Utilizing a cell culture based novel cellular thermal shift assay to understand the isoform-dependent thermal stability of ApoE variants

Apolipoprotein E (ApoE) is the primary genetic risk modifier of late-onset Alzheimers disease, with the {varepsilon}4 allele increasing risk up to 15-fold relative to {varepsilon}3. The structural differences between isoforms are thought to underlie their distinct effects on lipid transport, receptor binding, and disease risk. ApoE4 exhibits reduced thermodynamic stability compared to ApoE3, but prior characterisation has relied on purified recombinant protein, leaving open whether these differences are preserved in native cellular environments and how they relate to rare disease-associated variants. Here, we employed the cellular thermal shift assay (CETSA) and a bioluminescence-based thermal stability assay (BiTSA) to systematically characterise ApoE thermal stability across isoforms and variants. Using CETSA on brain tissue from humanised APOE knock-in mice and post-mortem human brain, we confirm that ApoE4 exhibits significantly reduced thermal stability compared to ApoE3 in native tissue, with this difference conserved across species despite variation in absolute melting temperatures. We developed BiTSA, which leverages a split-luciferase HiBiT tag to quantify soluble ApoE across a thermal gradient in living cells, providing a higher-throughput platform that faithfully recapitulates isoform stability differences. Applying BiTSA to rare AD-associated variants, we found that L28P exerts divergent, isoform-dependent effects, destabilising ApoE3 while paradoxically stabilising ApoE4--a finding supported by AlphaFold modelling revealing isoform-specific differences in helix 1 architecture. These results establish BiTSA as a robust cellular tool for ApoE variant characterisation and demonstrate that isoform background critically modulates the structural consequences of rare mutations.