Profiles of extracellular miRNA in cerebrospinal fluid and serum from patients with Alzheimer's and Parkinson's diseases correlate with disease status and features of pathology

Abstract

The discovery and reliable detection of markers for neurodegenerative diseases have been complicated by the inaccessibility of the diseased tissue--such as the inability to biopsy or test tissue from the central nervous system directly. RNAs originating from hard to access tissues, such as neurons within the brain and spinal cord, have the potential to get to the periphery where they can be detected non-invasively. The formation and extracellular release of microvesicles and RNA binding proteins have been found to carry RNA from cells of the central nervous system to the periphery and protect the RNA from degradation. Extracellular miRNAs detectable in peripheral circulation can provide information about cellular changes associated with human health and disease. In order to associate miRNA signals present in cell-free peripheral biofluids with neurodegenerative disease status of patients with Alzheimer's and Parkinson's diseases, we assessed the miRNA content in cerebrospinal fluid and serum from postmortem subjects with full neuropathology evaluations. We profiled the miRNA content from 69 patients with Alzheimer's disease, 67 with Parkinson's disease and 78 neurologically normal controls using next generation small RNA sequencing (NGS). We report the average abundance of each detected miRNA in cerebrospinal fluid and in serum and describe 13 novel miRNAs that were identified. We correlated changes in miRNA expression with aspects of disease severity such as Braak stage, dementia status, plaque and tangle densities, and the presence and severity of Lewy body pathology. Many of the differentially expressed miRNAs detected in peripheral cell-free cerebrospinal fluid and serum were previously reported in the literature to be deregulated in brain tissue from patients with neurodegenerative disease. These data indicate that extracellular miRNAs detectable in the cerebrospinal fluid and serum are reflective of cell-based changes in pathology and can be used to assess disease progression and therapeutic efficacy.

Figure 1. Potential sources of variation for the sample cohort.

Three-way ANOVA analysis of variation demonstrates that (A) expiration age, (B) postmortem interval (PMI) and (C) gender do not contribute significant variation to the miRNA expression data.

Figure 2. Ordinal regression analysis reveals miRNAs with progressive expression trends across increasing Braak stages.

(A) We plotted two miRNAs selected from Table? 4 (miR-9-3p and miR-708-3p) that are detected in CSF and change with increasing Braak stage. The y axis is the mean of normalized counts for each miRNA, while the x axis represents Braak stages. (B) miR-16-5p and miR-183b-5p are detected in SER and change with Braak stage.

Figure 3. Ordinal regression analysis reveals miRNAs with progressive expression trends across increasing neurofibrillary tangle density.

(A) We plotted four miRNAs (miR-181b-5p, miR-181d, miR-181a-5p and miR-9-3p) detected in CSF from Table? 5. (B) miR-7i-3p and miR-10a-5p were selected from Table? 5, significant for neurofibrillary tangle stage regression analysis in SER.

Figure 4. Ordinal regression analysis reveals miRNAs with progressive expression trends across increasing amyloid plaque density.

(A) We plotted two miRNAs (miR-195-5p, miR-101-3p) detected in CSF from Table? 6 that showed consistent expression changes with increased density of plaques. (B) miR-106-5p and miR-30b-5p, detected in SER and selected from Table? 6, showed significant fit across increasing plaque density stages.

Figure 5. Ordinal regression analysis reveals miRNAs with trends in Lewy body progression.

(A) We plotted two miRNAs (miR-34a-5p and miR-374-5p) detected in CSF from Table? 7 that showed consistent expression change with progression of Lewy bodies. (B) We plotted two miRNAs (miR-130b-3p and miR-181b-5p) detected in SER from Table? 7 that showed consistent expression changes with progression of Lewy bodies.