Background & Aims

Chromatin architecture governs cell lineages by regulating the specific gene expression; however, its role in the diversity of cancer development remains unknown. Among pancreatic cancers, pancreatic ductal adenocarcinoma (PDAC) and intraductal papillary mucinous neoplasms (IPMN) with an associated invasive carcinoma (IPMNinv) arise from 2 distinct precursors, and their fundamental differences remain obscure. Here, we aimed to assess the difference of chromatin architecture regulating the transcriptional signatures or biological features in pancreatic cancers.

Methods

We established 28 human organoids from distinct subtypes of pancreatic tumors, including IPMN, IPMNinv, and PDAC. We performed exome sequencing (seq), RNA-seq, assay for transposase-accessible chromatin-seq, chromatin immunoprecipitation-seq, high-throughput chromosome conformation capture, and phenotypic analyses with short hairpin RNA or clustered regularly interspaced short palindromic repeats interference.

Results

Established organoids successfully reproduced the histology of primary tumors. IPMN and IPMNinv organoids harbored GNAS, RNF43, or KLF4 mutations and showed the distinct expression profiles compared with PDAC. Chromatin accessibility profiles revealed the gain of stomach-specific open regions in IPMN and the pattern of diverse gastrointestinal tissues in IPMNinv. In contrast, PDAC presented an impressive loss of accessible regions compared with normal pancreatic ducts. Transcription factor footprint analysis and functional assays identified that MNX1 and HNF1B were biologically indispensable for IPMN lineages. The upregulation of MNX1 was specifically marked in the human IPMN lineage tissues. The MNX1-HNF1B axis governed a set of genes, including MYC, SOX9, and OLFM4, which are known to be essential for gastrointestinal stem cells. High-throughput chromosome conformation capture analysis suggested the HNF1B target genes to be 3-dimensionally connected in the genome of IPMNinv.

Conclusions

Our organoid analyses identified the MNX1-HNF1B axis to be biologically significant in IPMN lineages.

中文翻译：

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MNX1-HNF1B 轴对于导管内乳头状粘液性肿瘤谱系是必不可少的

背景与目标

染色质结构通过调节特定基因表达来控制细胞谱系；然而，它在癌症发展多样性中的作用仍然未知。在胰腺癌中，胰腺导管腺癌 (PDAC) 和导管内乳头状粘液性肿瘤 (IPMN) 与相关的浸润性癌 (IPMNinv) 起源于 2 个不同的前体，它们的基本区别仍然不清楚。在这里，我们旨在评估染色质结构在胰腺癌中调节转录特征或生物学特征的差异。

方法

我们从不同的胰腺肿瘤亚型（包括 IPMN、IPMNinv 和 PDAC）中建立了 28 个人类类器官。我们进行了外显子组测序 (seq)、RNA-seq、转座酶可及染色质-seq 测定、染色质免疫沉淀-seq、高通量染色体构象捕获，以及使用短发夹 RNA 或成簇的规则间隔短回文重复干扰的表型分析。

结果

已建立的类器官成功地再现了原发性肿瘤的组织学。IPMN 和 IPMNinv 类器官具有GNAS、RNF43或KLF4突变，并且与 PDAC 相比显示出不同的表达谱。染色质可及性概况揭示了 IPMN 中胃特异性开放区域的增加以及 IPMNinv 中不同胃肠道组织的模式。相比之下，与正常胰管相比，PDAC 表现出可及区域的显着损失。转录因子足迹分析和功能分析确定 MNX1 和 HNF1B 在生物学上对于 IPMN 谱系是必不可少的。MNX1 的上调在人类 IPMN 谱系组织中被特别标记。MNX1-HNF1B 轴控制着一组基因，包括MYC、SOX9和OLFM4，已知它们对胃肠道干细胞至关重要。高通量染色体构象捕获分析表明，HNF1B 靶基因在 IPMNinv 的基因组中是三维连接的。

结论

我们的类器官分析确定 MNX1-HNF1B 轴在 IPMN 谱系中具有生物学意义。