Literature DB >> 33972779

Reprogramming of the esophageal squamous carcinoma epigenome by SOX2 promotes ADAR1 dependence.

Zhong Wu1,2, Jin Zhou1,2, Xiaoyang Zhang1,2,3, Zhouwei Zhang1,2, Yingtian Xie4, Jie Bin Liu1, Zandra V Ho2, Arpit Panda1,5, Xintao Qiu4, Paloma Cejas4, Israel Cañadas1,6, Fahire Goknur Akarca1, James M McFarland2, Ankur K Nagaraja1,2,7, Louisa B Goss1, Nikolas Kesten1,4, Longlong Si8, Klothilda Lim4, Yanli Liu3, Yanxi Zhang1, Ji Yeon Baek1, Yang Liu1,2, Deepa T Patil9, Jonathan P Katz10, Josephine Hai1, Chunyang Bao1,2, Matthew Stachler1,9, Jun Qi11, Jeffrey J Ishizuka1,2, Hiroshi Nakagawa12, Anil K Rustgi12, Kwok-Kin Wong13, Matthew Meyerson1,2, David A Barbie1,2, Myles Brown1,4, Henry Long4, Adam J Bass14,15,16.   

Abstract

Esophageal squamous cell carcinomas (ESCCs) harbor recurrent chromosome 3q amplifications that target the transcription factor SOX2. Beyond its role as an oncogene in ESCC, SOX2 acts in development of the squamous esophagus and maintenance of adult esophageal precursor cells. To compare Sox2 activity in normal and malignant tissue, we developed engineered murine esophageal organoids spanning normal esophagus to Sox2-induced squamous cell carcinoma and mapped Sox2 binding and the epigenetic and transcriptional landscape with evolution from normal to cancer. While oncogenic Sox2 largely maintains actions observed in normal tissue, Sox2 overexpression with p53 and p16 inactivation promotes chromatin remodeling and evolution of the Sox2 cistrome. With Klf5, oncogenic Sox2 acquires new binding sites and enhances activity of oncogenes such as Stat3. Moreover, oncogenic Sox2 activates endogenous retroviruses, inducing expression of double-stranded RNA and dependence on the RNA editing enzyme ADAR1. These data reveal SOX2 functions in ESCC, defining targetable vulnerabilities.

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Year:  2021        PMID: 33972779      PMCID: PMC9124436          DOI: 10.1038/s41588-021-00859-2

Source DB:  PubMed          Journal:  Nat Genet        ISSN: 1061-4036            Impact factor:   41.307


  82 in total

1.  TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets.

Authors:  Ying Jin; Oliver H Tam; Eric Paniagua; Molly Hammell
Journal:  Bioinformatics       Date:  2015-07-23       Impact factor: 6.937

2.  Super-enhancers in the control of cell identity and disease.

Authors:  Denes Hnisz; Brian J Abraham; Tong Ihn Lee; Ashley Lau; Violaine Saint-André; Alla A Sigova; Heather A Hoke; Richard A Young
Journal:  Cell       Date:  2013-10-10       Impact factor: 41.582

3.  An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues.

Authors:  M Ryan Corces; Alexandro E Trevino; Emily G Hamilton; Peyton G Greenside; Nicholas A Sinnott-Armstrong; Sam Vesuna; Ansuman T Satpathy; Adam J Rubin; Kathleen S Montine; Beijing Wu; Arwa Kathiria; Seung Woo Cho; Maxwell R Mumbach; Ava C Carter; Maya Kasowski; Lisa A Orloff; Viviana I Risca; Anshul Kundaje; Paul A Khavari; Thomas J Montine; William J Greenleaf; Howard Y Chang
Journal:  Nat Methods       Date:  2017-08-28       Impact factor: 28.547

4.  Loss of ADAR1 in tumours overcomes resistance to immune checkpoint blockade.

Authors:  Jeffrey J Ishizuka; Robert T Manguso; Collins K Cheruiyot; Kevin Bi; Arpit Panda; Arvin Iracheta-Vellve; Brian C Miller; Peter P Du; Kathleen B Yates; Juan Dubrot; Ilana Buchumenski; Dawn E Comstock; Flavian D Brown; Austin Ayer; Ian C Kohnle; Hans W Pope; Margaret D Zimmer; Debattama R Sen; Sarah K Lane-Reticker; Emily J Robitschek; Gabriel K Griffin; Natalie B Collins; Adrienne H Long; John G Doench; David Kozono; Erez Y Levanon; W Nicholas Haining
Journal:  Nature       Date:  2018-12-17       Impact factor: 49.962

5.  limma powers differential expression analyses for RNA-sequencing and microarray studies.

Authors:  Matthew E Ritchie; Belinda Phipson; Di Wu; Yifang Hu; Charity W Law; Wei Shi; Gordon K Smyth
Journal:  Nucleic Acids Res       Date:  2015-01-20       Impact factor: 16.971

Review 6.  Reparative inflammation takes charge of tissue regeneration.

Authors:  Michael Karin; Hans Clevers
Journal:  Nature       Date:  2016-01-21       Impact factor: 49.962

7.  SOX2 and p63 colocalize at genetic loci in squamous cell carcinomas.

Authors:  Hideo Watanabe; Qiuping Ma; Shouyong Peng; Guillaume Adelmant; Danielle Swain; Wenyu Song; Cameron Fox; Joshua M Francis; Chandra Sekhar Pedamallu; David S DeLuca; Angela N Brooks; Su Wang; Jianwen Que; Anil K Rustgi; Kwok-kin Wong; Keith L Ligon; X Shirley Liu; Jarrod A Marto; Matthew Meyerson; Adam J Bass
Journal:  J Clin Invest       Date:  2014-03-03       Impact factor: 14.808

8.  Adenosine-to-inosine RNA editing mediated by ADARs in esophageal squamous cell carcinoma.

Authors:  Yan-Ru Qin; Jun-Jing Qiao; Tim Hon Man Chan; Ying-Hui Zhu; Fang-Fang Li; Haibo Liu; Jing Fei; Yan Li; Xin-Yuan Guan; Leilei Chen
Journal:  Cancer Res       Date:  2013-12-03       Impact factor: 12.701

9.  ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide.

