Genome-Wide Epigenetic Landscape of Lung Adenocarcinoma Links HOXB9 DNA Methylation to Intrinsic EGFR-TKI Resistance and Heterogeneous Responses

Abstract

PURPOSE Epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitors (TKIs) show efficacy in treating patients with lung adenocarcinoma with EGFR-activating mutations. However, a significant subset of targeted patients fail to respond. Unlike acquired resistance (AR), intrinsic resistance (IR) remains poorly understood. We investigated whether epigenomic factors contribute to patient-to-patient heterogeneity in the EGFR-TKI response and aimed to characterize the IR subpopulation that obtains no benefit from EGFR-TKIs. PATIENTS AND METHODS We conducted genome-wide DNA methylation profiling of 79 tumors sampled from patients with advanced lung adenocarcinoma before they received EGFR-TKI treatment and analyzed the patient responses. Pyrosequencing was performed in a validation cohort of 163 patients with EGFR-activating mutations. RESULTS A DNA methylation landscape of 216 CpG sites with differential methylation was established to elucidate the association of DNA methylation with the characteristics and EGFR-TKI response status of the patients. Functional analysis of 37 transcription-repressive sites identified the enrichment of transcription factors, notably homeobox ( HOX) genes. DNA methylation of HOXB9 (cg13643585) in the enhancer region yielded 88% sensitivity for predicting drug response (odds ratio [OR], 6.64; 95% CI, 1.98 to 25.23; P = .0009). Pyrosequencing validated that HOXB9 gained methylation in patients with a poor EGFR-TKI response (OR, 3.06; 95% CI, 1.13 to 8.19; P = .019). CONCLUSION Our data suggest that homeobox DNA methylation could be a novel tumor cellular state that can aid the precise categorization of tumor heterogeneity in the study of IR to EGFR-TKIs. We identified, for the first time, an epigenomic factor that can potentially complement DNA mutation status in discriminating patients with lung adenocarcinoma who are less likely to benefit from EGFR-TKI treatment, thereby leading to improved patient management in precision medicine.

Liquid biopsy uncovers distinct patterns of DNA methylation and copy number changes in NSCLC patients with different EGFR-TKI resistant mutations

“…The hyper-methylation status at transcriptional regulatory regions of those genes indicated their expression was suppressed in cases with EGFR dependent resistance mutations. Our finding was consistent with a recent study by Shu et al 48 showing that increased methylation of HOXB9 correlated with higher rate of resistance to EGFR-TKI. Thus, such consistent findings indicated that the hyper-methylation status of HOX genes could be exploited to predict and treat EGFR amplification mediated resistance.…”

Single‐cell RNA sequencing reveals cellular and molecular reprograming landscape of gliomas and lung cancer brain metastases

“…EGFR mutation promotes the expression of EGR1, 76,77 and high early growth response 1 (EGR1) expression correlates with resistance to anti‐EGFR treatment 78 . A higher level of DNA methylation of HOXB9 was found to be correlated with intrinsic EGFR‐TKI resistance and poor TKI response 79 . Expression of mutant EGFR (EGFRvIII) resulted in upregulation of a small group of genes, including FOSL1, 80 and EGFR‐PKM2 signalling induced the expression of FOSL1 to promote nasopharyngeal carcinoma cell invasion and metastasis 81 .…”

“…78 A higher level of DNA methylation of HOXB9 was found to be correlated with intrinsic EGFR-TKI resistance and poor TKI response. 79 Expression of mutant EGFR (EGFRvIII) resulted in upregulation of a small group of genes, including FOSL1, 80 and EGFR-PKM2 signalling induced the expression of FOSL1 to promote nasopharyngeal carcinoma cell invasion and metastasis. 81 Our results will help to improve the response to EGFR-TKI treatment.…”

DNA Methylation Analysis in Plasma Cell-Free DNA and Paired CTCs of NSCLC Patients before and after Osimertinib Treatment

“…A less common methylation-associated mechanism was found to be involved in the generation of T790M mutation that was induced by the activity of cytidine deaminase (AICDA) expression [ 65 ]. Very recently, a genome-wide DNA methylation analysis revealed that HOXB9 DNA methylation was linked to intrinsic EGFR-TKI resistance and complementary to mutation profiling could discern whether lung adenocarcinoma patients would benefit from EGFR-TKI treatment [ 66 ]. However, all these studies were performed in lung cancer cell lines or primary tissues and have not thus compared DNA methylation status before and after treatment.…”