Purpose: Histologic transformation to small cell lung cancer (SCLC) is a mechanism of treatment resistance in patients with advanced oncogene-driven lung adenocarcinoma (LUAD) that currently requires histologic review for diagnosis. Herein, we sought to develop an epigenomic cell-free (cf)DNA-based approach to non-invasively detect small cell transformation in patients with EGFR mutant (EGFRm) LUAD. Experimental Design: To characterize the epigenomic landscape of transformed (t)SCLC relative to LUAD and de novo SCLC, we performed chromatin immunoprecipitation sequencing (ChIP-seq) to profile the histone modifications H3K27ac, H3K4me3, and H3K27me3, methylated DNA immunoprecipitation sequencing (MeDIP-seq), assay for transposase-accessible chromatin sequencing (ATAC-seq), and RNA sequencing on 26 lung cancer patient-derived xenograft (PDX) tumors. We then generated and analyzed H3K27ac ChIP-seq, MeDIP-seq, and whole genome sequencing cfDNA data from 1 ml aliquots of plasma from patients with EGFRm LUAD with or without tSCLC. Results: Analysis of 126 epigenomic libraries from the lung cancer PDXs revealed widespread epigenomic reprogramming between LUAD and tSCLC, with a large number of differential H3K27ac (n=24,424), DNA methylation (n=3,298), and chromatin accessibility (n=16,352) sites between the two histologies. Tumor-informed analysis of each of these three epigenomic features in cfDNA resulted in accurate non-invasive discrimination between patients with EGFRm LUAD versus tSCLC (AUROC=0.82-0.87). A multi-analyte cfDNA-based classifier integrating these three epigenomic features discriminated between EGFRm LUAD versus tSCLC with an AUROC of 0.94. Conclusions: These data demonstrate the feasibility of detecting small cell transformation in patients with EGFRm LUAD through epigenomic cfDNA profiling of 1 ml of patient plasma.

中文翻译：

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通过表观基因组 cfDNA 分析检测晚期 EGFR 突变肺腺癌患者的小细胞转化


目的：组织学转化为小细胞肺癌（SCLC）是晚期癌基因驱动的肺腺癌（LUAD）患者的一种治疗耐药机制，目前需要组织学检查来诊断。在此，我们试图开发一种基于表观基因组无细胞 (cf)DNA 的方法，以非侵入性检测 EGFR 突变体 (EGFRm) LUAD 患者的小细胞转化。实验设计：为了表征转化 (t)SCLC 相对于 LUAD 和从头 SCLC 的表观基因组景观，我们进行了染色质免疫沉淀测序 (ChIP-seq) 来分析组蛋白修饰 H3K27ac、H3K4me3 和 H3K27me3，甲基化 DNA 免疫沉淀测序 (MeDIP) -seq）、转座酶可及染色质测序（ATAC-seq）分析以及 26 个肺癌患者来源的异种移植（PDX）肿瘤的 RNA 测序。然后，我们从患有或不患有 tSCLC 的 EGFRm LUAD 患者的 1 ml 等份血浆中生成并分析了 H3K27ac ChIP-seq、MeDIP-seq 和全基因组测序 cfDNA 数据。结果：对来自肺癌 PDX 的 126 个表观基因组文库的分析揭示了 LUAD 和 tSCLC 之间广泛的表观基因组重编程，具有大量差异 H3K27ac (n=24,424)、DNA 甲基化 (n=3,298) 和染色质可及性 (n=16,352)两种组织学之间的位点。对 cfDNA 中这三个表观基因组特征中每一个的肿瘤知情分析导致 EGFRm LUAD 与 tSCLC 患者之间准确的非侵入性区分 (AUROC=0.82-0.87)。基于多分析物 cfDNA 的分类器集成了这三种表观基因组特征，可区分 EGF​​Rm LUAD 与 tSCLC，AUROC 为 0.94。 结论：这些数据证明了通过 1 ml 患者血浆的表观基因组 cfDNA 分析检测 EGFRm LUAD 患者小细胞转化的可行性。