Protein misfolding and aggregation represent hallmark features of numerous degenerative diseases [1]. When exposed to different cellular stressors such as heat shock, osmotic changes, oxidative stress, heavy metal exposure, toxins, and aging, proteins in the cellular proteome encounter challenges in maintaining their specific three-dimensional structures. The failure to uphold proper protein folding can lead to misfolding and aggregation, ultimately contributing to the pathogenesis of neurodegenerative disorders like Alzheimer’s, Parkinson’s, Huntington’s diseases, and type II diabetes [2]. Chemotherapy-induced peripheral neuropathy (CIPN) presents a common side effect associated with specific chemotherapeutic agents, resulting in peripheral nerve damage. Prior studies have identified various mechanisms in the development of CIPN, including microtubule disruption, mitochondrial dysfunction, altered ion channel activity, myelin damage, DNA injury, immune responses, and neuroinflammation, etc (Fig. 1a) [3], [4]. Despite these complex and debated mechanisms, there remains a lack of evidence regarding proteome aggregation in neuronal cell models of CIPN. This absence may be attributed to the intricate structural composition of neuronal cells and the limitations of current analytical tools in directly detecting proteome misfolding and aggregation in living cells.

Unlike correctly folded and functional proteins, the 3-dimensional structures of misfolded and aggregated proteins are collapsed, posing challenges for the rational design of bio-/chemo sensors. Hong and Hatters showcased the efficacy of maleimide chemistry and AIEgens in globally targeting exposed cysteine residues, enabling the detection of the unfolded proteome in live cells under conditions of stress-induced proteome unfolding [5], [6], [7]. Additionally, a variety of fluorescent environment-sensitive probes, such as fluorescent molecular rotor probes and solvatochromic fluorescent probes, can be used to investigate changes in viscosity and polarity within protein aggregates in living cells [8], [9], [10], [11], [12], [13], [14], [15]. Furthermore, near-infrared fluorescent probes serve as valuable tools for imaging beta-amyloid and Tau protein polymers in Alzheimer’s disease [16], [17], [18], [19], [20], [21], [22], [23]. However, most of above-mentioned chemical sensors detecting protein aggregation, only provide spectroscopic signals for imaging purposes. In pursuit of resolving the composition of aggregated proteins, our groups have recently developed a chemical proteomics method to selectively capture and identify intracellular amorphous aggregated proteome in stressed cells [24], [25], [26]. Collectively, these tools enable systematic analysis of protein aggregation in the cellular context.

In this work, we presented an analytical platform using chemical sensors to detect and resolve proteome aggregation via imaging and proteomic analyses in neuronal cells upon chemotherapy-induced peripheral neuropathy (CIPN) (Fig. 1b). Initially, the fluorogenic imaging probe (AggStain) was utilized to visualize the formation of proteome aggregation in neuronal cells induced by various chemotherapeutic drugs [27]. Subsequently, chemical proteomics sensor (AggLink) was employed in paclitaxel treated cells to selectively capture and enrich the aggregated proteome for liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis [26]. Proteomic analysis revealed that paclitaxel disrupted cellular protein homeostasis by inducing the aggregation of pro-folding proteins, such as caseinolytic mitochondrial matrix peptidase chaperone subunit B (CLPB) protein and heat shock protein family D member 1 (HSPD1) protein [28], [29]. Together, these lines of evidence revealed by these protein aggregation sensors for the first time support the presence of proteome aggregation in CIPN neuronal model cells.