In vitro, cellular and in vivo studies of amyloid oligomers structure and toxicity: Challenges and advances

Oligomeric assemblies of amyloidogenic proteins, such as Aβ, tau, α-synuclein, amylin, transthyretin, and TDP-43, are increasingly recognized as key drivers of cellular dysfunction across a range of neurodegenerative and systemic disorders. However, their molecular properties remain poorly understood due to their low abundance, structural heterogeneity, and transient nature. This review outlines current methods for studying amyloid oligomers, including biophysical (NMR, cryo-EM, HS-AFM, mass spectrometry), computational (molecular dynamics simulations), and biological (cellular assays, organoids, and animal models) approaches. This review also covers emerging methods for detecting misfolded proteins within complex biological environments and live-cell systems. Furthermore, we discuss recent advances that specifically address the challenges of studying oligomers, which are yielding crucial data on how these pathogenic species impair cellular homeostasis. Given the heterogeneity and transient nature of the oligomers, it is essential to utilize findings across diverse experimental platforms that yield complementary data and apply methods that also ensure reproducibility and mechanistic clarity with the goal of translating these findings into effective therapeutic strategies.