Identification of selective SWI/SNF dependencies in enzalutamide-resistant prostate cancer

Authors: Bengul Gokbayrak, Umut Berkay Altintas, Shreyas Lingadahalli, Tunc Morova, Chia-Chi Flora Huang, Betul Ersoy Fazlioglu, Ivan Pak Lok Yu, Batuhan M. Kalkan, Paloma Cejas, Sonia H. Y. Kung, Ladan Fazli, Akane Kawamura, Henry W. Long, Ceyda Acilan, Tamer T. Onder, Tugba Bagci-Onder, James T. Lynch, Nathan A. Lack

Source: Communications Biology, Vol 8, Iss 1, Pp 1-12 (2025)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/2399-3642

Access URL: https://doaj.org/article/9273142519234b4fb532854e1afe6cb3

Increased nuclear factor I-mediated chromatin access drives transition to androgen receptor splice variant dependence in prostate cancer

Authors: Larysa Poluben, Mannan Nouri, Jiaqian Liang, Shaoyong Chen, Andreas Varkaris, Betul Ersoy-Fazlioglu, Olga Voznesensky, Irene I. Lee, Xintao Qiu, Laura Cato, Ji-Heui Seo, Matthew L. Freedman, Adam G. Sowalsky, Nathan A. Lack, Eva Corey, Peter S. Nelson, Myles Brown, Henry W. Long, Joshua W. Russo, Steven P. Balk

Source: Cell Reports, Vol 44, Iss 1, Pp 115089- (2025)

Subject Terms: CP: Cancer, CP: Molecular biology, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211124724014402; https://doaj.org/toc/2211-1247

Access URL: https://doaj.org/article/2f2b85dedf46431d9d37f79b462cfcfe

ZBTB7A is a modulator of KDM5-driven transcriptional networks in basal breast cancer

Authors: Benedetto DiCiaccio, Marco Seehawer, Zheqi Li, Andriana Patmanidis, Triet Bui, Pierre Foidart, Jun Nishida, Clive S. D’Santos, Evangelia K. Papachristou, Malvina Papanastasiou, Andrew H. Reiter, Xintao Qiu, Rong Li, Yijia Jiang, Xiao-Yun Huang, Anton Simeonov, Stephen C. Kales, Ganesha Rai, Madhu Lal-Nag, Ajit Jadhav, Myles Brown, Jason S. Carroll, Henry W. Long, Kornelia Polyak

Source: Cell Reports, Vol 43, Iss 12, Pp 114991- (2024)

Subject Terms: CP: Cancer, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211124724013421; https://doaj.org/toc/2211-1247

Access URL: https://doaj.org/article/d86443eea36b447cb9cbe10e44a6827f

Heterogeneity and transcriptional drivers of triple-negative breast cancer

Authors: Bojana Jovanović, Daniel Temko, Laura E. Stevens, Marco Seehawer, Anne Fassl, Katherine Murphy, Jayati Anand, Kodie Garza, Anushree Gulvady, Xintao Qiu, Nicholas W. Harper, Veerle W. Daniels, Huang Xiao-Yun, Jennifer Y. Ge, Maša Alečković, Jason Pyrdol, Kunihiko Hinohara, Shawn B. Egri, Malvina Papanastasiou, Raga Vadhi, Alba Font-Tello, Robert Witwicki, Guillermo Peluffo, Anne Trinh, Shaokun Shu, Benedetto Diciaccio, Muhammad B. Ekram, Ashim Subedee, Zachary T. Herbert, Kai W. Wucherpfennig, Anthony G. Letai, Jacob D. Jaffe, Piotr Sicinski, Myles Brown, Deborah Dillon, Henry W. Long, Franziska Michor, Kornelia Polyak

Source: Cell Reports, Vol 42, Iss 12, Pp 113564- (2023)

Subject Terms: CP: Cancer, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211124723015760; https://doaj.org/toc/2211-1247

