Proteomic Profiling of Breast Cancer

Breast tumor tissue and normal control breast tissue was excised from 23 breast cancer patients during surgery. Samples were then prepared and sequenced according to standard protocol^{56 (link)}. The women enrolled had the following demographics: 13 were post-menopausal, 4 were Estrogen Receptor (ER) negative, 16 were Human Epidermal Growth Factor Receptor (HER2) negative, 5 were Progesterone Receptor (PR) negative, 16 had invasive ductal carcinoma, and 2 had internal mammary chain involvement. Five women received treatment prior to sample collection. One woman was administered Taxotere, Carboplatin, Herceptin, Perjeta (TCHP). Three women were administered Adriamycin, cyclophosphamide, Taxol (AC-T). One woman was administered Anastrozole. Global proteomics data from primary breast tumors and matched normal tissues were generated through mass-spectrometry (MS) (PMID: 33212010)^{36 (link)} and pre-processed as previously described (PMID: 34552204). Data pertaining to mutated and overexpressed genes in human breast cancer was also sourced from the Catalogue of Somatic Mutations In Cancer (COSMIC)^{16 (link)}. This was divided into two sets, one containing only the most commonly mutated genes in breast cancer and the other containing only unmutated, overexpressed genes in breast cancer. For weighting purposes, the number of times a gene was mutated compared to the total number of times that gene was expressed served as the weight for the first set and the number of times the gene was overexpressed was used as the weight for the second set.