamics, we explored mitochondrial DNA (mtDNA) integrity and inflammation as disease modifiers in carriers of mutations in these genes. MtDNA integrity was investigated in a large collection of biallelic (n = 84) and monoallelic (n = 170) carriers of PINK1/PRKN mutations, idiopathic Parkinson’s disease patients (n = 67) and controls (n = 90). In addition, we studied global gene expression and serum cytokine levels in a subset. Affected and unaffected PINK1/PRKN monoallelic mutation carriers can be distinguished by heteroplasmic mtDNA variant load (AUC = 0.83, CI:0.74-0.93). Biallelic PINK1/PRKN mutation carriers harbor more heteroplasmic mtDNA variants in blood (p = 0.0006, Z = 3.63) compared to monoallelic mutation carriers. This enrichment was confirmed in iPSC-derived (controls, n = 3; biallelic PRKN mutation carriers, n = 4) and postmortem (control, n = 1; biallelic PRKN mutation carrier, n = 1) midbrain neurons. Lastly, the heteroplasmic mtDNA variant load correlated with IL6 levels in PINK1/PRKN mutation carriers (r = 0.57, p = 0.0074). PINK1/PRKN mutations predispose individuals to mtDNA variant accumulation in a dose- and disease-dependent manner.
Centre de recherche :
Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) Luxembourg Centre for Systems Biomedicine (LCSB)
Disciplines :
Génétique & processus génétiques Neurologie
Auteur, co-auteur :
Trinh, Joanne
Hicks, Andrew A.
König, Inke R.
DELCAMBRE, Sylvie ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Molecular and Functional Neurobiology
Lüth, Theresa
Schaake, Susen
Wasner, Kobi
GHELFI, Jenny ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Molecular and Functional Neurobiology
Borsche, Max
Vilariño-Güell, Carles
Hentati, Faycel
Germer, Elisabeth L.
Bauer, Peter
Takanashi, Masashi
Kostić, Vladimir
Lang, Anthony E.
Brüggemann, Norbert
Pramstaller, Peter P.
Pichler, Irene
Rajput, Alex
Hattori, Nobutaka
Farrer, Matthew J.
Lohmann, Katja
Weissensteiner, Hansi
MAY, Patrick ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core
Klein, Christine
GRÜNEWALD, Anne ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Molecular and Functional Neurobiology
FNR11250962 - Reduced Penetrance In Hereditary Movement Disorders: Elucidating Mechanisms Of Endogenous Disease Protection P1: Markers And Mechanisms Of Reduced Penetrance In Lrrk2 Mutation Carriers, 2016 (01/01/2017-30/06/2020) - Anne Grünewald
Intitulé du projet de recherche :
ProtectMove
Organisme subsidiant :
Fonds National de la Recherche - FnR (ProtectMove, MiRisk) DFG (ProtectMove) BMBF (MitoPD)
Dorsey ER, Sherer T, Okun MS, Bloem BR. The emerging evidence of the Parkinson pandemic. J Parkinsons Dis. 2018;8(s1): S3-S8.
Bloem BR, Okun MS, Klein C. Parkinson’s disease. Lancet. 2021; 397:2284-2303.
Hedrich K, Hagenah J, Djarmati A, et al. Clinical spectrum of homozygous and heterozygous PINK1 mutations in a large German family with Parkinson disease: Role of a single hit? Arch Neurol. 2006;63:833-838.
Pramstaller PP, Schlossmacher MG, Jacques TS, et al. Lewy body Parkinson’s disease in a large pedigree with 77 parkin mutation carriers. Ann Neurol. 2005;58:411-422.
Klein C, Lohmann-Hedrich K, Rogaeva E, Schlossmacher MG, Lang AE. Deciphering the role of heterozygous mutations in genes associated with parkinsonism. Lancet Neurol. 2007;6: 652-662.
Kasten M, Weichert C, Lohmann K, Klein C. Clinical and demographic characteristics of PINK1 mutation carriers–a meta-analysis. Mov Disord. 2010;25:952-954.
Weissbach A, Konig IR, Huckelheim K, et al. Influence of L-dopa on subtle motor signs in heterozygous parkin- and PINK1 mutation carriers. Parkinsonism Relat Disord. 2017;42:95-99.
Hilker R, Klein C, Ghaemi M, et al. Positron emission tomographic analysis of the nigrostriatal dopaminergic system in familial parkinsonism associated with mutations in the parkin gene. Ann Neurol. 2001;49:367-376.
