Identification of distinct pathological signatures induced by patient-derived α-synuclein structures in nonhuman primates

Machine learning–based approach unravels distinct pathological signatures induced by patient-derived α-synuclein seeds in monkeys. Dopaminergic neuronal cell death, associated with intracellular α-synuclein (α-syn)–rich protein aggregates [termed “Lewy bodies” (LBs)], is a well-established characteristic of Parkinson’s disease (PD). Much evidence, accumulated from multiple experimental models, has suggested that α-syn plays a role in PD pathogenesis, not only as a trigger of pathology but also as a mediator of disease progression through pathological spreading. Here, we have used a machine learning–based approach to identify unique signatures of neurodegeneration in monkeys induced by distinct α-syn pathogenic structures derived from patients with PD. Unexpectedly, our results show that, in nonhuman primates, a small amount of singular α-syn aggregates is as toxic as larger amyloid fibrils present in the LBs, thus reinforcing the need for preclinical research in this species. Furthermore, our results provide evidence supporting the true multifactorial nature of PD, as multiple causes can induce a similar outcome regarding dopaminergic neurodegeneration.

[1]  Elisabet Englund,et al.  Lewy bodies in grafted neurons in subjects with Parkinson's disease suggest host-to-graft disease propagation , 2008, Nature Medicine.

[2]  Davide Castelvecchi,et al.  Can we open the black box of AI? , 2016, Nature.

[3]  C. Dobson,et al.  Defining α-synuclein species responsible for Parkinson's disease phenotypes in mice , 2019, The Journal of Biological Chemistry.

[4]  Qin Li,et al.  Lack of additive role of ageing in nigrostriatal neurodegeneration triggered by α-synuclein overexpression , 2015, Acta neuropathologica communications.

[5]  J. Trojanowski,et al.  Pathological α-Synuclein Transmission Initiates Parkinson-like Neurodegeneration in Nontransgenic Mice , 2012, Science.

[6]  P. Hof,et al.  Lewy body densities in the entorhinal and anterior cingulate cortex predict cognitive deficits in Parkinson's disease , 2003, Acta Neuropathologica.

[7]  C D Marsden,et al.  Alterations in the levels of iron, ferritin and other trace metals in Parkinson's disease and other neurodegenerative diseases affecting the basal ganglia. , 1991, Brain : a journal of neurology.

[8]  M. Giugliano,et al.  α-Synuclein strains cause distinct synucleinopathies after local and systemic administration , 2015, Nature.

[9]  Qin Li,et al.  Lentiviral Overexpression of GRK6 Alleviates l-Dopa–Induced Dyskinesia in Experimental Parkinson’s Disease , 2010, Science Translational Medicine.

[10]  D. Krainc,et al.  α-synuclein toxicity in neurodegeneration: mechanism and therapeutic strategies , 2017, Nature Medicine.

[11]  Juan José Rodríguez Diez,et al.  On feature selection protocols for very low-sample-size data , 2018, Pattern Recognit..

[12]  M. Vila,et al.  Pathogenic Lysosomal Depletion in Parkinson's Disease , 2010, The Journal of Neuroscience.

[13]  R. Riek,et al.  Cryo-EM structure of alpha-synuclein fibrils , 2018, bioRxiv.

[14]  D. James Surmeier,et al.  Selective neuronal vulnerability in Parkinson disease , 2017, Nature Reviews Neuroscience.

[15]  Nicholas K. Sauter,et al.  Structure of the toxic core of α-synuclein from invisible crystals , 2015, Nature.

[16]  Federico N. Soria,et al.  Glucocerebrosidase deficiency in dopaminergic neurons induces microglial activation without neurodegeneration , 2017, Human molecular genetics.

[17]  E. Bézard,et al.  Rise and fall of minocycline in neuroprotection: need to promote publication of negative results , 2004, Experimental Neurology.

[18]  B. Mollenhauer,et al.  Novel One-step Immunoassays to Quantify α-Synuclein , 2012, The Journal of Biological Chemistry.

[19]  Xueming Li,et al.  Amyloid fibril structure of α-synuclein determined by cryo-electron microscopy , 2018, Cell Research.

[20]  N. Rougier,et al.  Identification of distinct pathological signatures induced by patient-derived α-synuclein structures in non-human primates , 2019, bioRxiv.

[21]  D. Eisenberg,et al.  Structures of fibrils formed by α-synuclein hereditary disease mutant H50Q reveal new polymorphs , 2019, Nature Structural & Molecular Biology.

[22]  H. Kretzschmar,et al.  Regional Distribution of Proteinase K‐Resistant α‐Synuclein Correlates with Lewy Body Disease Stage , 2004, Journal of neuropathology and experimental neurology.

[23]  R. Hauser,et al.  Lewy body–like pathology in long-term embryonic nigral transplants in Parkinson's disease , 2008, Nature Medicine.

[24]  Charles D. Schwieters,et al.  Solid-State NMR Structure of a Pathogenic Fibril of Full-Length Human α-Synuclein , 2016, Nature Structural &Molecular Biology.

[25]  J. Penney,et al.  The functional anatomy of basal ganglia disorders , 1989, Trends in Neurosciences.

[26]  E. Bézard,et al.  Birth Origin Differentially Affects Depressive-Like Behaviours: Are Captive-Born Cynomolgus Monkeys More Vulnerable to Depression than Their Wild-Born Counterparts? , 2013, PloS one.

