Biological and genetic characterization of a newly established human external auditory carcinoma cell line, SCEACono2. Biological and genetic characterization of a newly established human external auditory carcinoma cell line, SCEACono2

Squamous cell carcinoma of the external auditory canal (EACSCC) is an extraordinarily rare and aggressive malignant disease. Establishment of EACSCC cell line with robust molecular characteristics is essential for the basic and translational research of EACSCC. In this study, we showed the newly established EACSCC cell line SCEACono2, derived from a patient with well-to-moderately differentiated EACSCC. To elucidate the transctomic features of SCEACono2, we performed RNA-seq and revealed its unique characteristics and compared with publicly available head and neck squamous cell caricnoma (HNSCC)-derived cell lines HSC4 and SCC9. Overall design: Library preparation from RNA extracted from cultured cells and RNA sequencing were performed using a DNBSEQ-G400 sequencer at the Beijing Genomics Institute (Shenzhen, China). The sequenced reads were aligned to the human reference genome GRCh38 using STAR v2.7.9a with Gencode v38 annotations. Gene count tables were generated with RSEM v1.3.1.

外耳道鳞状细胞癌（external auditory canal squamous cell carcinoma, EACSCC）是一类极为罕见且侵袭性极强的恶性肿瘤。建立具备稳定可靠分子特征的EACSCC细胞系，对于该疾病的基础研究与转化研究均具有重要意义。本研究报道一株新建立的EACSCC细胞系SCEACono2，其分离自一名中-高分化EACSCC患者。为阐明SCEACono2的转录组特征，我们开展了RNA测序，揭示了其独特的分子特征，并将其与公开获取的头颈部鳞状细胞癌（head and neck squamous cell carcinoma, HNSCC）来源细胞系HSC4及SCC9进行了对比分析。实验整体设计：从培养细胞中提取RNA并完成文库构建，随后于中国深圳华大基因（Beijing Genomics Institute, Shenzhen, China）使用DNBSEQ-G400测序仪完成RNA测序。测序reads通过STAR v2.7.9a软件比对至人类参考基因组GRCh38，并以Gencode v38注释文件进行注释。基因计数表通过RSEM v1.3.1软件生成。