An Integrative Approach for Identifying Network Biomarkers of Breast Cancer Subtypes Using Genomic, Interactomic, and Transcriptomic Data

2017 ◽  
Vol 24 (8) ◽  
pp. 756-766 ◽  
Author(s):  
Forough Firoozbakht ◽  
Iman Rezaeian ◽  
Michele D'agnillo ◽  
Lisa Porter ◽  
Luis Rueda ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Breast Cancer Subtypes ◽  
Integrative Approach ◽  
Cancer Subtypes ◽  
Transcriptomic Data ◽  
Network Biomarkers

scholarly journals Discovering lncRNA Mediated Sponge Interactions in Breast Cancer Molecular Subtypes

2017 ◽  
Author(s):  
Gulden Olgun ◽  
Ozgur Sahin ◽  
Oznur Tastan
Keyword(s):  
Breast Cancer ◽  
Hox Genes ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Functional Enrichment ◽  
Breast Cancer Subtypes ◽  
Integrative Approach ◽  
Cancer Subtypes ◽  
Significant Difference

AbstractMotivationLong non-coding RNAs(lncRNAs) can indirectly regulate mRNAs expression levels by sequestering microRNAs (miRNAs), and act as competing endogenous RNAs (ceRNAs) or as sponges. Previous studies identified lncRNA-mediated sponge interactions in various cancers including the breast cancer. However, breast cancer subtypes are quite distinct in terms of their molecular profiles; therefore, ceRNAs are expected to be subtype-specific as well.ResultsTo find lncRNA-mediated ceRNA interactions in breast cancer subtypes, we develop an integrative approach. We conduct partial correlation analysis and kernel independence tests on patient gene expression profiles and further refine the candidate interactions with miRNA target information. We find that although there are sponges common to multiple subtypes, there are also distinct subtype-specific interactions. Functional enrichment of mRNAs that participate in these interactions highlights distinct biological processes for different subtypes. Interestingly, some of the ceRNAs also reside in close proximity in the genome; for example, those involving HOX genes, HOTAIR, miR-196a-1 and miR-196a-2. We also discover subtype-specific sponge interactions with high prognostic potential. For instance, when grouping is based on the expression patterns of specific sponge interactions, patients differ significantly in their survival distributions. If on the other hand, patients are grouped based on the individual RNA expression profiles of the sponge participants, they do not exhibit a significant difference in survival. These results can help shed light on subtype-specific mechanisms of breast cancer, and the methodology developed herein can help uncover sponges in other diseases.

Identification of new therapeutic leads for triple negative breast cancer subtypes

Planta Medica ◽  
2015 ◽  
Vol 81 (11) ◽  
Author(s):  
AJ Robles ◽  
L Du ◽  
S Cai ◽  
RH Cichewicz ◽  
SL Mooberry
Keyword(s):  
Breast Cancer ◽  
Triple Negative Breast Cancer ◽  
Triple Negative ◽  
Breast Cancer Subtypes ◽  
Cancer Subtypes ◽  
Therapeutic Leads

scholarly journals Clinical Significance of Annexin A2 Expression in Breast Cancer Patients

Cancers ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 2
Author(s):  
Lee D. Gibbs ◽  
Kelsey Mansheim ◽  
Sayantan Maji ◽  
Rajesh Nandy ◽  
Cheryl M. Lewis ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cancer Patients ◽  
Clinical Significance ◽  
Cell Lines ◽  
Breast Cancer Subtypes ◽  
Enzyme Linked Immunosorbent Assay ◽  
Breast Cancer Patients ◽  
Serum Samples ◽  
Cancer Subtypes ◽  
Tumor Tissues

Increasing evidence suggests that AnxA2 contributes to invasion and metastasis of breast cancer. However, the clinical significance of AnxA2 expression in breast cancer has not been reported. The expression of AnxA2 in cell lines, tumor tissues, and serum samples of breast cancer patients were analyzed by immunoblotting, immunohistochemistry, and enzyme-linked immunosorbent assay, respectively. We found that AnxA2 was significantly upregulated in tumor tissues and serum samples of breast cancer patients compared with normal controls. The high expression of serum AnxA2 was significantly associated with tumor grades and poor survival of the breast cancer patients. Based on molecular subtypes, AnxA2 expression was significantly elevated in tumor tissues and serum samples of triple-negative breast cancer (TNBC) patients compared with other breast cancer subtypes. Our analyses on breast cancer cell lines demonstrated that secretion of AnxA2 is associated with its tyrosine 23 (Tyr23) phosphorylation in cells. The expression of non-phosphomimetic mutant of AnxA2 in HCC1395 cells inhibits its secretion from cells compared to wild-type AnxA2, which further suggest that Tyr23 phosphorylation is a critical step for AnxA2 secretion from TNBC cells. Our analysis of AnxA2 phosphorylation in clinical samples further confirmed that the phosphorylation of AnxA2 at Tyr23 was high in tumor tissues of TNBC patients compared to matched adjacent non-tumorigenic breast tissues. Furthermore, we observed that the diagnostic value of serum AnxA2 was significantly high in TNBC compared with other breast cancer subtypes. These findings suggest that serum AnxA2 concentration could be a potential diagnostic biomarker for TNBC patients.

scholarly journals Breast Cancer Subtypes in Asian-Americans Differ According to Asian Ethnic Group

2012 ◽  
Vol 14 (5) ◽  
pp. 754-758 ◽  
Author(s):  
Ellen Chuang ◽  
Paul Christos ◽  
Arielle Flam ◽  
Katherine McCarville ◽  
Melissa Forst ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Ethnic Group ◽  
Asian Americans ◽  
Breast Cancer Subtypes ◽  
Cancer Subtypes

A retrospective study of breast cancer subtypes: the risk of relapse and the relations with treatments

2011 ◽  
Vol 130 (2) ◽  
pp. 489-498 ◽  
Author(s):  
Yahong Wang ◽  
Quangui Yin ◽  
Qi Yu ◽  
Jing Zhang ◽  
Ziyu Liu ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Retrospective Study ◽  
Breast Cancer Subtypes ◽  
Cancer Subtypes ◽  
Risk Of Relapse
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