Single-cell transcriptomics uncovers chromatin dysfunction in a human TDP-43 proteinopathy model of Amyotrophic Lateral Sclerosis

TDP-43 proteinopathy, characterised by nuclear depletion and cytoplasmic aggregation of TDP-43, is the defining pathological hallmark of amyotrophic lateral sclerosis (ALS) and a shared pathology across frontotemporal lobar degeneration with TDP-43 inclusions (FTLD-TDP), limbic-predominant age-related TDP-43 encephalopathy (LATE), and a substantial subset of Alzheimer’s disease. We recently developed a human model of TDP-43 proteinopathy that enables inducible mislocalisation of endogenous TDP-43 in iPSC-derived neurons without chemical stress or mutant protein overexpression.

Using single-cell RNA sequencing of this model, we dissected the transcriptomic consequences of TDP-43 nuclear depletion across motor neurons as well as V1 and V2 interneurons at single-cell resolution. This approach uncovered disruption of ATP-dependent chromatin remodelling as a convergent downstream pathway across all three spinal neuron subtypes. Master regulator analysis identified ACTL6B, the neuron-specific subunit of the nBAF (neuronal BRG1/BRM-associated factor) chromatin remodelling complex, as the most consistently inhibited transcription factor following TDP-43 mislocalisation. ACTL6B downregulation emerges early in the mislocalisation cascade and is confirmed in post-mortem ALS spinal cord. ACTL6B knockdown in post-mitotic motor neurons phenocopies both the morphological and transcriptional consequences of TDP-43 pathology. Together, these findings establish nBAF complex dysfunction as a principal, spinal cord-enriched driver of TDP-43-associated neurodegeneration and reveal chromatin remodelling defects as a key mechanism in ALS.