Article
Oncology
Navonil De Sarkar, Robert D. Patton, Anna-Lisa Doebley, Brian Hanratty, Mohamed Adil, Adam J. Kreitzman, Jay F. Sarthy, Minjeong Ko, Sandipan Brahma, Michael P. Meers, Derek H. Janssens, Lisa S. Ang, Ilsa M. Coleman, Arnab Bose, Ruth F. Dumpit, Jared M. Lucas, Talina A. Nunez, Holly M. Nguyen, Heather M. McClure, Colin C. Pritchard, Michael T. Schweizer, Colm Morrissey, Atish D. Choudhury, Sylvan C. Baca, Jacob E. Berchuck, Matthew L. Freedman, Kami Ahmad, Michael C. Haffner, R. Bruce Montgomery, Eva Corey, Steven Henikoff, Peter S. Nelson, Gavin Ha
Summary: By studying nucleosome positioning patterns in circulating tumor DNA (ctDNA), we identified distinct phenotypes of advanced prostate cancers and developed prediction models for phenotype classification. Nucleosome patterns associated with transcriptional activity were observed in ctDNA, providing insights into gene regulation and potential therapeutic targets. This study demonstrates the diagnostic advantages and precision oncology implications of ctDNA in cancer phenotyping.
Article
Multidisciplinary Sciences
Sidra Mumtaz, Muhammad Usman Rashid, Rizwan Ullah Khan, Naila Malkani
Summary: This study found that miR-4482 and miR-3912 can suppress ERG expression and its downstream target genes, thereby halting the progression of prostate cancer. These miRNAs may be employed as a potential therapeutic target for miRNA-based therapy against prostate cancer.
Article
Multidisciplinary Sciences
Meixia Che, Aashi Chaturvedi, Sarah A. Munro, Samuel P. Pitzen, Alex Ling, Weijie Zhang, Josh Mentzer, Sheng-Yu Ku, Loredana Puca, Yanyun Zhu, Andries M. Bergman, Tesa M. Severson, Colleen Forster, Yuzhen Liu, Jacob Hildebrand, Mark Daniel, Ting-You Wang, Luke A. Selth, Theresa Hickey, Amina Zoubeidi, Martin Gleave, Rohan Bareja, Andrea Sboner, Wayne Tilley, Jason S. Carroll, Winston Tan, Manish Kohli, Rendong Yang, Andrew C. Hsieh, Paari Murugan, Wilbert Zwart, Himisha Beltran, R. Stephanie Huang, Scott M. Dehm
Summary: Endocrine therapies for prostate cancer often lead to the reactivation of the androgen receptor, promoting disease progression. This study shows that the transcription factor KLF5 is induced during treatment, promoting cellular migration and the development of a basal epithelial cell phenotype.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Aileen Julia Riesle, Meijiang Gao, Marcus Rosenblatt, Jacques Hermes, Helge Hass, Anna Gebhard, Marina Veil, Bjorn Gruening, Jens Timmer, Daria Onichtchouk
Summary: This study investigates the combinatorial mechanisms of genome activation and shows that zebrafish genome activators Pou5f3 and Nanog exhibit different roles in the activation process. They act as pioneer-like transcription factors on synergistic enhancers, promoting histone acetylation and transcription activation. However, on antagonistic enhancers, one of the factors acts as a non-pioneer-like transcription factor, competing with the activator and blocking its effects. This activator-blocker mechanism restricts widespread transcriptional activation and prevents premature expression of late developmental genes in early embryos.
NATURE COMMUNICATIONS
(2023)
Review
Biochemistry & Molecular Biology
Zengde Chi, Yan Lu, Yinlong Yang, Bingqing Li, Peiyuan Lu
Summary: PD-1 serves as a crucial co-inhibitory receptor in regulating T cell immunity and peripheral tolerance. It plays a dual role in preventing T cell overactivation and maintaining T cell exhaustion. Additionally, the PD-1 signaling pathway is exploited by tumor cells to evade immune responses and is essential for maintaining peripheral tolerance and preventing autoimmune diseases.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Chao Wang, Jonathan Leavenworth, Chao Zhang, Zhichao Liu, Katherine Y. Yuan, Yicun Wang, Guangxin Zhang, Shuaibin Wang, Xuelian Cui, Yue Zhang, Sejong Bae, Jiangbing Zhou, Lizhong Wang, Runhua Liu
Summary: In prostate cancer, high expression of eIF4A1 is regulated by DNA methylation and it plays an oncogenic role through the BRD2 signaling pathway.
