Proteome and Network Analysis Provides Novel Insights Into Developing and Established Chemotherapy-Induced Peripheral Neuropathy

Abstract

Chemotherapy-induced peripheral neuropathy (CIPN) is a debilitating side-effect of cancer therapies. So far, the development of CIPN cannot be prevented, neither can established CIPN be reverted, often leading to the cessation of necessary chemotherapy. Thus, there is an urgent need to explore the mechanistic basis of CIPN to facilitate its treatment. Here we used an integrated approach of quantitative proteome profiling and network analysis in a clinically relevant rat model of paclitaxel-induced peripheral neuropathy. We analysed lumbar rat DRG at two critical time points: (1) day 7, right after cessation of paclitaxel treatment, but prior to neuropathy development (pre-CIPN); (2) 4 weeks after paclitaxel initiation, when neuropathy has developed (peak-CIPN). In this way we identified a differential protein signature, which shows how changes in the proteome correlate with the development and maintenance of CIPN, respectively. Extensive biological pathway and network analysis reveals that, at pre-CIPN, regulated proteins are prominently implicated in mitochondrial (dys)function, immune signalling, neuronal damage/regeneration, and neuronal transcription. Orthogonal validation in an independent rat cohort confirmed the increase of β-catenin (CTNNB1) at pre-CIPN. More importantly, detailed analysis of protein networks associated with β-catenin highlights translationally relevant and potentially druggable targets. Overall, this study demonstrates the enormous value of combining animal behaviour with proteome and network analysis to provide unprecedented insights into the molecular basis of CIPN. In line with emerging approaches of network medicine our results highlight new avenues for developing improved therapeutic options aimed at preventing and treating CIPN.

Transcriptomic and proteomic profiling of NaV1.8-expressing mouse nociceptors

“…We have recently shown the immense potential of defining pain-associated proteome dynamics in DRG by data-independent acquisition mass spectrometry (DIA-MS) (Rouwette et al, 2016 ; Barry et al, 2018 ; De Clauser et al, 2022 ). Here, we employed DIA-MS to reveal the previously unknown protein set-up of Na V 1.8 + nociceptors by using aforementioned DTA mice (Abrahamsen et al, 2008 ).…”

Transcriptomic and proteomic profiling of NaV1.8-expressing mouse nociceptors

“…Differences were considered significant at FDR adjusted P < 0.05 for transcriptome data. For proteome analysis, Benjamini-Hochberg (BH)-adjusted P-values were used for multiple testing and significantly altered proteins were defined by setting a cut-off of Q < 0.05 as previously described (De Clauser et al, 2022).…”

“…Data analysis was performed using mouse UniProt fasta downloaded 2018-07-01. We used two analysis pipelines as described previously (De Clauser et al, 2022): the spectral library-based search and the directDIA TM workflow developed at Biognosys using Biognosys Factory settings in Spectronaut X. Label-free Quantitation was executed on MS2-level using the area under the curve and data were filtered by Q-value sparse (precursors robustly found in at least one sample). Statistical testing of differential protein abundances between conditions was calculated in Spectronaut for each protein ID by performing a pairwise t-test.…”

“…We have recently shown the immense potential of defining pain-associated proteome dynamics in DRG by data-independent acquisition mass spectrometry (DIA-MS) (Barry et al, 2018; De Clauser et al, 2022; Rouwette et al, 2016). Here, we used DIA-MS to reveal the previously unknown protein set-up of nociceptors by using aforementioned DTA mice (Abrahamsen et al, 2008).…”

Inflammation-induced mitochondrial and metabolic disturbances in sensory neurons control the switch from acute to chronic pain

“…reduced ATP-production) in sensory neurons to chronic pain in rodents, although predominantly in chemotherapy-induced chronic pain models. [7] In addition, the mitochondrial protein ATPSc-KMT (formerly named FAM173B), a lysine (K)-specific methyltransferase (MTase), influences OXPHOS activity by methylating Lys-43 of the ATP synthase c-subunit (ATPSc) and promotes chronic pain development. [8] Finally, OXPHOS in sensory neurons adapts during transient inflammatory pain and donation of mitochondria from macrophages to sensory neurons is needed to resolve inflammatory pain.…”