INTEGRATED BULK MRNA-SEQ AND SYNAPTIC PROTEOMIC PROFILING OF VULNERABLE BRAIN REGIONS IN TDP-43 CONDITIONAL KNOCKOUT MICE

Recent meta-analyses of RNA-seq datasets from multiple TDP-43 knockdown cell models and from TDP-43–immunonegative neuronal nuclei in ALS/FTD brains demonstrate that many differentially expressed genes converge on pathways related to neuronal and synaptic function (Cao & Scotter, 2022). These include genes encoding presynaptic proteins involved in neurotransmitter release, synaptic vesicle cycling, and calcium signaling, as well as postsynaptic components. In parallel, recent studies have revealed a critical role for TDP-43 in maintaining RNA splicing fidelity by suppressing cryptic exon inclusion. Loss of nuclear TDP-43 results in hundreds of aberrant transcripts, many of which encode key synaptic proteins (Ma et al., 2022; Brown et al., 2022).
TDP-43 proteinopathies affect distinct brain regions in a disease-specific manner, with the cortex, hippocampus, and spinal cord particularly vulnerable. However, it remains unclear whether TDP-43 depletion across these tissues leads to convergent or region-specific changes in neuronal mRNA expression and synaptic protein composition. Identifying transcripts or proteins that are selectively or commonly dysregulated across vulnerable regions may reveal shared and region-specific disease mechanisms.
To address this, we generated primary neuronal sandwich co-cultures from the hippocampus, cortex, and striatum of CAGCre-ER; Tardbp^flox/flox mice. Conditional TDP-43 depletion was induced with 4-OH tamoxifen, followed by RNA isolation and bulk mRNA-seq. Transcriptome-wide analyses will identify shared and region-specific differential gene expression and splicing changes induced by TDP-43 loss.