RNA Expression Profiling Comparing ER+ Postpartum Breast Cancer with ER+ Nulliparous Breast Cancer

Purpose: To perform RNA-Seq expression profiling from Young Women's Breast Cancer FFPE tissues, comparing ER+ Postpartum Brest Cancer to ER+ Nulliparous Breast Cancer Methods: RNA was extracted and isolated from archival Estrogen Receptor Positive primary breast cancer FFPE tissues ( 9 Postpartum, 7 Nulliparous). RNA species selected for inclusion in library utilzing Illumina-Access bead based oligo library preparation representing > 98% of known protein coding genes. Results: We identified gene pathway differences in estrogen receptor signaling, t-cell immunity and cell cycle between nulliparous and postpartum breast cancer cases. Subset analysis also revealed an enrichment in extra-cellular matrix pathway related genes in postpartum compared to nulliparous and luminal A cases. Overall design: FFPE derived mRNA from 9 Postpartum and 7 Nulliparous Young Women's Breast Cancer cases generated by 100-cycle, single-ended, sequencing of approxinately 70 million reads per sample using Illumina HiSeq 2500 sequencer. Base call files were converted to fastq format using Bcl2Fastq.

研究目的：对青年女性乳腺癌福尔马林固定石蜡包埋（Formalin-Fixed Paraffin Embedded, FFPE）组织进行RNA测序表达谱分析，对比雌激素受体阳性（Estrogen Receptor Positive, ER+）产后乳腺癌与ER+未生育乳腺癌的基因表达差异。
实验方法：从存档的ER+原发性乳腺癌FFPE组织中提取并分离RNA，其中产后乳腺癌组9例，未生育乳腺癌组7例。采用基于Illumina-Access磁珠的寡核苷酸文库制备方案筛选目标RNA物种，该方案可覆盖超过98%的已知蛋白编码基因。
实验结果：本研究鉴定出未生育与产后乳腺癌样本在雌激素受体信号通路、T细胞免疫及细胞周期通路上的基因表达差异。亚组分析进一步显示，相较于未生育乳腺癌及腔面A型（luminal A）样本，产后乳腺癌样本中细胞外基质通路相关基因存在显著富集。
实验整体设计：采用Illumina HiSeq 2500测序仪，对9例产后青年女性乳腺癌及7例未生育青年女性乳腺癌的FFPE来源mRNA进行100循环单端测序，每个样本约产生7000万条读段。测序下机的碱基识别文件通过Bcl2Fastq工具转换为fastq格式。