Transcriptomic Analysis of EGFR and Downstream Pathway Expression in A549 and Healthy Lung 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, primarily for lung, breast, and ovarian, have been uncertain. These clinical tests lack specificity and sensitivity. We are interested in intronic single nucleotide polymorphisms (SNPs) in intronic regions. This work is an Insilco characterization and assessment of a lung adenocarcinoma cell line (A549) in association. With expression patterns of EGFR and associated pathways relative expression.
Purpose: Identify associated proteins from downstream pathways that are upregulated or downregulated in A549 compared to normal lung epithelium. Methods: The expression pipeline was applied to lung adenocarcinoma and healthy lung epithelium from publicly available cDNA short reads. This pipeline involved sequence alignment with a splice-aware aligner (STAR) and feature counting algorithm (feature Counts), and normalization, filtering and plotting with limma. Heteroscedasticity adjustment was performed with Voom.
Results/Conclusion: HRAS, FOS, JUN, and NFKB1 all are overexpressed, and TP53 is under-expressed in A549. This suggests typical cell cycle dysregulation for cancer. However, MAPK3/ERK1 suggests there is overactivity in a MAPK pathway. Under expression in SOS1 and AKT3 illicit the alternative MAPK pathways with careful attention to the JNK pathway. Also, CDH1/CDH2 differences in expression suggest that E-cadherin activity is much higher than N-cadherin activity and that they are abhorrently up and downregulated, respectively.
Transcriptomic Analysis of EGFR and Downstream Pathway Expression in A549 and Healthy Lung Epithelium
Student Center Ballroom
Introduction: Clinical tests utilizing EGFR isoforms as a method of cancer screening, primarily for lung, breast, and ovarian, have been uncertain. These clinical tests lack specificity and sensitivity. We are interested in intronic single nucleotide polymorphisms (SNPs) in intronic regions. This work is an Insilco characterization and assessment of a lung adenocarcinoma cell line (A549) in association. With expression patterns of EGFR and associated pathways relative expression.
Purpose: Identify associated proteins from downstream pathways that are upregulated or downregulated in A549 compared to normal lung epithelium. Methods: The expression pipeline was applied to lung adenocarcinoma and healthy lung epithelium from publicly available cDNA short reads. This pipeline involved sequence alignment with a splice-aware aligner (STAR) and feature counting algorithm (feature Counts), and normalization, filtering and plotting with limma. Heteroscedasticity adjustment was performed with Voom.
Results/Conclusion: HRAS, FOS, JUN, and NFKB1 all are overexpressed, and TP53 is under-expressed in A549. This suggests typical cell cycle dysregulation for cancer. However, MAPK3/ERK1 suggests there is overactivity in a MAPK pathway. Under expression in SOS1 and AKT3 illicit the alternative MAPK pathways with careful attention to the JNK pathway. Also, CDH1/CDH2 differences in expression suggest that E-cadherin activity is much higher than N-cadherin activity and that they are abhorrently up and downregulated, respectively.
