Background
MicroRNAs (miRNAs) play a critical role in the carcinogenesis and progression of breast cancer. MiRNA-205 has tumor suppressive properties, whereas miRNA-18a has both oncogenic and tumor ...suppressive roles. MiRNA-744’s role in breast cancer is unknown but is tumor-suppressive in vitro. We hypothesize that high expression of all three miRNAs is associated with a better survival based on their known functions in breast cancer.
Methods
All data was obtained from the Cancer Genome Atlas (TCGA). Expression patterns of miRNA-18a, miRNA-205, and miRNA-744 were retrieved from the Genomic Data Commons (GDC) data portal for analyses. After miRNA-specific thresholds were derived and used to group the patients into a high- or low-expression group, survival data was calculated by using the Cox proportional hazard model. Further subanalyses separating the patients based on receptor status and AJCC 7th edition TNM staging were similarly compared.
Results
In total, 1,052 of 1,097 samples logged in TCGA had clinical data and miRNA-sequence datasets on the miRNAs of interest. High expression of miRNA-18a (
p
= 0.079), miRNA-205 (
p
= 0.034), and miRNA-744 (
p
= 0.0135) was associated with better survival. On subanalysis, estrogen receptor (ER)-positive, progesterone receptor (PR)-positive, and lymph node-negative disease had a statistically significant survival advantage with miRNA-18a, miRNA-205, and miRNA-744 high expression.
Conclusions
By utilizing a big dataset (TCGA) with sufficient statistical power, we found that high expression of miRNA-18a, miRNA-205, and miRNA-744 in the breast tumor samples were all associated with better overall survival in ER/PR-positive, lymph node-negative disease supporting their role as a tumor suppressor in breast cancer.
MicroRNAs (miRNAs) have emerged as one of the crucial regulators of cancer progression. Some miRNAs are reported to be related to the response of breast cancer to tamoxifen (TAM). In this study, we ...investigated whether the levels of TAM response-related miRNAs translate to patient survival. The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets were used and Gene Set Enrichment Analysis (GSEA) was performed. Four TAM response-related miRNAs, miR-221, miR-222, miR-342, and miR-451, were identified by literature search. Patients with high expression of miR-342, related to TAM sensitivity, were associated with better survival in TCGA cohort (Overall Survival (OS), p=0.02; Disease Free Survival (DFS), p=0.03, respectively), and in two other independent GEO cohorts (OS, p=0.02 and p=0.0007, respectively). High expression of miR-342 was associated with significantly better survival in ER-positive patients (p=0.04), but not in ER-negative or triple-negative patients. Surprisingly, high expression of miR-451, reported to increase the sensitivity to TAM, was associated with worse survival (p=0.002). MiR-221 and miR-222 did not show any significance in survival. Lastly, GSEA demonstrated that lower miR-342 expression was significantly associated with the enrichment of TAM resistance-related gene expression, and higher miR-342 expression with TAM sensitivity-related gene expression, but miR-221, miR-222 and miR-451 were not. For the first time, we used "big data" from TCGA and GEO cohorts to analyze multiple miRNAs with respect to survival impact and TAM sensitivities. We demonstrated that TAM sensitivity-related miR-342 could be a promising biomarker, especially in luminal type breast cancer patients.
In testing differentially expressed genes between tumor and healthy tissues, data are usually collected in paired form. However, incomplete paired data often occur. While extensive statistical ...researches exist for paired data with incompleteness in both arms, hardly any recent work can be found on paired data with incompleteness in single arm. This paper aims to fill this gap by proposing some new methods, namely, P-value pooling methods and a nonparametric combination test. Simulation studies are conducted to investigate the performance of the proposed methods in terms of type I error and power at small to moderate sample sizes. A real data set from The Cancer Genome Atlas (TCGA) breast cancer study is analyzed using the proposed methods.
Sphingosine-1-phosphate (S1P), a bioactive sphingolipid mediator, has been implicated in regulation of many processes important for breast cancer progression. Previously, we observed that S1P is ...exported out of human breast cancer cells by ATP-binding cassette (ABC) transporter ABCC1, but not by ABCB1, both known multidrug resistance proteins that efflux chemotherapeutic agents. However, the pathologic consequences of these events to breast cancer progression and metastasis have not been elucidated. Here, it is demonstrated that high expression of ABCC1, but not ABCB1, is associated with poor prognosis in breast cancer patients. Overexpression of ABCC1, but not ABCB1, in human MCF7 and murine 4T1 breast cancer cells enhanced S1P secretion, proliferation, and migration of breast cancer cells. Implantation of breast cancer cells overexpressing ABCC1, but not ABCB1, into the mammary fat pad markedly enhanced tumor growth, angiogenesis, and lymphangiogenesis with a concomitant increase in lymph node and lung metastases as well as shorter survival of mice. Interestingly, S1P exported via ABCC1 from breast cancer cells upregulated transcription of sphingosine kinase 1 (SPHK1), thus promoting more S1P formation. Finally, patients with breast cancers that express both activated SPHK1 and ABCC1 have significantly shorter disease-free survival. These findings suggest that export of S1P via ABCC1 functions in a malicious feed-forward manner to amplify the S1P axis involved in breast cancer progression and metastasis, which has important implications for prognosis of breast cancer patients and for potential therapeutic targets.
