Locus-specific LINE-1 expression in clinical ovarian cancer specimens at the single-cell level

Long interspersed nuclear elements (LINE-1s or L1s) are a group of retrotransposons that can copy themselves within a genome. In our species, it is the most successful transposon in nucleotide content. L1 expression is generally mild in normal human tissues, but the activity has been shown to increase significantly in many cancers. Only few studies have examined L1 expression at single-cell resolution, thus it is undetermined whether L1 reactivation occurs solely in malignant cells within tumors. One of the cancer types with frequent L1 activity is high-grade serous ovarian carcinoma (HGSOC). Here, we identified locus-specific L1 expression with 3’ single-cell RNA sequencing in pre- and post-chemotherapy HGSOC sample pairs from 11 patients, and in fallopian tube samples from five healthy women. Although L1 expression quantification with the chosen technique was challenging due to the repetitive nature of L1 elements, we found evidence of genuine L1 expression. The expression levels were similar in pre- and post-chemotherapy samples, indicating that L1 transcriptional activity was unaffected by the treatment. Furthermore, we found that L1 activity was negatively associated with the expression of MYC target genes, a finding that supports earlier literature of MYC being an L1 suppressor. We studied LINE-1 expression in 22 high-grade serous ovarian cancer patient samples collected concurrently with both laparoscopy and interval debulking surgery from 11 women, as well as in five non-cancerous fallopian tube or fimbria tissue samples from five healthy post-menopausal women. We used scRNA-seq to get a single-cell level view of the expression profiles. ---------------------------- Authors state: Raw data files are not included. The raw data has been uploaded to EGA (EGAS00001006246 for fallopian tube/fibmriae samples, EGAS00001005010 for cancer samples) in order to comply with data protection regulations.

长散在核元件（Long interspersed nuclear elements，简称LINE-1s或L1s）是一类可在基因组内自主扩增的反转录转座子。在人类基因组中，它是核苷酸占比最高的转座子。正常人体组织中L1的表达水平通常较低，但多项研究证实其活性在多种癌症中显著升高。目前仅有少数研究以单细胞分辨率开展L1表达检测，因此尚不明确肿瘤内的L1激活是否仅局限于恶性细胞中。高频出现L1活性的癌症类型之一为高级别浆液性卵巢癌（high-grade serous ovarian carcinoma，HGSOC）。本研究通过3'端单细胞RNA测序，对11名患者的化疗前后高级别浆液性卵巢癌配对样本，以及5名健康女性的输卵管样本进行了位点特异性L1表达分析。尽管由于L1元件的重复序列特性，采用该技术进行L1表达定量存在较大挑战，但我们仍检测到了真实L1表达的相关证据。化疗前后样本的L1表达水平无显著差异，提示L1的转录活性不受化疗干预的影响。此外，我们发现L1活性与MYC靶基因的表达呈负相关，这一发现支持了"MYC作为L1抑制因子"的前期研究结论。本研究共纳入22例高级别浆液性卵巢癌患者样本，均来自11名同时接受腹腔镜手术与间隔减瘤术的女性；同时纳入5名健康绝经后女性的非癌性输卵管或输卵管伞部组织样本。我们采用单细胞RNA测序（single-cell RNA sequencing，简称scRNA-seq）获取了样本的单细胞水平表达谱。作者声明：本研究未提供原始数据文件。为符合数据保护法规要求，原始数据已上传至EGA数据库，其中输卵管/伞部样本的编号为EGAS00001006246，癌症样本的编号为EGAS00001005010。