Intra-tumor hypoxia is a common feature in many solid cancers. Although transcriptional targets of hypoxia-inducible factors (HIFs) have been well characterized, alternative splicing or processing of pre-mRNA transcripts which occurs during hypoxia and subsequent HIF stabilization is much less understood. Here, we identify many HIF-dependent alternative splicing events after whole transcriptome sequencing in pancreatic cancer cells exposed to hypoxia with and without downregulation of the aryl hydrocarbon receptor nuclear translocator (ARNT), a protein required for HIFs to form a transcriptionally active dimer. We correlate the discovered hypoxia-driven events with available sequencing data from pan-cancer TCGA patient cohorts to select a narrow set of putative biologically relevant splice events for experimental validation. We validate a small set of candidate HIF-dependent alternative splicing events in multiple human gastrointestinal cancer cell lines as well as patient-derived human pancreatic cancer organoids. Lastly, we report the discovery of a HIF-dependent mechanism to produce a hypoxia-dependent, long and coding isoform of the UDP-N-acetylglucosamine transporter SLC35A3.

肿瘤内缺氧是许多实体癌的共同特征。尽管缺氧诱导因子 (HIF) 的转录靶标已得到很好的表征，但在缺氧和随后的 HIF 稳定期间发生的前 mRNA 转录本的选择性剪接或加工却知之甚少。在这里，我们在暴露于缺氧的胰腺癌细胞中，在芳烃受体核易位蛋白（ARNT）下调或不下调的情况下进行全转录组测序后，发现了许多依赖于 HIF 的选择性剪接事件，ARNT 是 HIF 形成转录活性二聚体所需的蛋白质。我们将发现的缺氧驱动事件与泛癌 TCGA 患者队列的可用测序数据相关联，以选择一组狭窄的假定的生物学相关剪接事件进行实验验证。我们在多种人类胃肠道癌细胞系以及患者来源的人类胰腺癌类器官中验证了一小组候选 HIF 依赖性选择性剪接事件。最后，我们报告了 HIF 依赖性机制的发现，该机制可产生缺氧依赖性长编码 UDP -N-乙酰氨基葡萄糖转运蛋白 SLC35A3 亚型。