BBB Seminar: Annalisa Pastore
From aptamer in silico design to disease mechanism: the example of TDP-43
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Annalisa Pastore
King's College London, London, UK
The connection between neurodegeneration and protein misfolding and aggregation has been established over the past two decades. Only more recently, it was recognized that nucleic acids are also linked to protein aggregation in various ways. Aggregation of RNA-binding proteins can be triggered by defective transcription, which affects RNA processing and, consequently, leads to progressive cell death. A direct effect of RNA binding has also been reported as a possible cause of the aggregation of RNA-binding proteins. We have wondered what effect RNA could have on TDP-43, an RNA-binding protein whose aggregation is observed in amyotrophic lateral sclerosis and frontotemporal dementia. TDP-43 aggregates are also detected in 30-60% of Alzheimer's and Parkinson’s cases and correlate with the severity of cognitive deficits and neurodegeneration.
With this aim in mind, we have developed in silico and studied experimentally the effects of in silico-designed RNA aptamers on TDP-43 aggregation (1). We showed that high affinity binding RNA aptamers are able to interfere with TDP-43 aggregation as a function of their nucleotide composition, binding affinity, and length in vitro (2). We also demonstrated that the effect is sequence specific since aptamers that share compositional and sequence similarities with natural partners and that have a high affinity for the protein, have a strong inhibitory effect against aggregation already at equimolar protein:RNA ratio. Non-UG-rich RNA sequences that have low affinity have no effects or induce faster aggregation. Preliminary results suggested that the same concept holds in cellular models where transfection of specific RNA aptamers has remarkable effects on aggregate clearance. These important results have laid the ground towards understanding the mechanism which determines TDP-43-related pathologies and offer a hope for disease treatment.
(1) Zacco et. al (2021) In silico-designed RNA aptamers: A thread to explore protein condensation in vitro and in cell. Nature Methods, submitted.
(2) Zacco et al. (2019) RNA as a key factor in driving or preventing self-assembly of the TAR DNA-binding protein 43. J. Mol. Biol. 431(8):1671.
Chairperson: Anni Vedeler, Department of Biomedicine