Multidrug resistant transporter ABCC1 and activation of SPHK1 in breast cancer worsen patient's survival by export of S1P to the tumor microenvironment to enhance key processes involved in cancer progression.
.
Cytolytic activity score (CYT), defined by granzyme A and perforin expression, is a useful marker for underlying immunity. We hypothesized that CYT-high hepatocellular carcinomas (HCCs) have stronger ...immunogenicity and favorable tumor microenvironments, which would result in better clinical outcomes, using the cancer genome atlas (TCGA) cohort with 371 patients with HCC. We found CYT-high HCCs were associated with higher expressions of the apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3 (APOBEC3), well-known mutagenic enzymes. Further, higher numbers of anti-cancer immune cells, such as CD8+ T cells and M1 macrophages, were infiltrated in CYT-high HCCs. Major T cell exhaustion markers were expressed significantly higher in CYT-high HCCs, likely as a negative feedback loop. Additionally, CYT-high HCCs strongly enriched gene sets related with enhanced immune activity. With strong immunity, patients with CYT-high HCCs had significantly longer disease-specific survival (DSS) and overall survival (OS) (
= 0.03 and <0.01). Furthermore, when the OS is stratified by exhaustion marker expressions, the CYT-high/exhaustion-low group had the best and CYT-low/exhaustion-high groups had the worst OS. Lastly, high CYT was an independent protective factor for prognosis. In conclusion, CYT-high HCCs were associated with enhanced immunity and better survival. Our findings suggest that proper identification of tumor-immune microenvironments could stratify the patients for appropriate treatments.
Elderly patients are known to have a worse prognosis for breast cancer. This is commonly blamed on their medical comorbidities and access to care. However, in addition to these social issues, we ...hypothesized that the extreme elderly (octogenarians-patients over 80 years old) have biologically worse cancer with unfavorable tumor immune microenvironment. The Cancer Genomic Atlas (TCGA) and the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) breast cancer cohorts were analyzed. The control (aged 40-65) and octogenarians numbered 668 and 53 in TCGA and 979 and 118 in METABRIC, respectively. Octogenarians had significantly worse breast cancer-specific survival in both cohorts (
< 0.01). Octogenarians had a higher ER-positive subtype rate than controls in both cohorts. Regarding PAM50 classification, luminal-A and -B subtypes were significantly higher in octogenarians, whereas basal and claudin-low subtypes were significantly lower (
< 0.05) in octogenarians. There was no difference in tumor mutation load, intratumor heterogeneity, or cytolytic activity by age. However, the octogenarian cohort was significantly associated with high infiltration of pro-cancer immune cells, M2 macrophage, and regulatory T cells in both cohorts (
< 0.05). Our results demonstrate that octogenarians' breast cancer is associated with worse survival and with an unfavorable tumor immune microenvironment.
Triple‑negative breast cancer (TNBC) cells form angiogenesis‑independent vessel‑like structures to survive, known as vasculogenic mimicry (VM), contributing to a poor prognosis for cancer patients. ...Nuclear localized class I histone deacetylases (HDACs) enzymes, particularly HDACs 1, 2, 3 deacetylate chromatin histones, are overexpressed in cancers and epigenetically regulate the expression of genes involved in cancer initiation and progression. The specific HDAC inhibitor, entinostat, has been shown to attenuate tumor progression and metastasis in TNBC. In this study, we hypothesized that entinostat would enhance the expression of anti‑angiogenic and tumor suppressor genes and would thus suppress VM structures in TNBC cells in a 3D Matrigel cell culture preclinical model. Our data indicated that invasive triple‑negative MDA‑MB‑231, LM2‑4 and BT‑549 breast cancer cells, but not poorly invasive luminal MCF‑7 cells, efficiently underwent matrix‑associated VM formation. Approximately 80% of TNBC cells with the stem cell phenotype potential formed vessel‑like structures when mixed with Matrigel and cultured in the low attachment tissue culture plate. The molecular mechanisms of VM formation are rather complex, while angiogenesis inhibitor genes are downregulated and pro‑angiogenesis genes are upregulated in VM‑forming cells. Our data revealed that treatment of the TNBC VM phenotype cells with entinostat epigenetically led to the re‑expression of the anti‑angiogenic genes, serpin family F member 1 (SERPINF1) and thrombospondin 2 (THBS2), and to that of the tumor suppressor genes, phosphatase and tensin homolog (PTEN) and p21, and reduced VM structures. We also found that treatment of the TNBC VM phenotype cells with entinostat downregulated the expression of vascular endothelial growth factor A (VEGF‑A), and that of the epithelial‑mesenchymal transition (EMT)‑related genes, Vimentin and β‑catenin. METABIRC and TCGA breast cancer cohort mRNA expression data analysis revealed that a high expression of the anti‑angiogenesis‑associated genes, THBS2, SERPINF1 and serpin family B member 5 (SERPINB5), and of the tumor suppressor gene, PTEN, was associated with a better overall survival (OS) of breast cancer patients. Taken together, the findings of this study demonstrate that HDACs 1, 2, 3 partly contribute to VM formation in TNBC cells; thus, HDACs may be an important therapeutic target for TNBC.
