Phosphoproteomic analysis of neoadjuvant breast cancer suggests that increased sensitivity to paclitaxel is driven by CDK4 and filamin A

Abstract

Precision oncology research is challenging outside the contexts of oncogenic addiction and/or targeted therapies. We previously showed that phosphoproteomics is a powerful approach to reveal patient subsets of interest characterized by the activity of a few kinases where the underlying genomics is complex. Here, we conduct a phosphoproteomic screening of samples from HER2-negative female breast cancer receiving neoadjuvant paclitaxel (N = 130), aiming to find candidate biomarkers of paclitaxel sensitivity. Filtering 11 candidate biomarkers through 2 independent patient sets (N = 218) allowed the identification of a subgroup of patients characterized by high levels of CDK4 and filamin-A who had a 90% chance of achieving a pCR in response to paclitaxel. Mechanistically, CDK4 regulates filamin-A transcription, which in turn forms a complex with tubulin and CLIP-170, which elicits increased binding of paclitaxel to microtubules, microtubule acetylation and stabilization, and mitotic catastrophe. Thus, phosphoproteomics allows the identification of explainable factors for predicting response to paclitaxel.

Mapping the Protein Kinome: Current Strategy and Future Direction

“…However, traditional kinome analysis omits the spatial information in the process of tissue homogenization. The final obtained kinome information is the average level of kinase activity in the tissues or cell lysates [ 101 ]. However, it cannot reveal the differences in the spatial distribution of the kinome.…”

Recent Contributions of Mass Spectrometry-Based “Omics” in the Studies of Breast Cancer

“…Andromeda employs a target-decoy database search strategy for false discovery rate estimation and uses a scoring model (based on statistical scoring) to rank and identify peptides from MS/MS spectra. It supports various peptide fragmentation methods and database search algorithms, enabling high-throughput analysis of mass spectrometry data. , Proteome Discoverer is another widely used software platform developed by Thermo Fisher Scientific with data processing, peptide and protein identification, quantification, and statistical analysis. It supports different search algorithms, including SEQUEST, Mascot, and Byonic.…”

“…The authors deduced with their validations in cell line experiments that PTX sensitivity is mediated by CDK4, which regulates the activity of filamin A. Filamin-A interacts with tubulin and CLIP-170 to form a complex. This complex increased the binding of PTX to microtubules, leading to microtubule acetylation, stabilization, and cell death through catastrophes induced in the mitotic machinery …”

“…It supports various peptide fragmentation methods and database search algorithms, enabling highthroughput analysis of mass spectrometry data. 125,126 Proteome Discoverer is another widely used software platform developed by Thermo Fisher Scientific with data processing, peptide and protein identification, quantification, and statistical analysis. It supports different search algorithms, including SEQUEST, Mascot, and Byonic.…”

“…This complex increased the binding of PTX to microtubules, leading to microtubule acetylation, stabilization, and cell death through catastrophes induced in the mitotic machinery. 126 In an attempt to characterize paclitaxel resistance in breast cancer cells, Cao (2021) identified unique glycan-related protein, glycan, and glycoprotein signatures defining Paclitaxel chemoresistance in BC. Through the integration of transcriptomics, proteomics, glycomics, and glycoproteomics, which they combinatorially applied to arrive at dysregulations of glycogenes, glycan structures, and glycoproteins, they resulted in chemoresistance of BC cells.…”