Objective: To examine feasibility of obtaining microbiome data from frozen saliva and formalin-fixed, paraffin-embedded (FFPE) colon specimens.

Background: The gastrointestinal tract microbiome is of great interest in Parkinson’s disease (PD)^1-3. The Systemic Synuclein Sampling Study (S4) biobank contains specimens that would be useful for study of the microbiome, namely frozen saliva and FFPE colon biopsies^4-5. Developing protocols that allow use of these already-collected specimens for study of the PD microbiome will enhance efficiency and progress in this area.

Method: Specimens obtained as part of the S4 study from 5 PD participants and 4 healthy controls (HC) will be included. Genomic DNA from subject saliva specimens will be processed for 16S rRNA (16S) gene sequencing. To extract DNA from the paraffin-embedded colon, multiple methods will be tested for ability to remove formaldehyde-induced damage and provide sufficient DNA yield and quality for 16S sequencing. Sequence reads from samples will be taxonomically classified and per sample composition and diversity will be compared.

Results: We will report on the feasibility of generating microbiota data as 16S sequences from archived saliva and FFPE samples. If successful, these methods can be applied to additional specimens from 82 PD and HC subjects and consecutive inflammation activity in blood and cerebrospinal fluid. The resulting microbiota composition and diversity profiles can be associated with subject medications, motor and non-motor assessments, functional status, and olfaction using statistical models to better understand the role of the microbiome in PD versus HC.

Conclusion: This pilot study explores the use of existing biospecimen repositories to examine the GI tract microbiome in PD versus controls to enable the analysis of the spread of a possible pathogen across the gut barrier influencing peripheral inflammation.

References: 1. Braak H, Rub U, Gai WP, Del Tredici K. Idiopathic Parkinson’s disease: possible routes by which vulnerable neuronal types may be subject to neuroinvasion by an unknown pathogen. J Neural Transm. 2003; 110: 517-536. 2. van Kessel SP, Frye AK, El-Gendy AO, Castejon M, Keshavarzian A, van Dijk G, El Aidy S. Gut bacterial tyrosine decarboxylases restrict levels of levodopa in the treatment of Parkinson’s disease. Nat Commun. 2019; 10: 310-019-08294-y. 3. Schwiertz A, Spiegel J, Dillmann U, Grundmann D, Burmann J, Fassbender K, Schafer KH, Unger MM. Fecal markers of intestinal inflammation and intestinal permeability are elevated in Parkinson’s disease. Parkinsonism Relat Disord. 2018; 50: 104-107. 4. Visanji NP, Mollenhauer B, Beach TG, Adler CH, Coffey CS, Kopil CM, Dave KD, Foroud T, Chahine L, Jennings D, Systemic Synuclein Sampling Study (S4). The Systemic Synuclein Sampling Study: toward a biomarker for Parkinson’s disease. Biomark Med. 2017; 11: 359-368. 5. Chahine LM, Beach TG, Seedorff N, Caspell-Garcia C, Coffey CS, Adler CH, Serrano GE, Linder C, Mosovsky S, Foroud T, Riss H, Ecklund D, Seibyl J, Jennings D, Arnedo V, Riley L, Dave K, Mollenhauer B, on behalf of the Systemic Synuclein Sampling study. Feasibility and Safety of Multicenter Tissue and Biofluid Sampling for α-Synuclein in Parkinson’s Disease: The Systemic Synuclein Sampling Study. Journal of Parkinsons Disease. 2018; 8: 517-527.

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MDS Abstracts - https://www.mdsabstracts.org/abstract/feasibility-of-studying-the-pd-microbiome-in-frozen-saliva-and-formalin-fixed-colon-from-the-systemic-synuclein-sampling-study-s4/