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Updated: Jun 28, 2025
Optimization of a Multiplex RNA-based Expression Assay Using Breast Cancer Archival Material
Published on: August 1, 2018
Unlocking Overexpressed Membrane Proteins to Guide Breast Cancer Precision Medicine
Júlia Badaró Mendonça1,2, Priscila Valverde Fernandes3, Danielle C Fernandes3
1Translational Oncology Platform, Center for Technological Development in Health, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-900, RJ, Brazil.
Abstract:
Breast cancer (BC) is a prevalent form of cancer affecting women worldwide. However, the effectiveness of current BC drugs is limited by issues such as systemic toxicity, drug resistance, and severe side effects. Consequently, there is an urgent need for new therapeutic targets and improved tumor tracking methods. This study aims to address these challenges by proposing a strategy for identifying membrane proteins in tumors that can be targeted for specific BC therapy and diagnosis. The strategy involves the analyses of gene expressions in breast tumor and non-tumor tissues and other healthy tissues by using comprehensive bioinformatics analysis from The Cancer Genome Atlas (TCGA), UALCAN, TNM Plot, and LinkedOmics. By employing this strategy, we identified four transcripts (LRRC15, EFNA3, TSPAN13, and CA12) that encoded membrane proteins with an increased expression in BC tissue compared to healthy tissue. These four transcripts also demonstrated high accuracy, specificity, and accuracy in identifying tumor samples, as confirmed by the ROC curve. Additionally, tissue microarray (TMA) analysis revealed increased expressions of the four proteins in tumor tissues across all molecular subtypes compared to the adjacent breast tissue. Moreover, the analysis of human interactome data demonstrated the important roles of these proteins in various cancer-related pathways. Taken together, these findings suggest that LRRC15, EFNA3, TSPAN13, and CA12 can serve as potential biomarkers for improving cancer diagnosis screening and as suitable targets for therapy with reduced side effects and enhanced efficacy.
Insights
New research identifies four membrane proteins (LRRC15, EFNA3, TSPAN13, CA12) as promising biomarkers for breast cancer (BC) diagnosis and therapy. These proteins show increased expression in tumors, offering potential for improved treatment and reduced side effects.
Area of Science:
- Oncology
- Genomics
- Bioinformatics
Background:
- Breast cancer (BC) poses a significant global health challenge, with current treatments hampered by toxicity, resistance, and side effects.
- There is a critical need for novel therapeutic targets and enhanced methods for tumor tracking in BC management.
Purpose of the Study:
- To develop a strategy for identifying tumor-specific membrane proteins for targeted BC therapy and diagnosis.
- To evaluate the potential of identified membrane proteins as biomarkers for BC detection and treatment.
Main Methods:
- Comprehensive bioinformatics analysis of gene expression data from The Cancer Genome Atlas (TCGA), UALCAN, TNM Plot, and LinkedOmics.
- Analysis of breast tumor, non-tumor, and healthy tissues to identify differentially expressed membrane proteins.
- Validation using Receiver Operating Characteristic (ROC) curves and tissue microarray (TMA) analysis across molecular subtypes.
Main Results:
- Four transcripts (LRRC15, EFNA3, TSPAN13, CA12) encoding membrane proteins showed significantly increased expression in BC tissues compared to healthy tissues.
- These proteins demonstrated high accuracy and specificity in identifying tumor samples, confirmed by ROC curve analysis.
- TMA analysis confirmed elevated protein expression in tumors across all molecular subtypes; interactome data highlighted their roles in cancer pathways.
Conclusions:
- LRRC15, EFNA3, TSPAN13, and CA12 are identified as potential biomarkers for improving breast cancer diagnosis and screening.
- These proteins represent promising therapeutic targets for developing more effective BC treatments with potentially fewer side effects.
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