[27]  J. Koh,et al.  Cytosolic labile zinc accumulation in degenerating dopaminergic neurons of mouse brain after MPTP treatment , 2009, Brain Research.

[28]  J. Bolam,et al.  Living on the edge with too many mouths to feed: Why dopamine neurons die , 2012, Movement disorders : official journal of the Movement Disorder Society.

[29]  J. Trojanowski,et al.  Intrastriatal alpha-synuclein fibrils in monkeys: spreading, imaging and neuropathological changes. , 2019, Brain : a journal of neurology.

[30]  J. Altmann,et al.  Observational study of behavior: sampling methods. , 1974, Behaviour.

[31]  E. Bézard,et al.  Lewy body extracts from Parkinson disease brains trigger α‐synuclein pathology and neurodegeneration in mice and monkeys , 2014, Annals of neurology.

[32]  E. Bézard,et al.  Depressive-like behavioral profiles in captive-bred single- and socially-housed rhesus and cynomolgus macaques: a species comparison , 2014, Front. Behav. Neurosci..

[33]  R. Taschereau,et al.  Rank–rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures , 2010, Nucleic acids research.

[34]  D. Mann,et al.  Generation and characterization of novel conformation-specific monoclonal antibodies for α-synuclein pathology , 2015, Neurobiology of Disease.

[35]  A. Petrie,et al.  Regional differences in the severity of Lewy body pathology across the olfactory cortex , 2009, Neuroscience Letters.

[36]  G. Halliday,et al.  Structural heterogeneity of α-synuclein fibrils amplified from patient brain extracts , 2019, Nature Communications.

[37]  Michael Johnson,et al.  Triggers, Facilitators, and Aggravators: Redefining Parkinson’s Disease Pathogenesis , 2019, Trends in Neurosciences.

[38]  M. Fändrich,et al.  FTIR reveals structural differences between native β‐sheet proteins and amyloid fibrils , 2004, Protein science : a publication of the Protein Society.

[39]  E. Hirsch,et al.  Neuroinflammation in Parkinson's disease. , 2012, Parkinsonism & related disorders.

[40]  Alain Dagher,et al.  Dopamine neurons implanted into people with Parkinson's disease survive without pathology for 14 years , 2008, Nature Medicine.

[41]  Mingyan Liu,et al.  Decreased circulating Zinc levels in Parkinson’s disease: a meta-analysis study , 2017, Scientific Reports.

[42]  E. Bézard,et al.  Alpha‐synuclein propagation: New insights from animal models , 2016, Movement disorders : official journal of the Movement Disorder Society.

[43]  Gregory Piatetsky-Shapiro,et al.  Knowledge Discovery in Databases: An Overview , 1992, AI Mag..

[44]  P. Hantraye,et al.  Translational research for Parkinson׳s disease: The value of pre-clinical primate models. , 2015, European journal of pharmacology.

[45]  A. Ballabio,et al.  Brain tyrosinase overexpression implicates age-dependent neuromelanin production in Parkinson’s disease pathogenesis , 2019, Nature Communications.

[46]  B Bioulac,et al.  Relationship between the Appearance of Symptoms and the Level of Nigrostriatal Degeneration in a Progressive 1-Methyl-4-Phenyl-1,2,3,6-Tetrahydropyridine-Lesioned Macaque Model of Parkinson's Disease , 2001, The Journal of Neuroscience.

[47]  H. Braak,et al.  Staging of brain pathology related to sporadic Parkinson’s disease , 2003, Neurobiology of Aging.

[48]  Fred H. Gage,et al.  In vivo demonstration that α-synuclein oligomers are toxic , 2011, Proceedings of the National Academy of Sciences.

[49]  E. Bézard,et al.  Protein aggregation and neurodegeneration in prototypical neurodegenerative diseases: Examples of amyloidopathies, tauopathies and synucleinopathies , 2017, Progress in Neurobiology.

[50]  Joel Nothman,et al.  Author Correction: SciPy 1.0: fundamental algorithms for scientific computing in Python , 2020, Nature Methods.

[51]  A. Cuervo,et al.  Proteostasis and aging , 2015, Nature Network Boston.

[52]  Raphaella W. L. So,et al.  α-Synuclein strains target distinct brain regions and cell types , 2019, Nature Neuroscience.

[53]  A. Mackay-Sim,et al.  Parkinson's disease-associated human ATP13A2 (PARK9) deficiency causes zinc dyshomeostasis and mitochondrial dysfunction , 2014, Human molecular genetics.

[54]  Sebastian Thrun,et al.  Dermatologist-level classification of skin cancer with deep neural networks , 2017, Nature.

[55]  E. Bézard,et al.  Behavioural Profiles in Captive-Bred Cynomolgus Macaques: Towards Monkey Models of Mental Disorders? , 2013, PloS one.

[56]  Joel Nothman,et al.  SciPy 1.0-Fundamental Algorithms for Scientific Computing in Python , 2019, ArXiv.

[57]  Kurt Hornik,et al.  Multilayer feedforward networks are universal approximators , 1989, Neural Networks.

[58]  R. Wade-Martins,et al.  Alpha-synuclein oligomers: a new hope , 2017, Acta Neuropathologica.

[59]  V. Beneš,et al.  The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. , 2009, Clinical chemistry.

[60]  B. Meier,et al.  Structural and functional characterization of two alpha-synuclein strains , 2013, Nature Communications.