Plasma RNA profiling unveils transcriptional signatures associated with resistance to osimertinib in EGFR T790M positive non-small cell lung cancer patients

Andrey Alexeyenko; Odd Terje Brustugun; Inger Johanne Zwicky Eide; Radosveta Gencheva; Zeinab Kosibaty; Yi Lai; Luigi de Petris; Georgios Tsakonas; Oscar Grundberg; Bo Franzen; Kristina Viktorsson; Rolf Lewensohn; Per Hydbring; Simon Ekman

doi:10.21037/tlcr-22-236

Plasma RNA profiling unveils transcriptional signatures associated with resistance to osimertinib in EGFR T790M positive non-small cell lung cancer patients

Transl Lung Cancer Res. 2022 Oct;11(10):2064-2078. doi: 10.21037/tlcr-22-236.

Authors

Andrey Alexeyenko^{1

2

3}, Odd Terje Brustugun^{4

5

6}, Inger Johanne Zwicky Eide^{4

5

6}, Radosveta Gencheva⁷, Zeinab Kosibaty⁷, Yi Lai⁷, Luigi de Petris^{7

8}, Georgios Tsakonas^{7

8}, Oscar Grundberg⁸, Bo Franzen⁷, Kristina Viktorsson⁷, Rolf Lewensohn^{7

8}, Per Hydbring^#⁷, Simon Ekman^#^{7

8}

Affiliations

¹ Science for Life Laboratory, Box 1031, Solna, Sweden.
² Evi-networks consulting, Huddinge, Sweden.
³ Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden.
⁴ Section of Oncology, Drammen Hospital, Vestre Viken Hospital Trust, Drammen, Norway.
⁵ Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
⁶ Department of Cancer Genetics, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.
⁷ Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden.
⁸ Thoracic Oncology Center, Karolinska University Hospital, Stockholm, Sweden.

^# Contributed equally.

Abstract

Background: Targeted therapy with tyrosine kinases inhibitors (TKIs) against epidermal growth factor receptor (EGFR) is part of routine clinical practice for EGFR mutant advanced non-small cell lung cancer (NSCLC) patients. These patients eventually develop resistance, frequently accompanied by a gatekeeper mutation, T790M. Osimertinib is a third-generation EGFR TKI displaying potency to the T790M resistance mutation. Here we aimed to analyze if exosomal RNAs, isolated from longitudinally sampled plasma of osimertinib-treated EGFR T790M NSCLC patients, could provide biomarkers of acquired resistance to osimertinib.

Methods: Plasma was collected at baseline and progression of disease from 20 patients treated with osimertinib in the multicenter phase II study TKI in Relapsed EGFR-mutated non-small cell lung cancer patients (TREM). Plasma was centrifuged at 16,000 g followed by exosomal RNA extraction using Qiagen exoRNeasy kit. RNA was subjected to transcriptomics analysis with Clariom D.

Results: Transcriptome profiling revealed differential expression [log2(fold-change) >0.25, false discovery rate (FDR) P<0.15, and P(interaction) >0.05] of 128 transcripts. We applied network enrichment analysis (NEA) at the pathway level in a large collection of functional gene sets. This overall enrichment analysis revealed alterations in pathways related to EGFR and PI3K as well as to syndecan and glypican pathways (NEA FDR <3×10^-10). When applied to the 40 individual, sample-specific gene sets, the NEA detected 16 immune-related gene sets (FDR <0.25, P(interaction) >0.05 and NEA z-score exceeding 3 in at least one sample).

Conclusions: Our study demonstrates a potential usability of plasma-derived exosomal RNAs to characterize molecular phenotypes of emerging osimertinib resistance. Furthermore, it highlights the involvement of multiple RNA species in shaping the transcriptome landscape of osimertinib-refractory NSCLC patients.

Keywords: Non-small cell lung cancer (NSCLC); epidermal growth factor receptor (EGFR); exosomal RNA; osimertinib; transcriptome.