Authors:  Jason D Buenrostro; Beijing Wu; Howard Y Chang; William J Greenleaf
Journal:  Curr Protoc Mol Biol       Date:  2015-01-05

10.  Tumor innate immunity primed by specific interferon-stimulated endogenous retroviruses.

Authors:  Israel Cañadas; Rohit Thummalapalli; Jong Wook Kim; Shunsuke Kitajima; Russell William Jenkins; Camilla Laulund Christensen; Marco Campisi; Yanan Kuang; Yanxi Zhang; Evisa Gjini; Gao Zhang; Tian Tian; Debattama Rai Sen; Diana Miao; Yu Imamura; Tran Thai; Brandon Piel; Hideki Terai; Amir Reza Aref; Timothy Hagan; Shohei Koyama; Masayuki Watanabe; Hideo Baba; Anika Elise Adeni; Christine Anne Lydon; Pablo Tamayo; Zhi Wei; Meenhard Herlyn; Thanh Uyen Barbie; Ravindra Uppaluri; Lynnette Marie Sholl; Ewa Sicinska; Jacob Sands; Scott Rodig; Kwok Kin Wong; Cloud Peter Paweletz; Hideo Watanabe; David Allen Barbie
Journal:  Nat Med       Date:  2018-07-23       Impact factor: 53.440

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  11 in total

Review 1.  ADAR1 and its implications in cancer development and treatment.

Authors:  Allison R Baker; Frank J Slack
Journal:  Trends Genet       Date:  2022-04-19       Impact factor: 11.821

2.  Active endogenous retroviral elements in human pluripotent stem cells play a role in regulating host gene expression.

Authors:  Tianzhe Zhang; Ran Zheng; Mao Li; Chenchao Yan; Xianchun Lan; Bei Tong; Pei Lu; Wei Jiang
Journal:  Nucleic Acids Res       Date:  2022-05-20       Impact factor: 19.160

3.  Establishing transgenic murine esophageal organoids.

Authors:  Kyung-Pil Ko; Jie Zhang; Jae-Il Park
Journal:  STAR Protoc       Date:  2022-04-21

4.  Identifying a confused cell identity for esophageal squamous cell carcinoma.

Authors:  Xiangyu Pan; Jian Wang; Linjie Guo; Feifei Na; Jiajia Du; Xuelan Chen; Ailing Zhong; Lei Zhao; Lu Zhang; Mengsha Zhang; Xudong Wan; Manli Wang; Hongyu Liu; Siqi Dai; Ping Tan; Jingyao Chen; Yu Liu; Bing Hu; Chong Chen
Journal:  Signal Transduct Target Ther       Date:  2022-04-13

5.  Organoid models combined with genome engineering and epigenome studies to define SOX2 function evolution in esophageal squamous cell carcinoma.

Authors:  Fei-Yu Diao
Journal:  Thorac Cancer       Date:  2021-08-29       Impact factor: 3.500

6.  Epigenetic Regulator KDM4D Restricts Tumorigenesis via Modulating SYVN1/HMGB1 Ubiquitination Axis in Esophageal Squamous Cell Carcinoma.

Authors:  Wenjian Yao; Jianjun Wang; Li Zhu; Xiangbo Jia; Lei Xu; Xia Tian; Shuai Hu; Sen Wu; Li Wei
Journal:  Front Oncol       Date:  2021-11-08       Impact factor: 6.244

Review 7.  It's Getting Complicated-A Fresh Look at p53-MDM2-ARF Triangle in Tumorigenesis and Cancer Therapy.

Authors:  Che-Pei Kung; Jason D Weber
Journal:  Front Cell Dev Biol       Date:  2022-01-26

Review 8.  Genomic and Epigenomic Characterization of Tumor Organoid Models.

Authors:  Chehyun Nam; Benjamin Ziman; Megha Sheth; Hua Zhao; De-Chen Lin
Journal:  Cancers (Basel)       Date:  2022-08-24       Impact factor: 6.575

9.  Proteotranscriptomics of ocular adnexal B-cell lymphoma reveals an oncogenic role of alternative splicing and identifies a diagnostic marker.

Authors:  Jiahao Shi; Tianyu Zhu; Huimin Lin; Zhen Liu; Min Zhou; Ziyao Yu; Xiaowen Zhou; Xin Song; Yefei Wang; Renbing Jia; Xianqun Fan; Yixiong Zhou
Journal:  J Exp Clin Cancer Res       Date:  2022-07-30

10.  Non-genetic stratification reveals epigenetic heterogeneity and identifies vulnerabilities of glycolysis addiction in lung adenocarcinoma subtype.

Authors:  Xuming Song; Te Zhang; Hanlin Ding; Yipeng Feng; Wenmin Yang; Xuewen Yin; Bing Chen; Yingkuan Liang; Qixing Mao; Wenjie Xia; Guiping Yu; Lin Xu; Gaochao Dong; Feng Jiang
Journal:  Oncogenesis       Date:  2022-10-10       Impact factor: 6.524

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