Transcriptional profiling for CRISPR activation of a myeloma-preferential dependency. Transcriptional profiling for CRISPR activation of a myeloma-preferential dependency

Clinical progress in multiple myeloma (MM), an incurable plasma cell (PC) neoplasia, has been driven by therapies which have limited applications beyond MM/PC neoplasias and do not target specific oncogenic mutations in MM. Instead, these agents target pathways critical for PC biology yet largely dispensable for malignant or normal cells of most other lineages. We systematically characterized the lineage-preferential molecular dependencies of MM through genome-scale CRISPR gene editing studies in MM vs. hundreds of non-MM lines. This identified a collection of genes whose disruption has more pronounced or recurrent impact on the MM cell fitness compared to other malignancies. These genes, some known, others not previously linked to MM, encode transcription factors, chromatin modifiers, endoplasmic reticulum components, metabolic regulators or signaling molecules. The current dataset describes the transcriptional profiling of a MM cell line with CRISPR activation for the myeloma-preferential dependency, POU2AF1. The transcriptional profile of CRISPR activation of an additional gene (PANK1), which does not serve as a MM-preferential dependency in CRISPR gene editing studies, is also described. Overall design: LP1 cells were stably transduced with a construct for dCas9-Vp64 after lentiviral sgRNA transduction packaged with the pXPR-502 construct (RRID:Addgene_96923). LP1 cells transduced with POU2AF1 sgRNA for CRISPR-based activation of POU2AF1or control OR genes. The following sgRNA were used: PANK1_1 CACCGACGAGTTTCAACATG, PANK1_2 AGTTCTCTGGGCTTGCAGAG, POU2AF1_1 GCGCACAGTGGGGTGACAGG, POU2AF1_2 TGGCTGCAGAAACGTTGCAC, OR12D2 GAATGTCTGTCACTCCCAAG, OR6S1 GACCTGCAATTGGATAAACT

多发性骨髓瘤（multiple myeloma, MM）是一类不可治愈的浆细胞（plasma cell, PC）肿瘤，目前推动其临床进展的治疗手段存在两大局限：一是应用范围仅局限于MM/浆细胞肿瘤领域；二是无法靶向MM中的特异性致癌突变。此类治疗药物所靶向的是浆细胞生物学关键通路，但在绝大多数其他谱系的恶性或正常细胞中基本非必需。本研究通过在MM细胞系与数百种非MM细胞系中开展全基因组CRISPR基因编辑（CRISPR gene editing）实验，系统解析了MM的谱系偏好性分子依赖特征，最终鉴定出一组基因：相较于其他恶性肿瘤，这些基因的敲除对MM细胞适合度的影响更为显著或反复出现。其中部分基因此前已被证实与MM相关，另有部分尚未被关联至MM发病机制，它们分别编码转录因子、染色质修饰因子、内质网组分、代谢调控因子或信号分子。本数据集涵盖两类转录谱分析结果：一是对MM细胞系开展CRISPR激活（CRISPR activation）以靶向骨髓瘤偏好性依赖基因POU2AF1的转录谱；二是另一基因PANK1的CRISPR激活转录谱——该基因在CRISPR基因编辑研究中并未表现出骨髓瘤偏好性依赖特征。总体实验设计如下：将LP1细胞先使用包装有pXPR-502构建体（RRID:Addgene_96923）的慢病毒完成单向导RNA（single guide RNA, sgRNA）转导，随后将携带dCas9-Vp64的表达构建体稳定转导至LP1细胞。将LP1细胞分为若干实验组与对照组，分别转导靶向POU2AF1的sgRNA以实现CRISPR介导的POU2AF1激活，或转导对照开放读码框（open reading frame, OR）基因对应的sgRNA。本研究所用sgRNA序列如下：
PANK1_1：CACCGACGAGTTTCAACATG
PANK1_2：AGTTCTCTGGGCTTGCAGAG
POU2AF1_1：GCGCACAGTGGGGTGACAGG
POU2AF1_2：TGGCTGCAGAAACGTTGCAC
OR12D2：GAATGTCTGTCACTCCCAAG
OR6S1：GACCTGCAATTGGATAAACT