Krohn L, Grenn FP, Makarious MB, et al. Comprehensive assessment of PINK1 variants in Parkinson’s disease. medRxiv. 2020.
Yu E, Rudakou U, Krohn L, et al. Analysis of heterozygous PRKN variants and copy-number variations in Parkinson’s disease. Mov Disord. 2021;36:178-187.
Zhu W, Huang X, Yoon E, et al. Heterozygous PRKN mutations are common but do not increase the risk of Parkinson’s disease. Brain. 2022;145:2077-2091.
Pottier C, Rampersaud E, Baker M, et al. Identification of compound heterozygous variants in OPTN in an ALS-FTD patient from the CReATe consortium: A case report. Amyotroph Lateral Scler Frontotemporal Degener. 2018;19(5-6):469-471.
Greuel A, Trezzi JP, Glaab E, et al. GBA Variants in Parkinson’s disease: Clinical, metabolomic, and multimodal neuroimaging phenotypes. Mov Disord. 2020;35:2201-2210.
Kandul NP, Zhang T, Hay BA, Guo M. Selective removal of deletion-bearing mitochondrial DNA in heteroplasmic drosophila. Nat Commun. 2016;7:13100.
Gilkerson RW, De Vries RL, Lebot P, et al. Mitochondrial autophagy in cells with mtDNA mutations results from synergistic loss of transmembrane potential and mTORC1 inhibition. Hum Mol Genet. 2012;21:978-990.
Suen DF, Narendra DP, Tanaka A, Manfredi G, Youle RJ. Parkin overexpression selects against a deleterious mtDNA mutation in heteroplasmic cybrid cells. Proc Natl Acad Sci U S A. 2010; 107:11835-11840.
Sliter DA, Martinez J, Hao L, et al. Parkin and PINK1 mitigate STING-induced inflammation. Nature. 2018;561:258-262.
Trinh J, Lohmann K, Baumann H, et al. Utility and implications of exome sequencing in early-onset Parkinson’s disease. Mov Disord. 2019;34:133-137.
Kasten M, Hartmann C, Hampf J, et al. Genotype-phenotype relations for the Parkinson’s disease genes parkin, PINK1, DJ1: MDSGene systematic review. Mov Disord. 2018;33:730-741.
Lill CM, Mashychev A, Hartmann C, et al. Launching the movement disorders society genetic mutation database (MDSGene). Mov Disord. 2016;31:607-609.
Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754-1760.
Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet. 1999;23:147.
Li H, Handsaker B, Wysoker A, et al. The sequence alignment/ map format and SAMtools. Bioinformatics. 2009;25:2078-2079.
McKenna A, Hanna M, Banks E, et al. The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297-1303.
Okonechnikov K, Conesa A, Garcia-Alcalde F. Qualimap 2: Advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics. 2016;32:292-294.
Ewels P, Magnusson M, Lundin S, Kaller M. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016;32:3047-3048.
Weissensteiner H, Forer L, Fuchsberger C, et al. mtDNA-server: Next-generation sequencing data analysis of human mitochondrial DNA in the cloud. Nucleic Acids Res. 2016;44(W1): W64-W69.
Weissensteiner H, Forer L, Fendt L, et al. Contamination detection in sequencing studies using the mitochondrial phylogeny. Genome Res. 2021;31:309-316.
De Coster W, D’Hert S, Schultz DT, Cruts M, Van Broeckhoven C. Nanopack: Visualizing and processing long-read sequencing data. Bioinformatics. 2018;34:2666-2669.
Li H. Minimap2: Pairwise alignment for nucleotide sequences. Bioinformatics. 2018;34:3094-3100.
1000 Genomes Project Consortium, Auton A, Brooks LD, et al. A global reference for human genetic variation. Nature. 2015;526: 68-74.
Bolze A, Mendez F, White S, et al. Selective constraints and pathogenicity of mitochondrial DNA variants inferred from a novel database of 196,554 unrelated individuals. bioRxiv. [Preprint]. https://doi.org/10.1101/798264
Dayama G, Emery SB, Kidd JM, Mills RE. The genomic landscape of polymorphic human nuclear mitochondrial insertions. Nucleic Acids Res. 2014;42:12640-9.
Castellana S, Biagini T, Petrizzelli F, et al. Mitimpact 3: Modeling the residue interaction network of the respiratory chain subunits. Nucleic Acids Res. 2021;49(D1):D1282-D1288.
Pereira L, Soares P, Triska P, et al. Global human frequencies of predicted nuclear pathogenic variants and the role played by protein hydrophobicity in pathogenicity potential. Sci Rep. 2014;4:7155.
