RNA-seq data for LS180 and NCI-H358 Cancer cell lines

Despite exciting developments in cancer immunotherapy, its broad application is limited by the paucity of targetable antigens on the tumor cell surface. As an intrinsic cellular pathway, nonsense-mediated decay (NMD) conceals neoantigens through the destruction of the RNA products from genes harboring truncating mutations. We developed and conducted a high throughput screen, based on the ratiometric analysis of transcripts, to identify critical mediators of NMD. This screen revealed disruption of kinase SMG1’s phosphorylation of UPF1 as a potent disruptor of NMD. This led us to design a novel SMG1 inhibitor, KVS0001, that elevates the expression of transcripts and proteins resulting from truncating mutations in vivo and in vitro. Most importantly, KVS0001 concomitantly increased the presentation of immune-targetable HLA class I-associated peptides from NMD-downregulated proteins on the surface of cancer cells. KVS0001 provides new opportunities for studying NMD and the diseases in which..., Whole transcriptome RNA-seq LS180 or NCI-H358 cells were run in biological duplicate, treated with DMSO or 5µM LY3023414. For RNA extraction, cells were pelleted, frozen in liquid nitrogen, and stored at -80oC until RNA extraction. RNA extraction was performed using a Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Maryland, USA, Cat# 80204) per manufacturer’s instruction with cell homogenization and lysis in RLT buffer with a QIAshredder (Qiagen, Maryland, USA, Cat# 79656). RNA quality control using Agilent Tapestation 2200 (Agilent, California, USA, Cat# G2964AA) and the Agilent RNA ScreenTape (Agilent, California, USA, Cat# 5067- 5576) with Agilent RNA ScreenTape Sample Buffer and Ladder (Agilent, California, USA, Cat# 5067- 5577, Cat# 5067- 5578) per manufacturer’s instruction. Library prep using Illumina RNA library prep kit (Illumina, California, USA, Cat #RS-122-2001) and sequenced on an Illumina HiSeq 4000 150 cycle paired-end using manufacturer’s instructions. The data provided here i..., , # RNA-seq data for LS180 and NCI-H358 Cancer cell lines [https://doi.org/10.5061/dryad.69p8cz9dj](https://doi.org/10.5061/dryad.69p8cz9dj) ## Description of the data and file structure Data is RNA-seq fastq files from paired end 150 cycle NGS on an Illumina Hiseq 4000. There are two cell lines represented, LS180 and NCI-H358. Each were treated with either DMSO or the drug LY3023414. Both cell lines were treated, library prepared, and sequenced as biological replicates in duplicate, as indicated by a -1 and -2 in their file names. Both index and read files are included in this data set. ### Files and variables #### File: 9-H358-LY-1\_S9\_L002\_I1\_001.fastq.gz **Description:** NCI-H358 cell line treated with LY3023414 biological replicate 1 #### File: 10-H358-LY-2\_S10\_L002\_I1\_001.fastq.gz **Description:** NCI-H358 cell line treated with LY3023414 biological replicate 2 #### File: 11-H358-DMSO-1\_S11\_L002\_I1\_001.fastq.gz **Description:** NCI-H358 cell line treated with DM...尽管癌症免疫治疗领域已取得令人振奋的进展，但其广泛应用仍受限于肿瘤细胞表面可靶向抗原的匮乏。作为一种内在细胞通路，无义介导的mRNA降解（nonsense-mediated decay, NMD）可通过降解携带截短突变的基因所产生的RNA产物，从而隐藏新抗原（neoantigens）。我们基于转录本比例分析方法开发并开展了一项高通量筛选，以鉴定NMD的关键调控介质。该筛选结果显示，阻断激酶SMG1对UPF1的磷酸化过程，可强效抑制NMD通路活性。基于此发现，我们设计了一种新型SMG1抑制剂KVS0001，该抑制剂可在体内外提升携带截短突变的基因所产生的转录本与蛋白质的表达水平。尤为重要的是，KVS0001可同时增加癌细胞表面由NMD下调蛋白所产生的、可被免疫靶向的人类白细胞抗原I类（HLA class I）结合肽段的呈递。KVS0001为研究NMD及其相关疾病提供了新的研究思路。全转录组RNA测序（Whole transcriptome RNA-seq） 本实验采用LS180与NCI-H358细胞系进行生物学重复实验，每组设置二重复，分别用二甲基亚砜（DMSO）或5µM的LY3023414进行处理。RNA提取前，将细胞离心收集沉淀，置于液氮中速冻后保存于-80℃直至提取。RNA提取采用Qiagen AllPrep DNA/RNA Mini试剂盒（美国马里兰州Qiagen，货号80204），严格按照制造商说明书操作，使用RLT缓冲液结合QIAshredder（美国马里兰州Qiagen，货号79656）完成细胞均质化与裂解。RNA质量控制采用Agilent Tapestation 2200系统（美国加利福尼亚州Agilent，货号G2964AA），搭配Agilent RNA ScreenTape（美国加利福尼亚州Agilent，货号5067-5576）、Agilent RNA ScreenTape样品缓冲液与分子量标准（美国加利福尼亚州Agilent，货号5067-5577、5067-5578），严格遵循制造商指导流程进行。文库构建采用Illumina RNA文库制备试剂盒（美国加利福尼亚州Illumina，货号RS-122-2001），并使用Illumina HiSeq 4000平台进行150循环双端测序，操作流程严格遵循制造商说明书。本次提供的相关数据…… # LS180与NCI-H358癌细胞系RNA测序数据 https://doi.org/10.5061/dryad.69p8cz9dj ## 数据与文件结构说明 本数据集包含基于Illumina HiSeq 4000平台的150循环双端下一代测序（next-generation sequencing, NGS）所得的RNA测序fastq文件。实验涉及两种癌细胞系：LS180与NCI-H358，每组细胞分别经DMSO或LY3023414药物处理。两种细胞系均完成处理、文库构建与测序，且均设置生物学重复二重复，文件名中的-1与-2即对应这两个重复样本。本数据集同时包含索引文件与测序读段文件。 ### 文件与变量说明 #### 文件：9-H358-LY-1_S9_L002_I1_001.fastq.gz **描述：** 经LY3023414处理的NCI-H358细胞系生物学重复1样本 #### 文件：10-H358-LY-2_S10_L002_I1_001.fastq.gz **描述：** 经LY3023414处理的NCI-H358细胞系生物学重复2样本 #### 文件：11-H358-DMSO-1_S11_L002_I1_001.fastq.gz **描述：** 经DMSO处理的NCI-H358细胞系生物学重复1