Title

Exploring Structural Variations in EGFR Exon 19 Deletion: Insights into NSCLC Therapy

Authors

Donghoon Shin MD1, Jungwoo Kim MD2, Ivy Riano MD3 1 Department of Internal Medicine, MetroWest Medical Center/Tufts University School of Medicine, Framingham, MA, USA 2 Catholic University of Korea, College of Medicine, Seoul, Republic of Korea 3 Division of Hematology and Medical Oncology, Dartmouth Cancer Center, Geisel School of Medicine Dartmouth, Lebanon, NH

Introduction

Epidermal growth factor receptor (EGFR), a key receptor tyrosine kinase, plays crucial roles in tissue growth and repair and is a primary target for Tyrosine Kinase Inhibitors (TKIs). The majority of EGFR gene mutations are concentrated within exons 18-21 which encode the crucial tyrosine kinase (TK) domain and include exon 19 deletions (E19del)1. These deletions are the most prevalent activating mutation in advanced non–small cell lung cancer (NSCLC) among non-smoker patients. This project retrospectively analyzed the different subtypes of EGFR exon 19 deletions through TCGA database and investigate structural characteristics of one of the common exon 19 deletion(E19del) mutations in NSCLC, comparing it to the normal protein structure through PDB database.

Methods

Explored Ensemble gene browser and search in human (GRCh38.p14) to identify Exon 19 sequence and it’s domain in amino acid sequence by obtaining from the CCDS database. Analyzed lung adenocarcinoma (LUAD) data from The Cancer Genome Atlas (TCGA), downloaded and processed using the TCGAbiolinks R package. Explore the EGFR protein and one of its mutation subtypes by displaying the main protein structures of the normal protein and comparing the structural differences in the adjacent sequences of the deleted area in the PDB database

Results

The human EGFR gene (GRCh38.p14) was searched using the Ensembl genome browser, identifying the Exon 19 sequence under Transcript ID: ENST00000275493.7. Information on domain sequences and their functions was retrieved from UniProt (ID: P00533-1) revealing that the protein kinase domain spans amino acids 712-979. According to the TCGA-LUAD dataset, among 111 patients with EGFR mutations, exon 19 deletions were detected in 28 patients (25.2%). Seven varients of EGFR exon 19 deletions were identified, with the most frequent being delE746-A750 (64.3%), followed by delE746-S752insV (10.7%). Majority of deletions originate from either E746 or L747. Predominantly, deletions spanning 5 to 6 sequences were noted Through analysis of the Protein Data Bank (PDB) database, the normal structure of the Tyrosine Kinase Domain from human EGFR (Figure 1. PDB ID: 1M14) was accessed, identifying three crucial structural elements: the Activation loop (Asp831-Val852), the Nucleotide phosphate-binding loop (Gly695-Gly700), and the Catalytic loop (Arg812-Asn818). Interestingly, although the exon 19 deletion region is present within the kinase domain, these deletions are not within the key structures identified, above. An EGFR variant with the exon 19 deletion delL747_E749 was identified (Figure 2 PDB ID: 7TVD) The comparison of the 3D structures surrounding sequences 746 and 750 reveals significant disparities. The normal EGFR structure (Figure 3a, PDB ID: 1M14) exhibits dispersed sequences, while the Exon 19 deletion structure (Figure 3b, PDB ID: 7TVD) demonstrates a more compact conformation. Additionally, the adjacent helical structures spanning sequences 728-743 (highlighted in pink) and 772-780 (highlighted in orange) do not form coherent helical structures in the deletion variant

Conclusion

Utilizing bioinformatics tools to integrate structural, biochemical, and genomic data can provide valuable insights into the interactions between rare mutations and TKIs, further supporting the development of targeted therapeutic strategies.

References

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