Transcriptomic profiling of cerebrospinal fluid identifies ALS pathway enrichment and RNA biomarkers in MND individuals.
Alexander FröhlichAbigail L PfaffVivien J BubbJohn P QuinnSulev KõksPublished in: Experimental biology and medicine (Maywood, N.J.) (2023)
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.
Keyphrases
- amyotrophic lateral sclerosis
- cerebrospinal fluid
- single cell
- spinal cord
- gene expression
- genome wide
- oxidative stress
- rna seq
- endoplasmic reticulum stress
- dna methylation
- poor prognosis
- white matter
- stem cells
- signaling pathway
- electronic health record
- multiple sclerosis
- long non coding rna
- big data
- cell cycle arrest
- transcription factor
- brain injury
- functional connectivity
- nucleic acid