Oncotarget

Research Papers:

Genomic clustering analysis identifies molecular subtypes of thymic epithelial tumors independent of World Health Organization histologic type

Sukhmani K. Padda _, Yesim Gökmen-Polar, Jessica A. Hellyer, Sunil S. Badve, Neeraj K. Singh, Sumanth M. Vasista, Kabya Basu, Ansu Kumar and Heather A. Wakelee

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Oncotarget. 2021; 12:1178-1186. https://doi.org/10.18632/oncotarget.27978

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Abstract

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

Correspondence to:

Sukhmani K. Padda,email: sukhmani.padda@cshs.org

Keywords: thymic epithelial tumor; thymoma; genomics; clustering; computational analysis

Received: April 02, 2021     Accepted: May 15, 2021     Published: June 08, 2021

Copyright: © 2021 Padda et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

ABSTRACT

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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