Abstract A013: Induced pluripotent stem cells derived from normal human esophageal epithelial cells identify transcription factor networks contributing to esophageal carcinogenesis
Authors: Wang Haitao , Wang Ruihong , Prothro Katherine P. , Xi Sichuan , Hou Weilong , Wu Xinwei , Tolunay Tuana , Shukla Vivek , Zhang Mary R. , Shiffka Stephanie J. , Gara Sudheer , Schrump David S. 
Published: December 2022

Esophageal cancer (EsC) is the sixth leading cause of cancer-related mortality worldwide. Esophageal squamous cell cancers (ESCC) typically arise in the upper and mid-esophagus, whereas esophageal adenocarcinomas (EAC) arise in the distal esophagus and gastroesophageal junction. Presently, epigenetic mechanisms contributing to initiation, progression, and dissemination of EsC have not been fully elucidated. The present study was undertaken to determine if induced pluripotent stem cells (iPSCs) derived from normal esophageal epithelial cells (Eso-iPSCs), EsC cell lines cultured in stemness enriched conditions, and cancer stem-like cells isolated from primary EsC specimens could be used to identify unique primitive stem-like transcription factor networks associated with epigenetic plasticity, chemoresistance, and metastatic potential of EsC cells. RNA-seq analysis demonstrated that genes differentially expressed in Eso-iPSC overlapped with transcriptome signatures in lung-iPSC (Lu-iPSC) which we previously generated to identify novel therapeutic targets in lung cancers; similar to Lu-iPSC, Eso-iPSC transcriptome signatures overlapped considerably more with small cell lung cancers (SCLC) compared to non-small cell lung cancers (NSCLC), possibly reflecting greater stemness in SCLC. We next compared transcriptome signatures of Eso-iPSC with stem-like-EAC enrichment models (cell lines and PDX). 6% and 8% of differentially expressed genes in Eso-iPSC uniquely overlapped with EAC or ESCC lines, respectively, whereas 24% were common to Eso-iPSC, EAC cells, and ESCC cells. Culturing of EAC cells on matrigel or propagation of EAC as primary patient derived xenografts increased commonalities of Eso-iPSC and EAC transcriptome signatures. Lastly, we compared transcriptomes of Eso-iPSC with Barrett’s esophagus (BE; a premalignant condition in which the squamous epithelium of the distal esophagus is replaced by metaplastic columnar epithelial cells) and EAC samples. By combining and stringently filtering transcriptome, ATAC-seq, DNA methylome, and ChIP-seq datasets for tissue- and disease-specific signatures, we identified several potentially druggable, master TFs mediating stemness/plasticity, chemoresistance, and metastatic potential which are shared between EsC lines and primary tumor specimens. Enrichment techniques promoted acquisition of more stem-like states in cultured EAC cells as reflected in multi-omic signatures of these cells relative to Eso-iPSC and primary EAC specimens. Collectively, these findings establish proof of principal for our experimental approach which is now being used to further characterize epigenetic mechanisms contributing to esophageal carcinogenesis and to identify novel targets for EsC therapy.

Citation Format: Haitao Wang, Ruihong Wang, Katherine P. Prothro, Sichuan Xi, Weilong Hou, Xinwei Wu, Tuana Tolunay, Vivek Shukla, Mary R. Zhang, Stephanie J. Shiffka, Sudheer Gara, David S. Schrump. Induced pluripotent stem cells derived from normal human esophageal epithelial cells identify transcription factor networks contributing to esophageal carcinogenesis. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr A013.