NOVEL TRANSCRIPTOMIC APPROACHES IN BIOMARKER DISCOVERY IN HUNTINGTON'S DISEASE

Huntington’s disease (HD) is a fatal neurodegenerative disorder caused by CAG repeats expansion in the HTT gene. Transcriptional dysregulation is an early event in the pathogenic process in brain and peripheral tissues, justifying the use of transcriptomics approaches. We have explored novel methodologies in HD research: single-cell RNA-seq in patients’ blood (Chromium system) to face the high cellular complexity of this biofluid in biomarker discovery, and native RNA-seq (ONT system) in mouse model brain to capture the full-length complexity of the HD transcriptome and provide mechanistic insights.
In the first case, scRNA-seq supported an ubiquitous but mild effect on gene expression across peripheral blood mononuclear cells in symptomatic donors. Phenotypically characterized R6/1 mice allowed to correlate individual motor performance with transcriptional variations in both blood and striatum, identifying Irf7 as a promising candidate. In the second case, long read sequencing not only confirmed the differential expression in the R6/1 striatum reported in our lab but also enabled to reliably detect specific isoform switching and widespread disruption in poly(A) tail length, including some previously reported genes (e.g. Kctd17 and Auts2, respectively) besides extensive novel molecular alterations. This approach also permitted epitranscriptomic profiling of RNA (e.g., m6A and 5mC modifications).
Overall, the implementation of cutting-edge methodologies offers a framework for the proposal of clinically relevant biomarkers and new therapeutic strategies.
Funding: ISCIII-ERDF (PI19/00125, PI23/01858, CPII20/00025), Ministerio de Ciencia, Innovación y Universidades – NextGenerationEU (CNS2022-136169, FPU23/02176), ISABIAL (grants 2021-0406, 2022-0338, 2024/C/6, 2025/C.1/5, 2025/C.1/16), Generalitat Valenciana – NextGenerationEU (INVEST/2022/447).