TDP-43 Knockdown In Neuronal Vs Astrocytic Cell Lines Reveals Similarities And Differences In the Biological Functions Between These Two Cellular Contexts

Abstract

TAR DNA-binding protein 43 (TDP-43) is a ubiquitously expressed RNA/DNA-binding protein of the heterogeneous nuclear ribonucleoprotein (hnRNP) family, involved in multiple stages of RNA metabolism. Since its identification in 2006 as the principal pathological component of cytoplasmic inclusions in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD), TDP-43 has become central to neurodegeneration research. While ALS was initially considered a motor neuron-specific disorder, mounting evidence implicates non-cell-autonomous mechanisms—particularly involving astrocytes—in disease onset and progression. These glial cells contribute to neurodegeneration via neuroinflammation, metabolic disruption, and excitotoxicity. To investigate the molecular consequences of TDP-43 loss of function, we performed RNA sequencing on human SH-SY5Y neuroblastoma and U87 glioma cell lines following TDP-43 knockdown, simulating neuronal and glial environments. Transcriptomic profiling revealed both shared and cell type-specific changes. Gene Ontology enrichment analysis highlighted dysregulation in pathways related to cell cycle control, DNA replication, and chromatin organization in both lines, suggesting convergent stress responses relevant to ALS pathology. Meanwhile, certain pathways—such as mitotic spindle assembly (SH-SY5Y) and DNA damage response (U87)—were uniquely affected. We identified several commonly deregulated genes with either concordant expression trends or divergent regulation between the two cell types, suggesting shared versus distinct adaptive responses. qRT-PCR validation confirmed the reliability of the transcriptomic data. Notably, many validated targets are involved in RNA processing, cytoskeletal dynamics, synaptic function, and stress responses. Altogether, our findings underscore the critical role of TDP-43 in maintaining transcriptomic stability and support a model where both neuronal and glial dysfunction contribute to ALS pathogenesis via overlapping yet distinct molecular mechanisms.