Current Protocols: Approaches for Mapping and Analysis of R-loops (Bishop Lab)

Published On: April 29, 2024
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Pramiti Mukhopadhyay, Henry Miller, Aiola Stoja, Alexander J. R. Bishop Abstract R-loops are nucleic acid structures composed of a DNA: RNA hybrid with a displaced non-template single-stranded DNA. Current approaches to identify and map R-loop formation across the genome employ either an antibody targeted against R-loops (S9.6) or a catalytically inactivated form of RNase H1 (dRNH1), a nuclease [...] Read more

Patterns: Predicting drug response through tumor deconvolution by cancer cell lines (Chen Lab)

Published On: April 23, 2024
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Yu-Ching Hsu 1 2 3 4, Yu-Chiao Chiu 5 6, Tzu-Pin Lu 3, Tzu-Hung Hsiao 7, Yidong Chen 4 8 9 Highlights •Scaden-CA is a deep-learning model for tumor deconvolution •Tumor deconvolution facilitates the use of a drug response prediction algorithm •The model explores drug response mechanisms via DNA mutations and/or expression changes The bigger picture Drug repurposing involves utilizing approved or investigational drugs beyond the scope of the original medical application. This approach offers [...] Read more

Journal of the American Chemical Society: ights into Molecular Diversity within the FUS/EWS/TAF15 Protein Family: Unraveling Phase Separation of the N-Terminal Low-Complexity Domain from RNA-Binding Protein EWS (Libich Lab)

Published On: April 8, 2024
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Abstract The FET protein family, comprising FUS, EWS, and TAF15, plays crucial roles in mRNA maturation, transcriptional regulation, and DNA damage response. Clinically, they are linked to Ewing family tumors and neurodegenerative diseases such as amyotrophic lateral sclerosis. The fusion protein EWS::FLI1, the causative mutation of Ewing sarcoma, arises from a genomic translocation that fuses [...] Read more

Nature Communications: Development and crystal structures of a potent second-generation dual degrader of BCL-2 and BCL-xL (Sung)

Published On: April 2, 2024
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Digant Nayak, Dongwen Lv, Yaxia Yuan, Peiyi Zhang, Wanyi Hu, Anindita Nayak, Eliza A. Ruben, Zongyang Lv, Patrick Sung, Robert Hromas, Guangrong Zheng, Daohong Zhou & Shaun K. Olsen Abstract Overexpression of BCL-xL and BCL-2 play key roles in tumorigenesis and cancer drug resistance. Advances in PROTAC technology facilitated the recent development of the first BCL-xL/BCL-2 [...] Read more

Frontiers in Cell and Developmental Biology: Editorial: RNA-binding proteins in cancer: advances in translational research (Penalva)

Published On: March 27, 2024
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Caterina Mancarella1* Nadine Bley2 Luiz O. F. Penalva3,4 RNA-binding proteins (RBPs) regulate RNA metabolism, processing, and translation by establishing highly dynamic interactions with hundreds of coding and non-coding target RNAs within ribonucleoprotein complexes (Van Nostrand et al., 2020). Alterations in RBP expression levels or function contribute to several pathological conditions, including cancer. Though underappreciated in the [...] Read more

San Antonio Report: UT Health San Antonio President William Henrich has died

Published On: March 14, 2024
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Breaking News San Antonio Report: UT Health San Antonio President William Henrich has died (Back row, Middle) Dr. Henrich Originally posted, San Antonio Report 3/14/24 Dr. William L. Henrich, the president of UT Health San Antonio, has died, the school confirmed Thursday. Henrich helmed one of the state’s top health schools since 2009, leading UT [...] Read more

Greehey CCRI part of “CPRIT funding of $16.4 million over six months adds transformative expertise, bolsters cancer research.”

Published On: March 8, 2024
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Posted initially on UT Health San Antonio Newsroom on March 7, 2024 at 6:44 am. Shared by Steven Lee Contact: Steven Lee, 210-450-3823, lees22@uthscsa.edu Content contributed by Juanita Alvarez-Hernandez SAN ANTONIO, March 7, 2024 – The University of Texas Health Science Center at San Antonio (UT Health San Antonio) has secured approximately $16.4 million in funding from the Cancer Prevention [...] Read more

Patterns: shinyDeepDR: A user-friendly R Shiny app for predicting anti-cancer drug response using deep learning (Chen lab, et al)

Published On: February 20, 2024
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Li-Ju Wang 1, Michael Ning 1, Tapsya Nayak 2, Michael J. Kasper 1, Satdarshan P. Monga 3 4 5, Yufei Huang 5 6 7 8, Yidong Chen 2 9, Yu-Chiao Chiu 1 4 5 10 Show more Highlights shinyDeepDR is a web tool for predicting responses to 265 anti-cancer compounds It is applicable for researching both cancer cell lines and tumors Its interactive web interface facilitates result interpretation and investigation It identifies promising targets for an “undruggable” mutation in liver cancer The bigger picture Understanding how different [...] Read more

iScience: RNA helicase DDX3 regulates RAD51 localization and DNA damage repair in Ewing sarcoma (Bishop)

Published On: February 15, 2024
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Matthew E. Randolph 1 2, Marwa Afifi 3, Aparna Gorthi 4, Rachel Weil 1, Breelyn A. Wilky 5, Joshua Weinreb 1, Paul Ciero 1 2, Natalie ter Hoeve 7, Paul J. van Diest 7, Venu Raman 5 6 8, Alexander J.R. Bishop 4, David M. Loeb 1 2 5 9 Highlights •Impaired DDX3 RNA helicase [...] Read more

Genes & Cancer: Roles of USP1 in Ewing sarcoma (Shiio Lab)

Published On: February 13, 2024
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Panneerselvam Jayabal1, Xiuye Ma1 and Yuzuru Shiio1,2,3 ABSTRACT Ewing sarcoma is a cancer of bone and soft tissue in children and young adults that is driven by the EWS-ETS fusion transcription factor, most commonly EWS-FLI1. We previously reported that Ewing sarcoma harbors two populations of cells, the CD133high population displaying higher growth rate and the CD133low population displaying [...] Read more