Abstract PO-067: A multi-omics study in patient-derived organoids reveals MNX1-HNF1B axis to be indispensable for intraductal mucinous papillary neoplasm lineages
Authors: Kato Hiroyuki , Tateishi Keisuke , Yamamoto Keisuke , Iwadate Dousuke , Fujiwara Hiroaki , Nakatsuka Takuma , Miyabayashi Koji , Kudo Yotaro , Hideaki Ijichi , Koike Kazuhiko , Fujishiro Mitsuhiro 
Published: November 2021

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 invasive carcinoma with an associated intraductal papillary mucinous neoplasms (invasive IPMNs) arise from two distinct precursors, and their fundamental differences remain obscure. Here, we hypothesized that chromatin profiles may clarify their intrinsic molecular features. We originally established 28 human organoids from distinct subtypes of pancreatic tumors, including IPMN, invasive IPMN, and PDAC as well as from normal ductal cells and performed exome-seq, RNA-seq, ATAC-seq, ChIP-seq, Hi-C, and phenotypic analyses with shRNA or CRISPR interference. Established organoids successfully reproduced the histology of primary tumors. IPMN and invasive IPMN organoids specifically harbored GNAS, RNF43, and KLF4 mutations and showed the distinct lineage related expression profiles compared to PDAC. In addition, chromatin accessibility profiles well stratified the respective tumor groups. Notably, this analysis supported the histological features of tumor subtypes; gastric IPMN gained the stomach-specific accessible regions and the accessible pattern of invasive IPMN linked to diverse gastrointestinal tissues. In contrast, PDAC was characterized by the significant loss of chromatin accessibility seen in normal pancreatic ductal cells. Footprint analysis of transcription factors (TFs) identified specific TFs that are enriched in each tumor subtype. Of note we found the footprint of HNF1B to be active in IPMN lineages but not in PDAC. To address its biological significance, we analyzed the effects of HNF1B by knockdown (KD) experiments and revealed that HNF1B is biologically indispensable for IPMN lineages. We further identified MNX1 as an upstream regulator of HNF1B expression, another TF expressed in multipotent pancreatic progenitor cells. ChIP experiment revealed the enriched binding of MNX1 on the promoter elements of HNF1B in invasive IPMN. Importantly, KD or CRISPR interference of MNX1 impaired the survival of the organoids from invasive IPMN. Moreover, the correlated and high expression patterns of MNX1 and HNF1B in IPMN lineages were validated in a set of human tissues. To identify the common downstream genes of MNX1 and HNF1B, we analyzed RNA-seq and ATAC-seq after KD of the two genes. We found that MNX1-HNF1B axis governed a set of genes including MYC, SOX9, and OLFM4, which are known to regulate stem cell properties in gastrointestinal epithelium. Lastly, to get a broader view of chromatin architecture in these tumors, we performed Hi-C. We found that HNF1B target genes to be three-dimensionally condensed in the genome of invasive IPMN but not in that of PDAC, supporting the functional importance of those genes in invasive IPMN. Collectively, our organoid analyses unraveled the different lineage related chromatin structures correlating to the specific biological behaviors in pancreatic tumor subtypes.

Citation Format: Hiroyuki Kato, Keisuke Tateishi, Keisuke Yamamoto, Dousuke Iwadate, Hiroaki Fujiwara, Takuma Nakatsuka, Koji Miyabayashi, Yotaro Kudo, Ijichi Hideaki, Kazuhiko Koike, Mitsuhiro Fujishiro. A multi-omics study in patient-derived organoids reveals MNX1-HNF1B axis to be indispensable for intraductal mucinous papillary neoplasm lineages [abstract]. In: Proceedings of the AACR Virtual Special Conference on Pancreatic Cancer; 2021 Sep 29-30. Philadelphia (PA): AACR; Cancer Res 2021;81(22 Suppl):Abstract nr PO-067.