Genomics & Informatics

Korea Genome Organization (한국유전체학회)
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In-silico and structure-based assessment to evaluate pathogenicity of missense mutations associated with non-small cell lung cancer identified in the Eph-ephrin class of proteins

  • Shubhashish Chakraborty (Advanced Centre for Treatment, Research and Education in Cancer) ;
  • Reshita Baruah (Advanced Centre for Treatment, Research and Education in Cancer) ;
  • Neha Mishra (Advanced Centre for Treatment, Research and Education in Cancer) ;
  • Ashok K Varma (Advanced Centre for Treatment, Research and Education in Cancer)
  • Received : 2022.11.01
  • Accepted : 2023.08.03
  • Published : 2023.09.30
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Abstract

Ephs belong to the largest family of receptor tyrosine kinase and are highly conserved both sequentially and structurally. The structural organization of Eph is similar to other receptor tyrosine kinases; constituting the extracellular ligand binding domain, a fibronectin domain followed by intracellular juxtamembrane kinase, and SAM domain. Eph binds to respective ephrin ligand, through the ligand binding domain and forms a tetrameric complex to activate the kinase domain. Eph-ephrin regulates many downstream pathways that lead to physiological events such as cell migration, proliferation, and growth. Therefore, considering the importance of Eph-ephrin class of protein in tumorigenesis, 7,620 clinically reported missense mutations belonging to the class of variables of unknown significance were retrieved from cBioPortal and evaluated for pathogenicity. Thirty-two mutations predicted to be pathogenic using SIFT, Polyphen-2, PROVEAN, SNPs&GO, PMut, iSTABLE, and PremPS in-silico tools were found located either in critical functional regions or encompassing interactions at the binding interface of Eph-ephrin. However, seven were reported in nonsmall cell lung cancer (NSCLC). Considering the relevance of receptor tyrosine kinases and Eph in NSCLC, these seven mutations were assessed for change in the folding pattern using molecular dynamic simulation. Structural alterations, stability, flexibility, compactness, and solvent-exposed area was observed in EphA3 Trp790Cys, EphA7 Leu749Phe, EphB1 Gly685Cys, EphB4 Val748Ala, and Ephrin A2 Trp112Cys. Hence, it can be concluded that the evaluated mutations have potential to alter the folding pattern and thus can be further validated by in-vitro, structural and in-vivo studies for clinical management.

Keywords

Acknowledgement

We thank DBT-BTIS centre for providing access to necessary hardware and software. Funding for this study was supported by DBT (BT/PR40181/BTIS/137/15/2021); ICMR (No. BMI/12 (37)/2022 ID No. 2021-10100) to AKV

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