Transcriptomic Analysis of EGFR and Downstream Pathway Expression in MCF7 and Healthy Breast Epithelium
Category
Sciences and Technology
Department
Biology
Student Status
Undergraduate
Research Advisor
Dr. Christopher Ward
Document Type
Event
Location
Student Center Ballroom
Start Date
10-4-2025 2:00 PM
End Date
10-4-2025 4:00 PM
Description
Introduction: Clinical tests utilizing EGFR isoforms as a method of cancer screening have had an unreliable history to date. Our lab is interested in this gene's isoforms and downstream activation. We used an In-silco characterization and assessment of an Invasive Breast Ductal Carcinoma cell line (MCF7) in association with expression patterns of EGFR and associated pathways relative expression.
Purpose: Identify what proteins associated with downstream pathways are up or downregulated in MCF7 compared to the normal breast epithelium.
Methods: RNA-Seq data from publicly available breast adenocarcinoma and normal breast epithelium samples were analyzed using an isoform-level expression pipeline. Reads were aligned with a splice-aware aligner (STAR), followed by transcript assembly and quantification with featurecounts. Differential expression analysis and visualization were performed using Ballgown, allowing transcript-level resolution of EGFR isoforms and pathway-associated genes.
Results: Transcriptomic expressions trended in favor of under-expression, with the log fold change in gene expression of EGFR being nuanced among multiple samples.
Discussion: The breast ductal carcinoma cells show a general trend towards under-expression in the EGFR pathways. However, the expression of EGFR, being comparable to healthy breast epithelium, remains nuanced with increases in CDH2 expression suggesting increased N-Cadherin activity. This suggests that this pathway is not a primary driver in ER+, PR+, HER2- breast cancer. This does not rule out the possibility that isoforms may be elicited in downregulating this response.
Transcriptomic Analysis of EGFR and Downstream Pathway Expression in MCF7 and Healthy Breast Epithelium
Student Center Ballroom
Introduction: Clinical tests utilizing EGFR isoforms as a method of cancer screening have had an unreliable history to date. Our lab is interested in this gene's isoforms and downstream activation. We used an In-silco characterization and assessment of an Invasive Breast Ductal Carcinoma cell line (MCF7) in association with expression patterns of EGFR and associated pathways relative expression.
Purpose: Identify what proteins associated with downstream pathways are up or downregulated in MCF7 compared to the normal breast epithelium.
Methods: RNA-Seq data from publicly available breast adenocarcinoma and normal breast epithelium samples were analyzed using an isoform-level expression pipeline. Reads were aligned with a splice-aware aligner (STAR), followed by transcript assembly and quantification with featurecounts. Differential expression analysis and visualization were performed using Ballgown, allowing transcript-level resolution of EGFR isoforms and pathway-associated genes.
Results: Transcriptomic expressions trended in favor of under-expression, with the log fold change in gene expression of EGFR being nuanced among multiple samples.
Discussion: The breast ductal carcinoma cells show a general trend towards under-expression in the EGFR pathways. However, the expression of EGFR, being comparable to healthy breast epithelium, remains nuanced with increases in CDH2 expression suggesting increased N-Cadherin activity. This suggests that this pathway is not a primary driver in ER+, PR+, HER2- breast cancer. This does not rule out the possibility that isoforms may be elicited in downregulating this response.