Sphingolipids have emerged as key regulatory molecules in cancer cell survival and death. Although important roles of sphingolipids in breast cancer progression have been reported in experimental ...models, their roles in human patients are yet to be revealed. The aim of this study was to investigate the ceramide levels and its biosynthesis pathways in human breast cancer patients. Breast cancer, peri-tumor and normal breast tissue samples were collected from surgical specimens from a series of 44 patients with breast cancer. The amount of sphingolipid metabolites in the tissue were determined by mass spectrometry. The Cancer Genome Atlas was used to analyze gene expression related to the sphingolipid metabolism. Ceramide levels were higher in breast cancer tissue compared to both normal and peri-tumor breast tissue. Substrates and enzymes that generate ceramide were significantly increased in all three ceramide biosynthesis pathways in cancer. Further, higher levels of ceramide in breast cancer were associated with less aggressive cancer biology presented by Ki-67 index and nuclear grade of the cancer. Interestingly, patients with higher gene expressions of enzymes in the three major ceramide synthesis pathways showed significantly worse prognosis. This is the first study to reveal the clinical relevance of ceramide metabolism in breast cancer patients. We demonstrated that ceramide levels in breast cancer tissue were significantly higher than those in normal tissue, with activation of the three ceramide biosynthesis pathways. We also identified that ceramide levels have a significant association with aggressive phenotype and its enzymes have prognostic impact on breast cancer patients.
Abstract
Backgrounds: 40,000 US women still die with breast cancer every year. Vast majority of death occur after they develop metastasis, where bone is the most frequent site for breast cancer. New ...measures to identify the patients who develop metastasis allow us to intervene early, which is expected to prolong survival. The aim of this study is to establish a microRNA (miRNA) signature scoring system that can predict bone metastasis and survival utilizing integrated transcriptomics analyses in breast cancer.
Materials and Methods: Both clinical and RNA expression data, including microRNA and mRNA, of 1051 patients were retrieved from The Cancer Genome Atlas (TCGA). 1) Multivariate Cox proportional hazard model and Kaplan-Meier for overall survival were performed to construct and identify novel models of miRNAs signature for predicting patient survival. 2) Competing risk analysis using the miRNAs signature was conducted to clarify its association with metastatic distributions. 3) Gene Set Enrichment Analysis (GSEA) was performed to identify the genome-epigenome significance of the miRNAs signature.
Results: 1) Utilizing Cox model on TCGA cohort, we established a novel risk scoring system with three miRNAs signatures (miR-19a, miR-93, and miR-106a) that identified the patients population with extremely poor overall survival (p = 0.0004; 5-y survival rate, 49.2%). This result was reproduced in two other completely independent cohorts with microarray datasets (GSE19536, p = 0.0009; GSE22220, p = 0.0003, respectively). 2) Utilizing competing risk analysis for each metastatic sites of breast cancer, we found that the patients with bone metastasis demonstrated significantly high scores (p = 0.0052). The evaluation also showed a statistical tendency of association with lung metastasis (p = 0.0854). 3) We found that high score is associated with several critical gene sets such as angiogenesis (p < 0.0001) or epithelial mesenchymal transition (p = 0.0155) by GSEA that suggests that high signature score is associated with enhanced metastasis in breast cancer patients.
Conclusions: We established a miRNAs signature scoring system to predict bone metastasis and poor overall survival in breast cancer using novel integrated transcriptomics concept.
Citation Format: Tstutomu Kawaguchi, Li Yan, Qianya Qi, Song Liu, Kazuaki Takabe. Novel microRNA signature score to predict bone metastasis and prognosis of breast cancer abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4436. doi:10.1158/1538-7445.AM2017-4436
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