Transcriptomic profiling of cerebrospinal fluid identifies ALS pathway enrichment and RNA biomarkers in MND individuals

Abstract

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder and the most common form of motor neurone disease (MND) which is characterized by the damage and death of motor neurons in the brain and spinal cord of affected individuals. Due to the heterogeneity of the disease, a better understanding of the interaction between genetics and biochemistry with the identification of biomarkers is crucial for therapy development. In this study, we used cerebrospinal fluid (CSF) RNA-sequencing data from the New York Genome Center (NYGC) ALS Consortium and analyzed differential gene expression between 47 MND individuals and 29 healthy controls. Pathway analysis showed that the affected genes are enriched in many pathways associated with ALS, including nucleocytoplasmic transport, autophagy, and apoptosis. Moreover, we assessed differential expression on both gene- and transcript-based levels and demonstrate that the expression of previously identified potential biomarkers, including CAPG, CCL3, and MAP2, was significantly higher in MND individuals. Ultimately, this study highlights the transcriptomic composition of CSF which enables insights into changes in the brain in ALS and therefore increases the confidence in the use of CSF for biomarker development.

Keywords: Cerebrospinal fluid; RNA-seq; amyotrophic lateral sclerosis; biomarker; motor neurone disease; transcriptome.

Figure 1.

Overview of study. In this study, transcriptomic data set from the New York Genome Center ALS Consortium was used. RNA-seq data from cerebrospinal fluid of 47 MND and 29 healthy control individuals were available. The aim of the study was to perform differential gene expression analysis between MND and control individuals with a focus on biomarker expression and explore enriched pathways.

Figure 2.

UpSet plot to visualize intersections of differentially expressed genes. The bar chart represents the size of the gene set. The number of differentially expressed genes for single (filled-in cells) and intersecting (filled-in cells with connecting lines) pathways/diseases is shown. A full list of genes affected in the corresponding disease/pathway is listed in Supplementary Data 3.

Figure 3.

Several genes encoding potential biomarker proteins are significantly upregulated in CSF from MND individuals. Differential gene expression analysis was performed using transcriptomic data sets from 47 MND and 29 healthy control individuals. Expression changes were analyzed on a gene (A)- and transcript (B)-based level. Several genes which have been previously identified to encode potential biomarker proteins were significantly more highly expressed in MND individuals. Log2 fold changes (log2FC) and P-adjusted values are indicated. For transcript-based analysis, corresponding transcript IDs are shown.