Exome Sequencing Identifies Potentially Druggable Mutations in Nasopharyngeal Carcinoma

Yock Ping Chow,San Jiun Chai,Noor Kaslina Mohd Kornain,Soo Hwang Teo,Yoke Yeow Yap,Siew Woh Choo,Alan Soo-Beng Khoo,Vyomesh Patel,Chee Lun Lum,Tee Yong Tan,Norazlin Abdul Aziz,Kin Choo Pua,Lu Ping Tan,Rajadurai Pathmanathan,Paul Vey Hong Lim

doi:10.1038/srep42980

Abstract

In this study, we first performed whole exome sequencing of DNA from 10 untreated and clinically annotated fresh frozen nasopharyngeal carcinoma (NPC) biopsies and matched bloods to identify somatically mutated genes that may be amenable to targeted therapeutic strategies. We identified a total of 323 mutations which were either non-synonymous (n = 238) or synonymous (n = 85). Furthermore, our analysis revealed genes in key cancer pathways (DNA repair, cell cycle regulation, apoptosis, immune response, lipid signaling) were mutated, of which those in the lipid-signaling pathway were the most enriched. We next extended our analysis on a prioritized sub-set of 37 mutated genes plus top 5 mutated cancer genes listed in COSMIC using a custom designed HaloPlex target enrichment panel with an additional 88 NPC samples. Our analysis identified 160 additional non-synonymous mutations in 37/42 genes in 66/88 samples. Of these, 99/160 mutations within potentially druggable pathways were further selected for validation. Sanger sequencing revealed that 77/99 variants were true positives, giving an accuracy of 78%. Taken together, our study indicated that ~72% (n = 71/98) of NPC samples harbored mutations in one of the four cancer pathways (EGFR-PI3K-Akt-mTOR, NOTCH, NF-κB, DNA repair) which may be potentially useful as predictive biomarkers of response to matched targeted therapies.

Highlights

Targeted therapies with higher selectivity and minimal toxicity are frequently used as standard-of-care for treating several human cancers that include lung[1], breast[2] and colorectal[3] harboring specific genetic alterations
Our findings revealed that a subset of nasopharyngeal carcinoma (NPC) patients may be amenable to biomarker-guided therapies targeting epidermal growth factor receptor (EGFR)-PI3K-Akt-mTOR, NOTCH, NF-κB signaling and DNA repair pathways
The presence of the BRAF V600 variant in melanoma patients predicts benefit with FDA approved small molecule therapies, and vermurafenib has been shown to give benefit to BRAF V600E positive metastatic melanoma patients[37,40]

Summary

Introduction

Targeted therapies with higher selectivity and minimal toxicity are frequently used as standard-of-care for treating several human cancers that include lung[1], breast[2] and colorectal[3] harboring specific genetic alterations. Lung cancer patients expressing high epidermal growth factor receptor (EGFR) levels may not all benefit from anti-EGFR therapies (i.e. erlotinib/gefitinib), while those harboring gain of function mutations which led to constitutive activation of this mitogenic pathway are likely to be responsive and confer prolonged median survival[13,14]. Notwithstanding, the successful translation of mutation status in guiding oncology treatment decision has gained increasing attention and the growth in this field has been accelerated with the advent of generation sequencing[17,18] It follows that with the current generation sequencing capabilities, we are able to exquisitely tease out the complex genetic information underlying cancer development and concurrently identify relevant gene signatures that are unique to each tumor and link these to drug response with the clear view of identifying new therapies as treatment options[19,20,21]. Several ongoing clinical trials for example, NCI Molecular Analysis for Therapy Choice (MATCH) and FOCUS4, employ predetermined mutational profile of the cancer before giving the relevant targeted therapy[27]

Methods

Results

Conclusion