Biological correlates associated with high-risk breast cancer patients identified using a computational method Journal Article
| Authors: | Oh, J. H.; Pareja, F.; Elkin, R.; Xu, K.; Norton, L.; Deasy, J. O. |
| Article Title: | Biological correlates associated with high-risk breast cancer patients identified using a computational method |
| Abstract: | Using a novel unsupervised method to integrate multi-omic data, we previously identified a breast cancer group with a poor prognosis. In the current study, we characterize the biological features of this subgroup, defined as the high-risk group, using various data sources. Assessment of three published hypoxia signatures showed that the high-risk group exhibited higher hypoxia scores (p < 0.0001 in all three signatures), compared to the low-risk group. Our analysis of the immune cell composition using CIBERSORT and leukocyte fraction showed significant differences between the high and low-risk groups across the entire cohort, as well as within PAM50 subtypes. Within the basal subtype, the low-risk group had a statistically significantly higher spatial fraction of tumor-infiltrating lymphocytes (TILs) compared to the high-risk group (p = 0.0362). Our findings indicate that this subgroup with poor prognosis is driven by a distinct biological signature with high activation of hypoxia-related genes as well as a low number of TILs. © The Author(s) 2025. |
| Keywords: | adult; middle aged; overall survival; somatic mutation; methodology; cd8+ t lymphocyte; tumor associated leukocyte; gene; breast cancer; epidermal growth factor receptor 2; brca1 protein; brca2 protein; protein p53; high risk patient; hypoxia; cd4+ t lymphocyte; estrogen receptor; progesterone receptor; immunocompetent cell; tumor microenvironment; cell composition; biological functions; spatial analysis; leukocyte function; low risk patient; cancer prognosis; human; female; article; tumor mutational burden; pam50 gene; m1 macrophage; biological feature; computational method; estimated spatial fraction; leukocyte fraction |
| Journal Title: | npj Breast Cancer |
| Volume: | 11 |
| ISSN: | 2374-4677 |
| Publisher: | Nature Publishing Group |
| Date Published: | 2025-01-29 |
| Start Page: | 8 |
| Language: | English |
| DOI: | 10.1038/s41523-025-00725-y |
| PROVIDER: | scopus |
| PMCID: | PMC11775240 |
| PUBMED: | 39875417 |
| DOI/URL: | |
| Notes: | The MSK Cancer Center Support Grant (P30 CA008748) is acknowledged in the PubMed record and PDF. Corresponding MSK author is Jung Hun Oh -- Source: Scopus |
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