Access URL: https://doaj.org/article/5b7a46fb42fa443eac6a172b0b60048f

MYC drives aggressive prostate cancer by disrupting transcriptional pause release at androgen receptor targets

Authors: Xintao Qiu, Nadia Boufaied, Tarek Hallal, Avery Feit, Anna de Polo, Adrienne M. Luoma, Walaa Alahmadi, Janie Larocque, Giorgia Zadra, Yingtian Xie, Shengqing Gu, Qin Tang, Yi Zhang, Sudeepa Syamala, Ji-Heui Seo, Connor Bell, Edward O’Connor, Yang Liu, Edward M. Schaeffer, R. Jeffrey Karnes, Sheila Weinmann, Elai Davicioni, Colm Morrissey, Paloma Cejas, Leigh Ellis, Massimo Loda, Kai W. Wucherpfennig, Mark M. Pomerantz, Daniel E. Spratt, Eva Corey, Matthew L. Freedman, X. Shirley Liu, Myles Brown, Henry W. Long, David P. Labbé

Source: Nature Communications, Vol 13, Iss 1, Pp 1-17 (2022)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/bc90d144fd374a6387fda7079a332f9f

p16INK4A-deficiency predicts response to combined HER2 and CDK4/6 inhibition in HER2+ breast cancer brain metastases

Authors: Jing Ni, Sheheryar Kabraji, Shaozhen Xie, Yanzhi Wang, Peichen Pan, Xiaofang He, Zongming Liu, Jose Palbo Leone, Henry W. Long, Myles A. Brown, Eric P. Winer, Deborah A. R. Dillon, Nancy U. Lin, Jean J. Zhao

Source: Nature Communications, Vol 13, Iss 1, Pp 1-8 (2022)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/16bc242049ff4c6ca1e0501ace504822

Subtype heterogeneity and epigenetic convergence in neuroendocrine prostate cancer

Authors: Paloma Cejas, Yingtian Xie, Alba Font-Tello, Klothilda Lim, Sudeepa Syamala, Xintao Qiu, Alok K. Tewari, Neel Shah, Holly M. Nguyen, Radhika A. Patel, Lisha Brown, Ilsa Coleman, Wenzel M. Hackeng, Lodewijk Brosens, Koen M. A. Dreijerink, Leigh Ellis, Sarah Abou Alaiwi, Ji-Heui Seo, Sylvan Baca, Himisha Beltran, Francesca Khani, Mark Pomerantz, Alessandra Dall’Agnese, Jett Crowdis, Eliezer M. Van Allen, Joaquim Bellmunt, Colm Morrisey, Peter S. Nelson, James DeCaprio, Anna Farago, Nicholas Dyson, Benjamin Drapkin, X. Shirley Liu, Matthew Freedman, Michael C. Haffner, Eva Corey, Myles Brown, Henry W. Long

Source: Nature Communications, Vol 12, Iss 1, Pp 1-11 (2021)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/049dc4c6a6fd4e8a9fc4ad8f4f885b4e

Reprogramming of the FOXA1 cistrome in treatment-emergent neuroendocrine prostate cancer

Authors: Sylvan C. Baca, David Y. Takeda, Ji-Heui Seo, Justin Hwang, Sheng Yu Ku, Rand Arafeh, Taylor Arnoff, Supreet Agarwal, Connor Bell, Edward O’Connor, Xintao Qiu, Sarah Abou Alaiwi, Rosario I. Corona, Marcos A. S. Fonseca, Claudia Giambartolomei, Paloma Cejas, Klothilda Lim, Monica He, Anjali Sheahan, Amin Nassar, Jacob E. Berchuck, Lisha Brown, Holly M. Nguyen, Ilsa M. Coleman, Arja Kaipainen, Navonil De Sarkar, Peter S. Nelson, Colm Morrissey, Keegan Korthauer, Mark M. Pomerantz, Leigh Ellis, Bogdan Pasaniuc, Kate Lawrenson, Kathleen Kelly, Amina Zoubeidi, William C. Hahn, Himisha Beltran, Henry W. Long, Myles Brown, Eva Corey, Matthew L. Freedman

