From the Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh, Pittsburgh, PA.
Department of Pediatrics, University of Minnesota Medical Center and Masonic Children's Hospital.
Pancreas. 2020 Sep;49(8):1037-1043. doi: 10.1097/MPA.0000000000001607.
To determine if RNA collected from pancreatic tissue, without the use of RNAlater, is useful for RNA sequencing (RNA-seq) despite degradation, and if so, then, via RNA-seq analysis, how does gene expression vary between pancreatitis etiologies.
Data were assessed in 2 dimensions, based on RNA-seq signal shape assessed by RSeQC v.2.6.4 and RNA expression after accounting for different degrees of degradation.
Six measures of RNA characteristics (median RNA fragment size, reads per million kilobases saturation, transcript integrity number, distribution of hexamers, percentage of nucleotides that are guanine or cytosine, and duplicated reads) were significantly different between hereditary pancreatitis and idiopathic pancreatitis. Differential expression analysis revealed that 150 genes were differentially expressed between hereditary and idiopathic etiologies, 197 genes were differentially expressed between alcoholic and idiopathic etiologies, and 200 genes were differentially expressed between alcoholic and hereditary etiologies. We then determined that many enriched pathways between hereditary and idiopathic etiologies are related to the matrisome, and many of the enriched pathways between alcoholic and idiopathic etiology or hereditary etiology are related to ion transport.
We found distinct RNA-seq signals between different pancreatitis etiologies in both of the dimensions in critical pathways for pancreas biology.
确定在不使用 RNAlater 的情况下，从胰腺组织中提取的 RNA 是否可用于 RNA 测序 (RNA-seq)，即使存在降解，以及如果可以，那么通过 RNA-seq 分析，不同胰腺炎病因之间的基因表达如何变化。
根据 RSeQC v.2.6.4 评估的 RNA-seq 信号形状和不同程度降解后的 RNA 表达，从 2 个维度评估数据。
在遗传性胰腺炎和特发性胰腺炎之间，有 6 个 RNA 特征测量值（中位数 RNA 片段大小、每百万千碱基的读频数饱和度、转录完整性数、六聚体分布、鸟嘌呤或胞嘧啶核苷酸百分比和重复读）有显著差异。差异表达分析显示，150 个基因在遗传性和特发性病因之间存在差异表达，197 个基因在酒精性和特发性病因之间存在差异表达，200 个基因在酒精性和遗传性病因之间存在差异表达。然后，我们确定遗传性和特发性病因之间许多富集的途径与基质体有关，酒精性和特发性病因或遗传性病因之间许多富集的途径与离子转运有关。
我们在关键胰腺生物学途径的两个维度上发现了不同胰腺炎病因之间的明显 RNA-seq 信号。
