Targeted Profiling of Epitranscriptomic Reader, Writer, and Eraser Proteins Accompanied with Radioresistance in Breast Cancer Cells

Abstract

Epitranscriptomic reader, writer, and eraser (RWE) proteins recognize, install, and remove modified nucleosides in RNA, which are known to play crucial roles in RNA processing, splicing, and stability. Here, we established a liquid chromatographyparallel-reaction monitoring (LC-PRM) method for high-throughput profiling of a total of 152 epitranscriptomic RWE proteins. We also applied the LC-PRM method, in conjunction with stable isotope labeling by amino acids in cell culture (SILAC), to quantify these proteins in two pairs of matched parental/radioresistant breast cancer cells (i.e., MDA-MB-231 and MCF-7 cells and their corresponding radioresistant C5 and C6 clones), with the goal of assessing the roles of these proteins in radioresistance. We found that eight epitranscriptomic RWE proteins were commonly altered by over 1.5-fold in the two pairs of breast cancer cells. Among them, TRMT1 (an m 2,2 G writer) may play a role in promoting breast cancer radioresistance due to its clinical relevance and its correlation with DNA repair gene sets. To our knowledge, this is the first report of a targeted proteomic method for comprehensive quantifications of epitranscriptomic RWE proteins. We envision that the LC-PRM method is applicable for studying the roles of these proteins in the metastatic transformation of cancer and therapeutic resistance of other types of cancer in the future.

Targeted Proteomic Analysis of Small GTPases in Radioresistant Breast Cancer Cells

“…Radioresistant C5 and C6 cell lines were generated previously. − MDA-MB-231/C5 and MCF7/C6 pairs of breast cancer cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Thermo Fisher) supplemented with 10% fetal bovine serum (FBS, Thermo Fisher) and 1% penicillin–streptomycin solution (PS, GE Healthcare). The cells were maintained at 37 °C in a humidified chamber supplemented with 5% CO 2 .…”

Advancements in Oncoproteomics Technologies: Treading toward Translation into Clinical Practice

“…It can be applied to intact proteins and could enable robust, multiplexed quantitation for top-down experiments [ 161 ]. The advancements in SILAC have enhanced our understanding of cancer biology and serve as a tool for biomarker discovery [ 169 , 170 , 171 , 172 , 173 , 174 , 175 ].…”

Recent advances in cold atmospheric plasma (CAP) for breast cancer therapy

“…Numerous studies also offer that breast cancer cells frequently acquire chemo-and radio-resistance by leveraging their inherent resistance to apoptosis and modifying their proliferation and survival pathways (Ogbu et al, 2022;Qi et al, 2022). CAP treatment varies from radiation, chemotherapy, and electromagnetic fields; chemotherapy has clinical systemic adverse effects while electromagnetic waves enter and kill the surrounding tissue (Akiyama et al, 2018;Bauer & Graves, 2016;Stupp et al, 2005).…”

“…Although ionizing radiation and chemotherapy are by far the most widely utilized breast cancer treatment strategies, both have severe systemic side effects because they target both tumor and healthy cells (Errahmani et al, 2022; Sjöström et al, 1999). Numerous studies also offer that breast cancer cells frequently acquire chemo‐ and radio‐resistance by leveraging their inherent resistance to apoptosis and modifying their proliferation and survival pathways (Ogbu et al, 2022; Qi et al, 2022). CAP treatment varies from radiation, chemotherapy, and electromagnetic fields; chemotherapy has clinical systemic adverse effects while electromagnetic waves enter and kill the surrounding tissue (Akiyama et al, 2018; Bauer & Graves, 2016; Stupp et al, 2005).…”