To demonstrate proof-of-concept for the utility of transcriptional profiling as a disease biomarker by functionally validating SETX mutations in patients clinically suspected of having Ataxia with Oculomotor Apraxia Type 2 (AOA2).

Genetic ataxias are clinically heterogenous neurodegenerative conditions often involving rare or private mutations. It is often challenging for clinicians and geneticists to assign pathogenicity to rare gene variations solely based on DNA sequencing for clinically heterogenous conditions. An effective functional biomarker from an easy-to-obtain biospecimen would aid this assessment and be of high clinical value. The SETX gene encodes the protein senataxin, a ubiquitous DNA/RNA helicase crucial for resolving R-loops and maintaining genome stability. Loss-of-function mutations in SETX cause a recessive neurodegenerative disorder, Ataxia with Oculomotor Apraxia Type 2 (AOA2). 

RNA-sequencing data was generated from peripheral blood from 20 AOA2 families (32 patients and 35 carrier controls). Weighted Gene Co-expression Network Analysis (WGCNA) was performed to construct an AOA2-specific transcriptomic signature for use as a functional biomarker to validate SETX variants as loss-of-function mutations.

WGCNA identified five disease-specific gene network modules, which were validated using additional genomic datasets from AOA2 patient blood, fibroblasts, and SETX-knockout mouse models. One of these modules was found to be modestly effective in distinguishing individuals with AOA2 from carriers (sensitivity 64%, specificity 97%) and to robustly differentiate AOA2 patients from those with genetically distinct, yet phenotypically similar, neurological disorders or other SETX-related genetic disorders (sensitivity 100%, specificity 100%). As a further demonstration of efficacy, we utilized this transcriptomic biomarker to verify the first pathogenic AOA2 mutation in a non-canonical SETX transcript, expanding the spectrum of mutations that contribute to AOA2.

Transcriptional profiling-based biomarkers can functionally resolve variants of uncertain clinical significance in disease genes that are expressed in accessible tissues to improve diagnosis of genetic neurological disorders.