Article
Multidisciplinary Sciences
Nozomu Takata, Jason M. Miska, Marc A. Morgan, Priyam Patel, Leah K. Billingham, Neha Joshi, Matthew J. Schipma, Zachary J. Dumar, Nikita R. Joshi, Alexander V. Misharin, Ryan B. Embry, Luciano Fiore, Peng Gao, Lauren P. Diebold, Gregory S. McElroy, Ali Shilatifard, Navdeep S. Chandel, Guillermo Oliver
Summary: Using eye organoids and mouse models, the authors demonstrate that lactate plays a bioenergetic independent role as a cell signaling molecule during early eye formation in mice. The study reveals the importance of aerobic glycolysis in retinal development and identifies specific glucose transporters and glycolytic genes involved. Lactate-mediated upregulation of eye-field transcription factors is controlled by epigenetic modifications.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Sakshi Goel, Vipul Bhatia, Sushmita Kundu, Tanay Biswas, Shannon Carskadon, Nilesh Gupta, Mohammad Asim, Colm Morrissey, Nallasivam Palanisamy, Bushra Ateeq
Summary: DLX1 serves as a crucial factor in prostate cancer, and its high levels are associated with aggressive disease and poor prognosis. Through regulating the transcriptional activity of DLX1, ERG and AR contribute to tumorigenesis and metastasis. Inhibiting ERG/AR-mediated transcription of DLX1 using BET inhibitors and anti-androgens can reduce its expression and downstream oncogenic effects.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Kaiqin Sheng, Yuecheng Wu, Hanbin Lin, Menghan Fang, Chaorong Xue, Xu Lin, Xinjian Lin
Summary: Sialic acid-binding immunoglobulin-like lectin 15 (Siglec-15) is a critical immune suppressor in human cancers, similar to programmed cell death 1 ligand (PD-L1). The study reveals that transcription factors ETS-1 and ETS-2 bind to the Siglec-15 promoter, enhancing its transcription and expression in hepatocellular carcinoma (HCC) cells. Transforming growth factor beta-1 (TGF-beta 1) upregulates ETS-1 and ETS-2 expression and facilitates their binding to the Siglec-15 promoter. TGF-beta 1 also activates the Ras/C-Raf/MEK/ERK1/2 signaling pathway, leading to phosphorylation of ETS-1 and ETS-2, which in turn increases the transcription and expression of Siglec-15. These findings provide valuable insights into the molecular regulation of Siglec-15 and its potential for HCC immunotherapy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Nilton Jose Santos, Caroline Nascimento Barquilha, Isabela Correa Barbosa, Rodrigo Tavares Macedo, Flavio Oliveira Lima, Luis Antonio Justulin, Guilherme Oliveira Barbosa, Hernandes F. Carvalho, Sergio Luis Felisbino
Summary: Prostate cancer, a leading cause of cancer-related death in men, requires new biomarkers. Research on the expression pattern of proteoglycans and syntenin-1 in mouse models and human prostate tumors revealed SDC1, SDC3, SDC2, and SDC4 differences associated with cancer development, with SDC3 expression linked to shorter prostate-specific survival.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Ziwei Wang, Tao Wang, Danni Hong, Baijun Dong, Yan Wang, Huaqiang Huang, Wenhui Zhang, Bijun Lian, Boyao Ji, Haoqing Shi, Min Qu, Xu Gao, Daofeng Li, Colin Collins, Gonghong Wei, Chuanliang Xu, Hyung Joo Lee, Jialiang Huang, Jing Li
Summary: This study characterized ADPC and NEPC in prostate tumors using scRNA-seq and identified NEPC-specific gene expression signatures. The findings revealed different paths by which NEPC diverges from ADPC and inferred a hierarchical transcription factor network involved in NEPC progression.
Article
Biochemistry & Molecular Biology
Yuzhou Wang, Yu Zhang, Ning Yu, Bingyan Li, Jiazhen Gong, Yide Mei, Jianqiang Bao, Shisong Ma
Summary: Researchers developed a universal human gene expression predictor called EXPLICIT-Human and used it to decode transcriptional regulation. The predictor accurately reconstructed transcriptomes for a wide range of tissues and conditions using the expression of 1613 transcription factors. It extracted significant interacting TF-target gene pairs, enabling inference of TF regulators for various pathways. The method showed better performance in recovering the correct TF regulators compared to existing tools.
JOURNAL OF GENETICS AND GENOMICS
(2023)
Article
Biochemistry & Molecular Biology
Zhe Wang, Jianfang Chen, Fengjun Sun, Xiang Zhao, Yan Dong, Songtao Yu, Jianjun Li, Houjie Liang
Summary: This study identified a clinically significant lncRNA, CRLM1, in colorectal cancer metastasis, which was found to promote metastasis and regulate gene expression. This discovery suggests that CRLM1 could serve as a potential biomarker and therapeutic target for colorectal liver metastases.
CELL AND BIOSCIENCE
(2022)
Article
Biology
Nehal Gupta, Hanbing Song, Wei Wu, Rovingaile K. Ponce, Yone K. Lin, Ji Won Kim, Eric J. Small, Felix Y. Feng, Franklin W. Huang, Ross A. Okimoto
Summary: This study reveals that the concurrent loss of CIC and ERF can drive prostate oncogenesis by mutually repressing ETS transcription factor ETV1. Targeting ETV1 can limit the growth of CIC and ERF-deficient prostate cancer.
Article
Biochemistry & Molecular Biology
Meng Xiao He, Michael S. Cuoco, Jett Crowdis, Alice Bosma-Moody, Zhenwei Zhang, Kevin Bi, Abhay Kanodia, Mei-Ju Su, Sheng-Yu Ku, Maria Mica Garcia, Amalia R. Sweet, Christopher Rodman, Laura DelloStritto, Rebecca Silver, John Steinharter, Parin Shah, Benjamin Izar, Nathan C. Walk, Kelly P. Burke, Ziad Bakouny, Alok K. Tewari, David Liu, Sabrina Y. Camp, Natalie I. Vokes, Keyan Salari, Jihye Park, Sebastien Vigneau, Lawrence Fong, Joshua W. Russo, Xin Yuan, Steven P. Balk, Himisha Beltran, Orit Rozenblatt-Rosen, Aviv Regev, Asaf Rotem, Mary-Ellen Taplin, Eliezer M. Van Allen
Summary: The study revealed pervasive coexpression of androgen receptor isoforms in cancer cells and explored the mechanisms of treatment resistance in metastatic castration-resistant prostate cancer.