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ASPSCR1-TFE3 reprograms transcription by organizing enhancer loops around hexameric VCP/p97.
Pozner A, Li L, Verma SP, Wang S, Barrott JJ, Nelson ML, Yu JSE, Negri GL, Colborne S, Hughes CS, Zhu JF, Lambert SL, Carroll LS, Smith-Fry K, Stewart MG, Kannan S, Jensen B, John CM, Sikdar S, Liu H, Dang NH, Bourdage J, Li J, Vahrenkamp JM, Mortenson KL, Groundland JS, Wustrack R, Senger DL, Zemp FJ, Mahoney DJ, Gertz J, Zhang X, Lazar AJ, Hirst M, Morin GB, Nielsen TO, Shen PS, Jones KB. Pozner A, et al. Among authors: zhang x. Nat Commun. 2024 Feb 7;15(1):1165. doi: 10.1038/s41467-024-45280-5. Nat Commun. 2024. PMID: 38326311 Free PMC article.
Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas.
Schaub FX, Dhankani V, Berger AC, Trivedi M, Richardson AB, Shaw R, Zhao W, Zhang X, Ventura A, Liu Y, Ayer DE, Hurlin PJ, Cherniack AD, Eisenman RN, Bernard B, Grandori C; Cancer Genome Atlas Network. Schaub FX, et al. Among authors: zhang x. Cell Syst. 2018 Mar 28;6(3):282-300.e2. doi: 10.1016/j.cels.2018.03.003. Cell Syst. 2018. PMID: 29596783 Free PMC article.
A predominant enhancer co-amplified with the SOX2 oncogene is necessary and sufficient for its expression in squamous cancer.
Liu Y, Wu Z, Zhou J, Ramadurai DKA, Mortenson KL, Aguilera-Jimenez E, Yan Y, Yang X, Taylor AM, Varley KE, Gertz J, Choi PS, Cherniack AD, Chen X, Bass AJ, Bailey SD, Zhang X. Liu Y, et al. Among authors: zhang x. Nat Commun. 2021 Dec 8;12(1):7139. doi: 10.1038/s41467-021-27055-4. Nat Commun. 2021. PMID: 34880227 Free PMC article.
Illuminating the noncoding genome in cancer.
Zhang X, Meyerson M. Zhang X, et al. Nat Cancer. 2020 Sep;1(9):864-872. doi: 10.1038/s43018-020-00114-3. Epub 2020 Sep 14. Nat Cancer. 2020. PMID: 35121955 Free PMC article. Review.
3D genomic analysis reveals novel enhancer-hijacking caused by complex structural alterations that drive oncogene overexpression.
Mortenson KL, Dawes C, Wilson ER, Patchen NE, Johnson HE, Gertz J, Bailey SD, Liu Y, Varley KE, Zhang X. Mortenson KL, et al. Among authors: zhang x. bioRxiv [Preprint]. 2024 Jun 21:2024.01.23.576965. doi: 10.1101/2024.01.23.576965. bioRxiv. 2024. Update in: Nat Commun. 2024 Jul 20;15(1):6130. doi: 10.1038/s41467-024-50387-w PMID: 38328209 Free PMC article. Updated. Preprint.
HiChIP-Based Epigenomic Footprinting Identifies a Promoter Variant of UXS1 That Confers Genetic Susceptibility to Gastroesophageal Cancer.
Gnanapragasam A, Kirbizakis E, Li A, White KH, Mortenson KL, Cavalcante de Moura J, Jawhar W, Yan Y, Falter R, Russett C, Giannias B, Camilleri-Broët S, Bertos N, Cools-Lartigue J, Garzia L, Sangwan V, Ferri L, Zhang X, Bailey SD. Gnanapragasam A, et al. Among authors: zhang x. Cancer Res. 2024 Jul 15;84(14):2377-2389. doi: 10.1158/0008-5472.CAN-23-2397. Cancer Res. 2024. PMID: 38748784 Free PMC article.
Multi-Omics Analysis Identifies MGA as a Negative Regulator of the MYC Pathway in Lung Adenocarcinoma.
Llabata P, Mitsuishi Y, Choi PS, Cai D, Francis JM, Torres-Diz M, Udeshi ND, Golomb L, Wu Z, Zhou J, Svinkina T, Aguilera-Jimenez E, Liu Y, Carr SA, Sanchez-Cespedes M, Meyerson M, Zhang X. Llabata P, et al. Among authors: zhang x. Mol Cancer Res. 2020 Apr;18(4):574-584. doi: 10.1158/1541-7786.MCR-19-0657. Epub 2019 Dec 20. Mol Cancer Res. 2020. PMID: 31862696 Free PMC article.
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