Transcriptomic silencing as a potential mechanism of treatment resistance.

Jacob J Adashek,Razelle Kurzrock,Christopher W Szeto,J Zachary Sanborn,Charles J Vaske,Sandeep K Reddy,Shumei Kato,Rahul Parulkar,Stephen C Benz

doi:10.1172/jci.insight.134824

Abstract

Next-generation sequencing (NGS) has not revealed all the mechanisms underlying resistance to genomically matched drugs. Here, we performed in 1417 tumors whole-exome tumor (somatic)/normal (germline) NGS and whole-transcriptome sequencing, the latter focusing on a clinically oriented 50-gene panel in order to examine transcriptomic silencing of putative driver alterations. In this large-scale study, approximately 13% of the somatic single nucleotide variants (SNVs) were unexpectedly not expressed as RNA; 23% of patients had ≥1 nonexpressed SNV. SNV-bearing genes consistently transcribed were TP53, PIK3CA, and KRAS; those with lower transcription rates were ALK, CSF1R, ERBB4, FLT3, GNAS, HNF1A, KDR, PDGFRA, RET, and SMO. We also determined the frequency of tumor mutations being germline, rather than somatic, in these and an additional 462 tumors with tumor/normal exomes; 33.8% of germline SNVs within the gene panel were rare (not found after filtering through variant information domains) and at risk of being falsely reported as somatic. Both the frequency of silenced variant transcription and the risk of falsely identifying germline mutations as somatic/tumor related are important phenomena. Therefore, transcriptomics is a critical adjunct to genomics when interrogating patient tumors for actionable alterations, because, without expression of the target aberrations, there will likely be therapeutic resistance.

Highlights

Clinical-grade next-generation sequencing (NGS) is being increasingly used as a tool to direct the treatment of cancers
Additional resistance mechanisms may be due to one or more of the following: the tumor microenvironment, which secretes various hormones, growth factors, and cytokines that can propel cell growth and survival [5]; cancer progenitor cells that increase the expression of drug efflux transporter genes that pump drugs out of the cell and into the interstitium [6]; mutations within drug transporter genes that attenuate drug binding and influx into the cell and/or absorption [7]; increased expression of antiapoptotic proteins and decreased expression of proapoptotic proteins [7]; amplification of oncogenes and protumorigenic genes [8]; mutations within drug target domains, such as the kinase motifs [9]; and changes in genes, such as BRCA, that revert them to “normal,” abrogating sensitivity to PARP inhibitors [10]
All of these patients were used for tumor/normal Next-generation sequencing (NGS), that is, known tumor tissue NGS data were compared with those from normal nontumor tissue, which here was either same-patient blood or buccal tissue

Summary

Introduction

Clinical-grade next-generation sequencing (NGS) is being increasingly used as a tool to direct the treatment of cancers. By revealing alterations in some of the most commonly affected and instrumental genes in cancer development and progression, NGS ostensibly identifies potentially actionable targets [1]. The outcome for many patients with metastatic tumors remains grim even in the era of precision oncology, with responses often being unpredictable, even when clinical-grade NGS is used. Additional resistance mechanisms may be due to one or more of the following: the tumor microenvironment, which secretes various hormones, growth factors, and cytokines that can propel cell growth and survival [5]; cancer progenitor cells that increase the expression of drug efflux transporter genes that pump drugs out of the cell and into the interstitium [6]; mutations within drug transporter genes that attenuate drug binding and influx into the cell and/or absorption [7]; increased expression of antiapoptotic proteins and decreased expression of proapoptotic proteins [7]; amplification of oncogenes and protumorigenic genes [8]; mutations within drug target domains, such as the kinase motifs [9]; and changes in genes, such as BRCA, that revert them to “normal,” abrogating sensitivity to PARP inhibitors [10].

Methods

Results

Conclusion