Source: Nature Communications, Vol 12, Iss 1, Pp 1-12 (2021)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/c9b61c7dcf794ef5947cc08ad8806fa3

Response to supraphysiological testosterone is predicted by a distinct androgen receptor cistrome

Authors: Xintao Qiu, Lisha G. Brown, Jennifer L. Conner, Holly M. Nguyen, Nadia Boufaied, Sarah Abou Alaiwi, Ji-Heui Seo, Talal El Zarif, Connor Bell, Edward O’Connor, Brian Hanratty, Mark Pomerantz, Matthew L. Freedman, Myles Brown, Michael C. Haffner, Peter S. Nelson, Felix Y. Feng, David P. Labbé, Henry W. Long, Eva Corey

Source: JCI Insight, Vol 7, Iss 10 (2022)

Subject Terms: Endocrinology, Oncology, Medicine

File Description: electronic resource

Relation: https://doaj.org/toc/2379-3708

Access URL: https://doaj.org/article/31afe18a58f34ea88bc2519a68bd658c

Chromatin accessibility promotes hematopoietic and leukemia stem cell activity

Authors: Lucia Cabal-Hierro, Peter van Galen, Miguel A. Prado, Kelly J. Higby, Katsuhiro Togami, Cody T. Mowery, Joao A. Paulo, Yingtian Xie, Paloma Cejas, Takashi Furusawa, Michael Bustin, Henry W. Long, David B. Sykes, Steven P. Gygi, Daniel Finley, Bradley E. Bernstein, Andrew A. Lane

Source: Nature Communications, Vol 11, Iss 1, Pp 1-18 (2020)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/f424d9b406fb49f7a429fe6474f60a2d

Androgen Receptor Is a Non-canonical Inhibitor of Wild-Type and Mutant Estrogen Receptors in Hormone Receptor-Positive Breast Cancers

Authors: Suriyan Ponnusamy, Sarah Asemota, Lee S. Schwartzberg, Fouzia Guestini, Keely M. McNamara, Mariaelena Pierobon, Alba Font-Tello, Xintao Qiu, Yingtian Xie, Prakash K. Rao, Thirumagal Thiyagarajan, Brandy Grimes, Daniel L. Johnson, Martin D. Fleming, Frances E. Pritchard, Michael P. Berry, Roy Oswaks, Richard E. Fine, Myles Brown, Hironobu Sasano, Emanuel F. Petricoin, Henry W. Long, Ramesh Narayanan

Source: iScience, Vol 21, Iss , Pp 341-358 (2019)

Subject Terms: Science

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2589004219304183; https://doaj.org/toc/2589-0042

Access URL: https://doaj.org/article/dff52cda825c431a910313dacdb4bf32

Perturbed myoepithelial cell differentiation in BRCA mutation carriers and in ductal carcinoma in situ

Authors: Lina Ding, Ying Su, Anne Fassl, Kunihiko Hinohara, Xintao Qiu, Nicholas W. Harper, Sung Jin Huh, Noga Bloushtain-Qimron, Bojana Jovanović, Muhammad Ekram, Xiaoyuan Zi, William C. Hines, Maša Alečković, Carlos Gil del Alcazar, Ryan J. Caulfield, Dennis M. Bonal, Quang-De Nguyen, Vanessa F. Merino, Sibgat Choudhury, Gabrielle Ethington, Laura Panos, Michael Grant, William Herlihy, Alfred Au, Gedge D. Rosson, Pedram Argani, Andrea L. Richardson, Deborah Dillon, D. Craig Allred, Kirsten Babski, Elizabeth Min Hui Kim, Charles H. McDonnell, Jon Wagner, Ron Rowberry, Kristie Bobolis, Celina G. Kleer, E. Shelley Hwang, Joanne L. Blum, Simona Cristea, Piotr Sicinski, Rong Fan, Henry W. Long, Saraswati Sukumar, So Yeon Park, Judy E. Garber, Mina Bissell, Jun Yao, Kornelia Polyak

