TRPS1 is a lineage-specific transcriptional dependency in breast cancer [Seq]

We performed an unbiased cell viability-based pooled shRNA screen on 59 cell lines to identify novel epigenetic and transcriptional dependencies of multiple cancer types, including leukemia, neuroblastoma, breast, colorectal, prostate, and rhabdoid tumors. Here, we identified Tricho-Rhino-Phalangeal Syndrome Type I protein (TRPS1) as one of the most significant hits specific for breast cancer cell lines. Downregulation of TRPS1 resulted in cell cycle arrest and apoptosis increase in vitro and impaired tumorigenic capacity in vivo. We characterized TRPS1 genomic targets and protein interactome. We identified GATAD2B as an important partner of TRPS1, uncovering novel epigenetic network crucial for breast cancer cell survival. Overall design: Bulk RNA-Seq: Gene expression analysis of 57 cell lines used in the screen and HCC3153 and SUM159 cell lines with TET-inducible shRNA against TRPS1 with the following variables: Two different shRNA labeled sh1 (sh41) and sh2 (sh43), doxycyclin (plus/treatment) and no doxycyclin (minus/control), 3, 4 and 5 days after doxycyclin treatment. All conditions were sequenced without replicates (24 samples). ChIP-Seq: Examination of H3K27me3, GATAD2A, GATAD2B, H3K27ac, and TRPS1 in three different cell lines, in duplicates. HCC3153 cell line included the following variables: Two different shRNA labeled sh1 (sh41) and sh2 (sh43), doxycyclin (plus/treatment) and no doxycyclin (minus/control). Please note that the 'DFCI_EpiCluster_RNA-Seq.reads.gct' processed data file includes 4 re-analyzed samples, which were submitted as a part of series GSE63582 and the data columns correspond to the following samples; SUM149PT - GSM1842497 [SUM149_DMSO_12H_R1] SUM149PT_JQ1R_w_JQ1 - GSM1842493 [SUM149R_DMSO_12H_R1] SUM159PT - GSM1553156 [SUM159_DMSO_3H_1] SUM159PT_JQ1R_w_JQ1 - GSM1553147 [SUM159R_DMSO_3H_2]

本研究针对59株细胞系开展了基于细胞活力的无偏混合shRNA筛选，以鉴定多种癌症类型（包括白血病、神经母细胞瘤、乳腺癌、结直肠癌、前列腺癌以及横纹肌样瘤）的新型表观遗传与转录依赖特性。本研究将毛发-鼻-指（趾）综合征I型蛋白（Tricho-Rhino-Phalangeal Syndrome Type I protein，TRPS1）鉴定为乳腺癌细胞系特异性的最显著阳性靶点之一。体外实验表明，下调TRPS1可引发细胞周期阻滞与细胞凋亡增加，并在体内削弱肿瘤发生能力。本研究对TRPS1的基因组靶标与蛋白质互作组进行了系统表征，鉴定出GATAD2B为TRPS1的重要互作伴侣，揭示了对乳腺癌细胞存活至关重要的新型表观遗传调控网络。

整体实验设计如下：
1. 批量RNA测序（Bulk RNA-Seq）：针对筛选所用的57株细胞系，以及携带TET诱导型靶向TRPS1的shRNA的HCC3153与SUM159细胞系开展基因表达分析，实验变量包含：两种分别标记为sh1（sh41）与sh2（sh43）的shRNA、是否添加多西环素（处理组/对照组）、多西环素处理后第3、4、5天。所有实验条件均未设置生物学重复，共完成24个样本的测序。
2. 染色质免疫共沉淀测序（ChIP-Seq）：针对三种不同的细胞系，对H3K27me3、GATAD2A、GATAD2B、H3K27ac以及TRPS1进行检测，每个实验设置生物学重复。其中HCC3153细胞系的实验变量包括：两种分别标记为sh1（sh41）与sh2（sh43）的shRNA、是否添加多西环素（处理组/对照组）。

请注意，处理后的数据文件"DFCI_EpiCluster_RNA-Seq.reads.gct"包含4份重新分析的样本，这些样本作为GSE63582系列数据集的一部分提交，数据列对应如下样本：
SUM149PT - GSM1842497 [SUM149_DMSO_12H_R1]
SUM149PT_JQ1R_w_JQ1 - GSM1842493 [SUM149R_DMSO_12H_R1]
SUM159PT - GSM1553156 [SUM159_DMSO_3H_1]
SUM159PT_JQ1R_w_JQ1 - GSM1553147 [SUM159R_DMSO_3H_2]