High miR-99b expression is associated with cell proliferation and worse patient outcomes in breast cancer

Abstract

Background: Although miR-99b is a known suppressive microRNA in several cancer types, its role in breast cancer is not elucidated. In this study, we examine the clinical relevance of miR-99b expression in breast cancer. Methods: We analyzed microRNA and messenger RNA expressions and their relationships with clinical parameters for 1,961 breast cancer samples from two independent large cohorts, the Cancer Genome Atlas (TCGA) and the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC). Several algorithms including Gene Set Enrichment Analysis (GSEA) and xCell were used to investigate biological function and the tumor microenvironment. Results: High miR-99b expression significantly enriched the mTORC1 signaling gene set in breast cancer (normalized enrichment score (NES)=1.63, false discovery rate (FDR)=0.03, and NES=1.58, FDR=0.10, in METABRIC and TCGA, respectively). No other mechanisms including the epithelial mesenchymal transition, or nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kB) and transforming growth factor (TGF)-β signaling, were consistently enriched consistently in both cohorts. miR-99b-high breast cancer was associated with high homologous recombination deficiencies, intratumor heterogeneity, and higher rates of mutation and neoantigens. Further miR-99b-high specimens have increased E2F targets, G2/M checkpoint, and mitotic spindle signaling, and are significantly associated with pathogenesis in both cohorts (p = 0.011, <0.001). High miR-99b was also associated with low stromal cell fractions in the tumor microenvironment, including adipocytes, keratinocytes, and lymphatic endothelial cells (p < 0.001). However, in both cohorts, miR-99b expression was not associated with significant infiltration of immune cells, except for dendritic cells (p = 0.006, 0.020). Finally, in both cohorts, breast cancer with high miR-99b expression was significantly associated with worse and disease-free survival (DSS) and overall survival (OS), particularly in estrogen receptor (ER)-positive/human epidermal growth factor (HER)2-negative breast cancer (DSS hazard ratio (HR) 1.29, 95% confidence interval (CI) 1.10-1.51, p < 0.001 in the METABRIC cohort, and HR 1.82, 95% CI 1.12-2.98, p = 0.017 in the TCGA cohort). Conclusions: Breast cancer with high miR-99b expression was significantly associated with mTORC1 signaling, cell proliferation, and decreased patient survival, particularly in ER-positive/HER2-negative subtype.

Identification of a Panel of miRNAs Associated with Resistance to Palbociclib and Endocrine Therapy

“…Importantly, E2F is a downstream effector of CDK4 and CDK6 on the cell cycle and its overexpression may hamper the activity of CDK4/6i. Moreover, high miR-99b expression was associated with worse patient survival, particularly in HR+/HER2− tumors [23]. Our results seem to support an oncomiR function for this miRNA in patients treated with ET and CDK4/6i.…”

“…An inverse relationship between the expression of miR-99b-5p and mTOR has been described either in BCCL and tumor specimens [22]. Oppositely, an analysis of two large datasets of breast cancer patients consisting of 1961 cases downloaded from the METABRIC and TCGA databases showed that high miR-99b expression correlated significantly with enriched mTORC1 gene sets and that the mTOR pathway, but no other signaling pathway, was activated in miR-99b-high-expressing breast cancer specimens [23]. In the same datasets, miR-99b-high breast cancer specimens were significantly enriched in three genes related to cell proliferation: E2F targets, the G2/M checkpoint, and mitotic spindle gene sets.…”

Decreased Lipid Phosphate Phosphatase 1/3 and Increased Lipid Phosphate Phosphatase 2 Expression in the Human Breast Cancer Tumor Microenvironment Promotes Tumor Progression and Immune System Evasion

“…Clinical and mRNA expression breast cancer data were obtained from the Cancer Genome Atlas Program (TCGA) (whole database, n = 1090; estrogen receptor positive and human epidermal growth factor receptor negative tumors (ER+ HER2−), n = 593; human epidermal growth factor receptor positive tumors (HER2+), n = 184; and triple negative breast cancer (TNBC), n = 160), the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) (whole database, n = 1094; ER+ HER2−, n = 1355; HER2+, n = 236; and TNBC, n = 313), and GSE96058 (whole database, n = 3069; ER+ HER2−, n = 2277; HER2+, n = 392; and TNBC, n = 155). These three databases were obtained via the cBioPortal ( (accessed on 9 October 2022)) and the Gene Expression Omnibus (GEO) repository of the United States National Institutes of Health ( (accessed on 9 October 2022)), as previously described [ 32 , 33 ]. Gene expression data from 114 samples of normal breast tissue were obtained from the Genotype-Tissue Expression (GTex) Portal ( (accessed on 9 October 2022)) [ 34 ].…”

“…Functional enrichment analysis of the LPP genes ( PLPP1–3 ) was performed by gene set enrichment analysis (GSEA) [ 33 ] on the Molecular Signatures Database Hallmark collection ( (accessed on 9 October 2022)) [ 37 ]. A false discovery rate (FDR) of <0.25 indicated enriched signaling gene sets [ 38 ].…”

Lysophosphatidic Acid Receptor Signaling in the Human Breast Cancer Tumor Microenvironment Elicits Receptor-Dependent Effects on Tumor Progression

“…Clinical outcomes and mRNA expression for breast cancer patients were obtained from three large databases: the Cancer Genome Atlas Program (TCGA) (whole database n = 1090; estrogen-receptor-positive and human-epidermal-growth-factor-receptor-negative (ER+ HER2-) n = 593; HER2+ n = 184; triple-negative breast cancer (TNBC) n = 160), the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) (whole database n = 1094, ER+ HER2-n = 1355, HER2+ n = 236, and TNBC n = 313), and GSE96058 (whole database n = 3069, ER+ HER2-n = 2277, HER2+ n = 392, and TNBC n = 155). These data were retrieved from the cBioPortal (https://www.cbioportal.org (accessed on 22 September 2022)) and the Gene Expression Omnibus (GEO) repository of the United States National Institutes of Health (https://www.ncbi.nlm.nih.gov/geo (accessed on 22 September 2022)), as previously described [45,46]. Gene expression data from 114 normal breast tissue samples were retrieved from the Genotype-Tissue Expression (GTex) Portal (https://gtexportal.org (accessed on 22 September 2022)) [47].…”