Transcriptome Profiling of Acquired Gefitinib Resistant Lung Cancer Cells Reveals Dramatically Changed Transcription Programs and New Treatment Targets

Abstract

Background: Targeted therapy for lung cancer with epidermal growth factor receptor (EGFR) mutations with tyrosine kinase inhibitors (TKIs) represents one of the major breakthroughs in lung cancer management. However, gradually developed resistance to these drugs prevents sustained clinical benefits and calls for resistant mechanism research and identification of new therapeutic targets. Acquired T790M mutation accounts for the majority of resistance cases, yet transcriptome changes in these cells are less characterized, and it is not known if new treatment targets exist by available drugs. Methods: Transcriptome profiling was performed for lung cancer cell line PC9 and its resistant line PC9GR after long-term exposure to gefitinib through RNA sequencing. Differentially expressed genes and changed pathways were identified along with existing drugs targeting these upregulated genes. Using 144 lung cancer cell lines with both gene expression and drug response data from the cancer cell line encyclopedia (CCLE) and Cancer Therapeutics Response Portal (CTRP), we screened 549 drugs whose response was correlated with these upregulated genes in PC9GR cells, and top drugs were evaluated for their response in both PC9 and PC9GR cells. Results: In addition to the acquired T790M mutation, the resistant PC9GR cells had very different transcription programs from the sensitive PC9 cells. Multiple pathways were changed with the top ones including TNFA signaling, androgen/estrogen response, P53 pathway, MTORC1 signaling, hypoxia, and epithelial mesenchymal transition. Thirtytwo upregulated genes had available drugs that can potentially be effective in treating the resistant cells. From the response profiles of CCLE, we found 17 drugs whose responses were associated with at least four of these upregulated genes. Among the four drugs evaluated (dasatinib, KPT-185, trametinib, and pluripotin), all except trametinib demonstrated strong inhibitory effects on the resistant PC9GR cells, among which KPT185 was the most potent. KPT-185 suppressed growth, caused apoptosis, and inhibited migration of the PC9GR cells at similar (or better) rates as the sensitive PC9 cells in a dose-dependent manner. Wei et al. New Targets for Lung Cancer Conclusions: Acquired TKI-resistant lung cancer cells (PC9GR) have dramatically changed transcription and pathway regulation, which expose new treatment targets. Existing drugs may be repurposed to treat those patients with developed resistance to TKIs.

Selinexor inhibits growth of patient derived chordomas in vivo as a single agent and in combination with abemaciclib through diverse mechanisms

“…Each of these pathways can drive oncogenesis when dysregulated, and interestingly, E2F and GR signaling have been shown to be targetable by XPO1 inhibitors ( 43 , 46 , 63 ). Specific to the CF466 sacral chordoma model, TGFA was among the most significantly reduced genes, which is notable because it encodes an EGFR ligand, and SINE compounds are effective against cancer cells with engineered resistance to EGFR-tyrosine kinase inhibitors ( 64 ). Notably, direct EGFR inhibitors have shown promise as anti-cancer agents in chordoma and are being clinically evaluated ( 65 ).…”

Modulating undruggable targets to overcome cancer therapy resistance

“…In addition to the acquired T790M mutation, the resistant PC9GR cells had very different transcription programs from the sensitive PC9 cells. suppressed growth, caused apoptosis, and inhibited migration of the PC9GR cells at similar (or better) rates as the sensitive PC9 cells in a dosedependent manner (Wei et al, 2020). Both compounds 48 and 49 (KPT-276) were investigated for the antileukemic activity in vitro and in vivo in AML.…”

“…S109 45 Niu et al, 2015a verdinexor KPT-335) 46 Jorquera et al, 2019 eltanexor Z-isomer, KPT-8602) 47 Verbeke et al, 2020 KPT-185 48 Wei et al, 2020 KPT-276 49 Ranganathan et al, 2012 Immunogenic Cell Death ICD) cyclophosphamide 50 Vanmeerbeek et al 2020 oxaliplatin DACH-Pt)* 51 Vanmeerbeek et al 2020 epirubicin 52 Vanmeerbeek et al 2020 bortezomib 53 Vanmeerbeek et al 2020 ferrocifen P722* 54 Jaouen. 2015;Top, 2003;Vessieres, 2019…”

Curcumin alters distinct molecular pathways in breast cancer subtypes revealed by integrated miRNA/mRNA expression analysis

“…RNA‐seq has been employed to study the changes in tumorigenesis in the presence of different drugs such as curcumin, 23 shikonin, 14 gefitinib, 24 Gallic acid, 25 benzo[α]pyrene (BaP), 26 Fructus Meliae Toosendan (FMT), 27 citral, 28 Quercetin 29 and so on. In this study, we have explored the whole transcriptome (mRNA and miRNA) effect post‐curcumin treatment in MDA‐MB‐231, MCF7, and T47D cells.…”