TDP43 proteinopathy exhibits disease, tissue, and context-specific cryptic splicing signatures

Mislocalization of the nuclear protein TAR DNA-binding protein 43 (TDP43) is a hallmark of ALS and FTD which leads to de-repression and inclusion of cryptic exons. These cryptic exons represent promising biomarkers of TDP43 pathology in a spectrum of neurodegenerative diseases. However, most cryptic exons to date have been identified from in vitro models or a single cortical FTD dataset, limiting our understanding of tissue and cell-specific splices as well as differences between in vitro and in vivo processes. We meta-analyzed published bulk RNAseq datasets representing 1,778 RNAseq profiles of ALS and FTD post-mortem tissue, and in vitro models with experimentally depleted TDP43. We identified 142 cryptic splices, including 76 novel events, and identified cryptic splicing signatures with distinct cortical and spinal cord enrichment, among other context-specific profiles. Using RNAseq and RT-qPCR, we validated a subset of these splices in an independent spinal cord cohort, and demonstrated a correlation of TDP43 pathology severity with degree of cryptic splicing. Leveraging multiple public single-nucleus RNAseq datasets of ALS and FTD motor and frontal cortex, we confirmed the elevation of cortical-enriched splices in disease and localized them to layer-specific neuronal populations. This catalog of cryptic splices could inform efforts to develop biomarkers for tissue-specific and cell type-specific TDP43 pathology.