Genomic clustering analysis identifies molecular subtypes of thymic epithelial tumors independent of World Health Organization histologic type
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Sukhmani K. Padda1, Yesim Gökmen-Polar2, Jessica A. Hellyer1, Sunil S. Badve2, Neeraj K. Singh3, Sumanth M. Vasista3, Kabya Basu3, Ansu Kumar3 and Heather A. Wakelee1
1 Stanford University School of Medicine/Stanford Cancer Institute, Stanford, CA, USA
2 Indiana University School of Medicine, Indianapolis, IN, USA
3 Cellworks Group, San Jose, CA, USA
|Sukhmani K. Padda,||email:||firstname.lastname@example.org|
Keywords: thymic epithelial tumor; thymoma; genomics; clustering; computational analysis
Received: April 02, 2021 Accepted: May 15, 2021 Published: June 08, 2021
Further characterization of thymic epithelial tumors (TETs) is needed. Genomic information from 102 evaluable TETs from The Cancer Genome Atlas (TCGA) dataset and from the IU-TAB-1 cell line (type AB thymoma) underwent clustering analysis to identify molecular subtypes of TETs. Six novel molecular subtypes (TH1-TH6) of TETs from the TCGA were identified, and there was no association with WHO histologic subtype. The IU-TAB-1 cell line clustered into the TH4 molecular subtype and in vitro testing of candidate therapeutics was performed. The IU-TAB-1 cell line was noted to be resistant to everolimus (mTORC1 inhibitor) and sensitive to nelfinavir (AKT1 inhibitor) across the endpoints measured. Sensitivity to nelfinavir was due to the IU-TAB-1 cell line’s gain-of function (GOF) mutation in PIK3CA and amplification of genes observed from array comparative genomic hybridization (aCGH), including AURKA, ERBB2, KIT, PDGFRA and PDGFB, that are known upregulate AKT, while resistance to everolimus was primarily driven by upregulation of downstream signaling of KIT, PDGFRA and PDGFB in the presence of mTORC1 inhibition. We present a novel molecular classification of TETs independent of WHO histologic subtype, which may be used for preclinical validation studies of potential candidate therapeutics of interest for this rare disease.
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