Breast cancer

Breast cancer is a cancer that forms in the cells of the breasts. Breast cancer can occur in both men and women, but is far more common in women. Cancer begins when healthy cells in the breast change and grow out of control, forming a mass or sheet of cells called a tumor. Breast cancer arises in the epithelial cells which line the ducts (85%) or lobules (15%) in the glandular tissue of the breast. Cancers developing from the ducts are known as ductal carcinomas, while those developing from lobules are known as lobular carcinomas. Breast cancer can be non-invasive, which does not go beyond the milk ducts or lobules in the breast, or invasive, which spreads into surrounding tissues and/or distant organs. Over time, these in situ cancers may progress and invade the surrounding breast tissue then spread to the nearby lymph nodes or to other organs in the body. The stage of breast cancer describes how much the cancer has grown, and if or where it has spread. If a woman dies from breast cancer, it is because of widespread metastasis. However, breast cancer treatment can be highly effective, especially when the disease is identified early. Breast cancer is the most prevalent cancer worldwide and is the fifth most common cause of cancer deaths.

Figure 1. The volcano plot shows the adjusted p-value compared to the difference in average protein expression (NPX) for all proteins in breast cancer compared to all other cancers. The lollipop plot shows the top 10 most important proteins resulting from the cancer prediction model with importance scores ranging between 0 to 100.

Pan-cancer protein panel

8 proteins have been selected by the model to predict breast cancer (Table 1). An interesting protein is Her2 (ERBB2), well-known for its overexpression in certain subtypes of breast cancer and it has been shown (Magis AT et al. (2020)) to be upregulated in blood from such breast cancer patients. As expected, we observed higher plasma levels in only a fraction of the patients and this protein was therefore not selected to be included in the panel. Instead, the top protein for prediction of breast cancer in our model (PRTG) is a developmental membrane protein with enriched transcription in retina with, to our knowledge, no previous known involvement in breast cancer.

Cancer Protein Importance p.adjusted NPX fold change
Breast cancer PRTG 64.9 1.1e-10 0.2
Breast cancer LAMP3 58.1 8.5e-3 0.2
Breast cancer OXT 56.1 9.6e-4 0.6
Breast cancer SDC4 56.1 1.5e-10 0.6
Breast cancer HSD11B1 53.2 4.6e-3 0.1
Breast cancer BTC 52.3 4.0e-4 0.4
Breast cancer LPL 51.7 6.6e-5 0.2
Breast cancer MSMB 51.6 2.9e-2 0.2
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