Source: Nature Communications, Vol 10, Iss 1, Pp 1-16 (2019)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/784cf49197cf4d50824d3974f6c39d75

Super-Enhancer-Associated LncRNA UCA1 Interacts Directly with AMOT to Activate YAP Target Genes in Epithelial Ovarian Cancer

Authors: Xianzhi Lin, Tassja J. Spindler, Marcos Abraão de Souza Fonseca, Rosario I. Corona, Ji-Heui Seo, Felipe Segato Dezem, Lewyn Li, Janet M. Lee, Henry W. Long, Thomas A. Sellers, Beth Y. Karlan, Houtan Noushmehr, Matthew L. Freedman, Simon A. Gayther, Kate Lawrenson

Source: iScience, Vol 17, Iss , Pp 242-255 (2019)

Subject Terms: Science

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2589004219302081; https://doaj.org/toc/2589-0042

Access URL: https://doaj.org/article/93bb63abbf5e4c2688944d7226861c60

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis

Authors: MacIntosh Cornwell, Mahesh Vangala, Len Taing, Zachary Herbert, Johannes Köster, Bo Li, Hanfei Sun, Taiwen Li, Jian Zhang, Xintao Qiu, Matthew Pun, Rinath Jeselsohn, Myles Brown, X. Shirley Liu, Henry W. Long

Source: BMC Bioinformatics, Vol 19, Iss 1, Pp 1-14 (2018)

Subject Terms: RNA-seq, Analysis, Pipeline, Snakemake, Gene fusion, Immunological infiltrate, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12859-018-2139-9; https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/05f5ce1145074e0bbe0ea6794782fc82

Enhancer-Mediated Oncogenic Function of the Menin Tumor Suppressor in Breast Cancer

Authors: Koen M.A. Dreijerink, Anna C. Groner, Erica S.M. Vos, Alba Font-Tello, Lei Gu, David Chi, Jaime Reyes, Jennifer Cook, Elgene Lim, Charles Y. Lin, Wouter de Laat, Prakash K. Rao, Henry W. Long, Myles Brown

Source: Cell Reports, Vol 18, Iss 10, Pp 2359-2372 (2017)

Subject Terms: breast cancer, MEN1, tumor suppressor, oncogene, transcription, epigenetics, menin, histone H3K4 trimethylation, enhancer, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211124717302061; https://doaj.org/toc/2211-1247

Access URL: https://doaj.org/article/3f77d4a5a1b546718b544e4e56c72eda

Trisomy of a Down Syndrome Critical Region Globally Amplifies Transcription via HMGN1 Overexpression

Authors: Cody T. Mowery, Jaime M. Reyes, Lucia Cabal-Hierro, Kelly J. Higby, Kristen L. Karlin, Jarey H. Wang, Robert J. Kimmerling, Paloma Cejas, Klothilda Lim, Hubo Li, Takashi Furusawa, Henry W. Long, David Pellman, Bjoern Chapuy, Michael Bustin, Scott R. Manalis, Thomas F. Westbrook, Charles Y. Lin, Andrew A. Lane

Source: Cell Reports, Vol 25, Iss 7, Pp 1898-1911.e5 (2018)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211124718316504; https://doaj.org/toc/2211-1247

Access URL: https://doaj.org/article/70783644fe2f43be951838ad8302663a

Atlas of prostate cancer heritability in European and African-American men pinpoints tissue-specific regulation

