The landscape of angiogenesis subtypes for breast cancer: a comprehensive analysis based on the Cancer Genome Atlas.

PURPOSE: Breast cancer is a common malignant tumor in women with a poor prognosis. This study aimed to investigate angiogenesis subtypes of breast cancer and unveil the etiology and molecular features of breast cancer. METHODS: Based on the angiogenesis gene set derived from AmiGO2, and breast cancer data in the Cancer Genome Atlas (TCGA), we define a novel cluster of angiogenesis subtypes for patients by consensus clustering. The gene regulation, immune landscape, molecular characteristics, and clinical features as well as enrichment pathways were explored in the angiogenesis subtypes of breast cancer. RESULTS: Two angiogenesis subtypes were established through consensus clustering, among which subtype1 included 275 patients and subtype2 included 813 patients. A total of 643 differential expressed genes and 109 miRNAs were found between the two subtypes. The gene set enrichment analysis showed that the enriched hallmark pathways in subtype2 were related to the cancer tumorigenesis and breast cancer progression, including estrogen response early estrogen response late, epithelial-mesenchymal transition (EMT), especially angiogenesis. The mutant-allele tumor heterogeneity and tumor mutation burden of non-angiogenesis subtype were significantly higher than that in the angiogenesis subtype. The stroma score, immune score and ESTIMATE score were significantly higher in angiogenesis subtype, while the tumor purity in angiogenesis subtype was considerably lower. Finally, most immune checkpoints were expressed higher in the angiogenesis subtype. CONCLUSIONS: The omics analysis has established a novel angiogenesis subtype of breast cancer and identified the characteristics of the immune microenvironment and genomic alteration of breast cancer. Thus, this angiogenesis subtype might provide new evidence for inhibiting the progression and immunotherapy response in breast cancer.

Novel immune subtypes of lung adenocarcinoma identified through bioinformatic analysis.

The magnitude of the immune response is closely associated with clinical outcome in patients with cancer. However, finding potential therapeutic targets for lung cancer in the immune system remains challenging. Here, we constructed a vital immune-prognosis genes (VIPGs) based cluster of lung adenocarcinoma (LUAD) from IMMPORT databases and The Cancer Genome Atlas. A transcription factor regulatory network for the VIPGs was also established. The tumor microenvironment of LUAD was analyzed using the ESTIMATE (Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data) algorithm and single-sample Gene Set Enrichment Analysis. The immune checkpoints and genomic alterations were explored in the different immune clusters. We identified 15 VIPGs for patients with LUAD and clustered the patients into low-immunity and high-immunity subtypes. The immune score, stromal score and ESTIMATE score were significantly higher in the high-immunity subtype, whereas tumor purity was higher in the low-immunity subtype. In addition, the immune checkpoints cytotoxic T lymphocyte associate protein-4(CTLA4), programmed cell death protein-1 and programmed death-ligand were elevated in the low-immunity subtype. The genomic results also showed that the tumor mutation burden was higher in the high-immunity subtype. Finally, Gene Set Enrichment Analysis showed that several immune-related gene sets, including interleukin-2/STAT5 signaling, inflammatory response, interleukin-6/Janus kinase(JAK)/signal transducer and activator of transcription 3 (STAT3) signaling, interferon-gamma response and allograft rejection, were elevated in the high-immunity subtype. Finally, high-immunity patients exhibited greater overall and disease-specific survival outcome compared with low-immunity patients (log rank P = 0.013 and P = 0.0097). Altogether, here we have identified 15 immune-prognosis genes and a potential immune subtype for patients with LUAD, which may provide new insights into the prognosis and treatment of LUAD.