Association Analysis of Deep Genomic Features Extracted by Denoising Autoencoders in Breast Cancer

Artificial intelligence-based unsupervised deep learning (DL) is widely used to mine multimodal big data. However, there are few applications of this technology to cancer genomics. We aim to develop DL models to extract deep features from the breast cancer gene expression data and copy number alteration (CNA) data separately and jointly. We hypothesize that the deep features are associated with patients’ clinical characteristics and outcomes. Two unsupervised denoising autoencoders (DAs) were developed to extract deep features from TCGA (The Cancer Genome Atlas) breast cancer gene expression and CNA data separately and jointly. A heat map was used to view and cluster patients into subgroups based on these DL features. Fisher’s exact test and Pearson’ Chi-square test were applied to test the associations of patients’ groups and clinical information. Survival differences between the groups were evaluated by Kaplan–Meier (KM) curves. Associations between each of the features and patient’s overall survival were assessed using Cox’s proportional hazards (COX-PH) model and a risk score for each feature set from the different omics data sets was generated from the survival regression coefficients. The risk scores for each feature set were binarized into high- and low-risk patient groups to evaluate survival differences using KM curves. Furthermore, the risk scores were traced back to their gene level DAs weights so that the three gene lists for each of the genomic data points were generated to perform gene set enrichment analysis. Patients were clustered into two groups based on concatenated features from the gene expression and CNA data and these two groups showed different overall survival rates (p-value = 0.049) and different ER (Estrogen receptor) statuses (p-value = 0.002, OR (odds ratio) = 0.626). All the risk scores from the gene expression and CNA data and their concatenated one were significantly associated with breast cancer survival. The patients with the high-risk group were significantly associated with patients’ worse outcomes (p-values ≤ 0.0023). The concatenated risk score was enriched by the AMP-activated protein kinase (AMPK) signaling pathway, the regulation of DNA-templated transcription, the regulation of nucleic acid-templated transcription, the regulation of apoptotic process, the positive regulation of gene expression, the positive regulation of cell proliferation, heart morphogenesis, the regulation of cellular macromolecule biosynthetic process, with FDR (false discovery rate) less than 0.05. We confirmed DAs can effectively extract meaningful genomic features from genomic data and concatenating multiple data sources can improve the significance of the features associated with breast cancer patients’ clinical characteristics and outcomes.