Authors: Alexander Gusev, Huwenbo Shi, Gleb Kichaev, Mark Pomerantz, Fugen Li, Henry W. Long, Sue A. Ingles, Rick A. Kittles, Sara S. Strom, Benjamin A. Rybicki, Barbara Nemesure, William B. Isaacs, Wei Zheng, Curtis A. Pettaway, Edward D. Yeboah, Yao Tettey, Richard B. Biritwum, Andrew A. Adjei, Evelyn Tay, Ann Truelove, Shelley Niwa, Anand P. Chokkalingam, Esther M. John, Adam B. Murphy, Lisa B. Signorello, John Carpten, M. Cristina Leske, Suh-Yuh Wu, Anslem J. M. Hennis, Christine Neslund-Dudas, Ann W. Hsing, Lisa Chu, Phyllis J. Goodman, Eric A. Klein, John S. Witte, Graham Casey, Sam Kaggwa, Michael B. Cook, Daniel O. Stram, William J. Blot, Rosalind A. Eeles, Douglas Easton, ZSofia Kote-Jarai, Ali Amin Al Olama, Sara Benlloch, Kenneth Muir, Graham G. Giles, Melissa C. Southey, Liesel M. Fitzgerald, Henrik Gronberg, Fredrik Wiklund, Markus Aly, Brian E. Henderson, Johanna Schleutker, Tiina Wahlfors, Teuvo L. J. Tammela, Børge G. Nordestgaard, Tim J. Key, Ruth C. Travis, David E. Neal, Jenny L. Donovan, Freddie C. Hamdy, Paul Pharoah, Nora Pashayan, Kay-Tee Khaw, Janet L. Stanford, Stephen N. Thibodeau, Shannon K. McDonnell, Daniel J. Schaid, Christiane Maier, Walther Vogel, Manuel Luedeke, Kathleen Herkommer, Adam S. Kibel, Cezary Cybulski, Dominika Wokolorczyk, Wojciech Kluzniak, Lisa Cannon-Albright, Craig Teerlink, Hermann Brenner, Aida K. Dieffenbach, Volker Arndt, Jong Y. Park, Thomas A. Sellers, Hui-Yi Lin, Chavdar Slavov, Radka Kaneva, Vanio Mitev, Jyotsna Batra, Amanda Spurdle, Judith A. Clements, Manuel R. Teixeira, Hardev Pandha, Agnieszka Michael, Paula Paulo, Sofia Maia, Andrzej Kierzek, The PRACTICAL consortium, David V. Conti, Demetrius Albanes, Christine Berg, Sonja I. Berndt, Daniele Campa, E. David Crawford, W. Ryan Diver, Susan M. Gapstur, J. Michael Gaziano, Edward Giovannucci, Robert Hoover, David J. Hunter, Mattias Johansson, Peter Kraft, Loic Le Marchand, Sara Lindström, Carmen Navarro, Kim Overvad, Elio Riboli, Afshan Siddiq, Victoria L. Stevens, Dimitrios Trichopoulos, Paolo Vineis, Meredith Yeager, Gosia Trynka, Soumya Raychaudhuri, Frederick R. Schumacher, Alkes L. Price, Matthew L. Freedman, Christopher A. Haiman, Bogdan Pasaniuc

Source: Nature Communications, Vol 7, Iss 1, Pp 1-13 (2016)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/e4bbdf2c86b748b69179c08e3173c667

Regulation of the glucocorticoid receptor via a BET-dependent enhancer drives antiandrogen resistance in prostate cancer

Authors: Neel Shah, Ping Wang, John Wongvipat, Wouter R Karthaus, Wassim Abida, Joshua Armenia, Shira Rockowitz, Yotam Drier, Bradley E Bernstein, Henry W Long, Matthew L Freedman, Vivek K Arora, Deyou Zheng, Charles L Sawyers

Source: eLife, Vol 6 (2017)

Subject Terms: prostate cancer, resistance to targeted therapies, epigenetics, Medicine, Science, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://elifesciences.org/articles/27861; https://doaj.org/toc/2050-084X

Access URL: https://doaj.org/article/61db683fcfe74955afcc80092315405e