Prediction of Bone Metastasis in Breast Cancer Based on Minimal Driver Gene Set in Gene Dependency Network

Abstract

Bone is the most frequent organ for breast cancer metastasis, and thus it is essential to predict the bone metastasis of breast cancer. In our work, we constructed a gene dependency network based on the hypothesis that the relation between one gene and the risk of bone metastasis might be affected by another gene. Then, based on the structure controllability theory, we mined the driver gene set which can control the whole network in the gene dependency network, and the signature genes were selected from them. Survival analysis showed that the signature could distinguish the bone metastasis risks of cancer patients in the test data set and independent data set. Besides, we used the signature genes to construct a centroid classifier. The results showed that our method is effective and performed better than published methods.

Immune‑related genes and gene sets for predicting the response to anti‑programmed death 1 therapy in patients with primary or metastatic non‑small cell lung cancer

“…Li et al ( 58 ) have established a 4-gene set biomarker that predicts early relapse in advanced epithelial ovarian cancer after initial platinum-paclitaxel chemotherapy with an accuracy ~65.5%. In addition, a minimal driver gene set has been developed to predict bone metastasis in breast cancer ( 59 ). Another study has proposed that an immune gene-set based signature may serve as a promising biomarker for estimating overall survival of patients with ovarian cancer ( 60 ).…”

FDG-PET/CT for Response Monitoring in Metastatic Breast Cancer: The Feasibility and Benefits of Applying PERCIST

“…Today, the contrast-enhanced computed tomography (CE-CT) and the corresponding Response Evaluation Criteria in Solid Tumors (RECIST) 1.1 are recommended in clinical trials [ 3 , 4 , 5 ] while no specific recommendations are given for response monitoring in patients with MBC in current clinical guidelines [ 6 ]. The development of new metastases is the main challenge when monitoring patients with MBC, especially in the bones [ 7 ], which is a predilection site for metastases in breast cancer [ 8 ]. 18 F-Fluorodeoxyglucose Positron Emission Tomography/Computed Tomography (FDG-PET/CT) has shown higher accuracy for the detection of bone metastases than CE-CT [ 9 ].…”

Innovative Options for Bone Metastasis Treatment: An Extensive Analysis on Biomaterials-Based Strategies for Orthopedic Surgeons

“…More recently, Li J.-N. et al (2019) set up another useful bioinformatic tool based on a minimal driver gene set in gene dependency network to distinguish patients that will develop BM from low risk ones. Specifically, the tool exploits an algorithm based on gene dependency network, with the hypothesis that the relation between one gene and the risk of BM is potentially influenced by another gene.…”

“…Specifically, the tool exploits an algorithm based on gene dependency network, with the hypothesis that the relation between one gene and the risk of BM is potentially influenced by another gene. In addition, Li J.-N. et al (2019) found that their signature is specific to BM, excluding tropism for other organs.…”