Deep sncRNA-seq of the PPMI cohort to study Parkinson’s disease progression

Abstract

Coding and non-coding RNAs have diagnostic and prognostic importance in Parkinson's diseases (PD). We studied circulating small non-coding RNAs (sncRNAs) in 7, 003 samples from two longitudinal PD cohorts (Parkinson's Progression Marker Initiative (PPMI) and Luxembourg Parkinson's Study (NCER-PD)) and modelled their influence on the transcriptome. First, we sequenced sncRNAs in 5, 450 blood samples of 1, 614 individuals in PPMI. The majority of 323 billion reads (59 million reads per sample) mapped to miRNAs. Other covered RNA classes include piRNAs, rRNAs, snoRNAs, tRNAs, scaRNAs, and snRNAs. De-regulated miRNAs were associated with the disease and disease progression and occur in two distinct waves in the third and seventh decade of live. Originating mostly from a characteristic set of immune cells they resemble a systemic inflammation response and mitochondrial dysfunction, two hallmarks of PD. By profiling 1, 553 samples from 1, 024 individuals in the NCER-PD cohort using an independent technology, we validate relevant findings from the sequencing study. Finally, network analysis of sncRNAs and transcriptome sequencing of the original cohort identified regulatory modules emerging in progressing PD patients.miRNA studies to date, covering over 3, 000 patients and controls 21 .Advanced biomarker studies however require carefully designed cohorts. Already a few large-scale PD studies aiming to advance diagnosis, prognosis and therapeutics fulfil respective requirements 22-24 . Among them, the Parkinson's Progression Marker Initiative (PPMI) is a multi-cohort, longitudinal observational study designed to discover and validate objective biomarkers of Parkinson's 25 . The PPMI project constitutes a global effort of 33 clinical sites in 11 countries with regular study participant assessments (Figure 1a). It also features comprehensive clinical phenotyping to observe hundreds of characteristics of the known subtypes of the disease, such as the idiopathic and genetic forms. Further, longitudinal biosampling following rigorous Standard Operating Procedures (SOPs) is performed to set a framework for the discovery and validation of early-onset and prognostic biomarkers. To identify potential non-coding RNA and transcriptomic markers in PPMI we performed RNA-seq on blood samples drawn at each clinical visit. For short and long RNAs, we carried out optimized assays and sequenced separate aliquots from the same blood samples for paired RNA analyses. Here, we present the evaluation of the sncRNA-seq fraction for disease detection and progression tracking. We examine the potential of different classes of small RNAs but emphasise the role of miRNAs. We also validate relevant findings for miRNAs on the Luxembourg Parkinson's Study in the framework of the National Centre for Excellence in Research on PD (NCER-PD) cohort 22 , which was performed independently and with a different technology. Finally, we provide insights on how the key non-coding RNAs regulate gene expression by utilizing the long RNA sequencing data. Specific ana...

Genetic Risk Profiling in Parkinson’s Disease and Utilizing Genetics to Gain Insight into Disease-Related Biological Pathways

“…Additionally, dysregulation of small noncoding transcripts, particularly microRNAs, is increasingly recognized as a potential mediator of reactive oxygen species production and mitochondrial dysfunction in PD and other neurodegenerative diseases [ 57 ]. Recent RNA-seq experiments in longitudinal PD cohorts associated PD with dysregulation of miRNAs implicated in function of mitochondria and inflammatory immune cells such as leukocytes [ 58 ].…”

Non-Coding RNAs in the Brain-Heart Axis: The Case of Parkinson’s Disease

“… Role of microRNAs in Parkinson’s disease [ 28 , 52 , 54 , 63 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 , 74 , 75 , 76 , 77 , 78 , 79 , 80 , 81 , 82 , 83 , 84 , 85 , 86 , 87 , 88 , 89 , 90 , 91 , 92 , 93 , 94 , 95 , 96 , 97 , 98 , 99 , 100 , 101 ]. …”

“…A Taqman PCR-based study in RNA samples isolated from peripheral lymphocytes of 20 non-medicated PD patients and 18 PD patients under medication revealed that several miRNAs, including brain-enriched miRNAs, were upregulated after treatment (miR-7, miR9-5p, miR-9-3p, miR-129, and miR-132) whilst other miRNAs were unaffected (miR-133b, miR-153, miR-191, miR-346, miR-433, miR-598) [55]. A large scale study used whole blood samples from two different cohorts-PPMI (2802 PD vs. 1538 controls) and NCER-PD (947 PD vs. 493 controls) to highlight the de-regulated small ncRNAs, in particular miRNAs, in PD and demonstrated that the occurrence of their de-regulation is related to disease progression and aging [63]. Whether these changes merely reflect the control of inflammation or the amelioration of the neurological status of the patients remains to be determined.…”