Bender A, Krishnan KJ, Morris CM, et al. High levels of mitochondrial DNA deletions in substantia nigra neurons in aging and Parkinson disease. Nat Genet. 2006;38:515-517.
Rocha MC, Rosa HS, Grady JP, et al. Pathological mechanisms underlying single large-scale mitochondrial DNA deletions. Ann Neurol. 2018;83:115-130.
Grady JP, Murphy JL, Blakely EL, et al. Accurate measurement of mitochondrial DNA deletion level and copy number differences in human skeletal muscle. PLoS ONE. 2014;9:e114462.
Yu-Wai-Man P, Lai-Cheong J, Borthwick GM, et al. Somatic mitochondrial DNA deletions accumulate to high levels in aging human extraocular muscles. Invest Ophthalmol Vis Sci. 2010;51: 3347-3353.
Nicholls TJ, Zsurka G, Peeva V, et al. Linear mtDNA fragments and unusual mtDNA rearrangements associated with pathological deficiency of MGME1 exonuclease. Hum Mol Genet. 2014; 23:6147-6162.
Grünewald A, Rygiel KA, Hepplewhite PD, Morris CM, Picard M, Turnbull DM. Mitochondrial DNA depletion in respiratory chain-deficient Parkinson disease neurons. Ann Neurol. 2016; 79:366-378.
Wasner K, Smajic S, Ghelfi J, et al. Parkin deficiency impairs mitochondrial DNA dynamics and propagates inflammation. Mov Disord. 2022;37:1405-1415.
Reinhardt P, Glatza M, Hemmer K, et al. Derivation and expansion using only small molecules of human neural progenitors for neurodegenerative disease modeling. PLoS ONE. 2013;8: e59252.
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
A language and environment for statistical computing. R Foundation for Statistical Computing. 2020. https://www.Rproject.org/
Luth T, Schaake S, Grunewald A, May P, Trinh J, Weissensteiner H. Benchmarking low-frequency variant calling with long-read data on mitochondrial DNA. Front Genet. 2022;13:887644.
Wei W, Gaffney DJ, Chinnery PF. Cell reprogramming shapes the mitochondrial DNA landscape. Nat Commun. 2021;12:5241.
Matheoud D, Cannon T, Voisin A, et al. Intestinal infection triggers Parkinson’s disease-like symptoms in Pink1(-/-) mice. Nature. 2019;571:565-569.
Payne BA, Wilson IJ, Yu-Wai-Man P, et al. Universal heteroplasmy of human mitochondrial DNA. Hum Mol Genet. 2013;22: 384-390.
Kraytsberg Y, Kudryavtseva E, McKee AC, Geula C, Kowall NW, Khrapko K. Mitochondrial DNA deletions are abundant and cause functional impairment in aged human substantia nigra neurons. Nat Genet. 2006;38:518-520.
Grunewald A, Kumar KR, Sue CM. New insights into the complex role of mitochondria in Parkinson’s disease. Prog Neurobiol. 2019;177:73-93.
Rothfuss O, Fischer H, Hasegawa T, et al. Parkin protects mitochondrial genome integrity and supports mitochondrial DNA repair. Hum Mol Genet. 2009;18:3832-3850.
Zanon A, Kalvakuri S, Rakovic A, et al. SLP-2 interacts with parkin in mitochondria and prevents mitochondrial dysfunction in parkin-deficient human iPSC-derived neurons and drosophila. Hum Mol Genet. 2017;26:2412-2425.
Dolle C, Flones I, Nido GS, et al. Defective mitochondrial DNA homeostasis in the substantia nigra in Parkinson disease. Nat Commun. 2016;7:13548.
LaVoie MJ, Hastings TG. Dopamine quinone formation and protein modification associated with the striatal neurotoxicity of methamphetamine: Evidence against a role for extracellular dopamine. J Neurosci. 1999;19:1484-1491.
Yakes FM, Van Houten B. Mitochondrial DNA damage is more extensive and persists longer than nuclear DNA damage in human cells following oxidative stress. Proc Natl Acad Sci U S A. 1997;94:514-519.
Pickrell AM, Huang CH, Kennedy SR, et al. Endogenous parkin preserves dopaminergic substantia nigral neurons following mitochondrial DNA mutagenic stress. Neuron. 2015;87:371-381.
Borsche M, Konig IR, Delcambre S, et al. Mitochondrial damage-associated inflammation highlights biomarkers in PRKN/PINK1 parkinsonism. Brain. 2020;143:3041-3051.