High throughput sequencing of small cell lung cancer chemosensitive H69 and corresponding chemoresistant H69AR

Small cell lung cancer (SCLC) is the most aggressive subtype of lung cancer. Although most patients are initially sensitive to first-line chemotherapy with combined cisplatin and etoposide, chemotherapy drugs resistance easily develops and quickly leads to tumor progression. Therefore, understanding mechanisms of chemotherapy drugs resistance and how to reverse it is key to improving the prognosis of patients with SCLC. The parental SCLC cell lines H69 and corresponding doxorubicin-induced multidrug resistant variant (H69AR) were used to explore the mechanism of chemoresistance in SCLC. Overall design: RNA was extracted from SCLC cells (H69 and H69AR). The RNA quality was assessed with a Bioanalyzer 2100 DNA Chip 7500 (Agilent Technologies), and samples with an RNA integrity number (RIN) of over 7 were further analyzed by RNA-seq. All sequencing reactions were performed on an Illumina HiSeq 2000 instrument (Illumina, San Diego, CA, USA). We used HISAT2 (version 2.1.0) with the default setting to map the RNA-seq data to the human reference genome (NCBI38/hg38).We aggregated the read counts at the gene level using HTSeq.

小细胞肺癌（Small cell lung cancer, SCLC）是恶性程度最高的肺癌亚型。尽管多数患者初始对顺铂联合依托泊苷的一线化疗方案敏感，但极易产生化疗药物耐药性，并快速导致肿瘤进展。因此，阐明化疗耐药的机制并探索其逆转策略，是改善小细胞肺癌患者预后的关键。
本研究以亲本小细胞肺癌细胞系H69及其阿霉素诱导的多药耐药亚株（H69AR）为模型，探究小细胞肺癌的化疗耐药机制。
实验整体设计如下：从H69和H69AR两种小细胞肺癌细胞中提取总RNA。采用安捷伦科技（Agilent Technologies）的生物分析仪2100 DNA Chip 7500评估RNA质量，选取RNA完整性数（RIN）≥7的样本进行后续RNA测序（RNA-seq）分析。所有测序实验均于Illumina HiSeq 2000测序仪（Illumina，美国加利福尼亚州圣地亚哥）上开展。采用默认参数的HISAT2（版本2.1.0）将RNA-seq数据比对至人类参考基因组（NCBI38/hg38）。采用HTSeq工具对基因水平的测序reads计数进行汇总。