Greehey CCRI Archives

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Cell Death & Disease: Impact of the thyroid hormone T3 and its nuclear receptor TRα1 on colon cancer stem cell phenotypes and response to chemotherapies (Penalva)

May 2, 2024

Maria Virginia Giolito, Serguei Bodoirat, Theo La Rosa, Mathieu Reslinger, Gabriela D. A. Guardia, Jana Mourtada, Leo Claret, Alain Joung, Pedro A. F. Galante, Luiz O. F. Penalva & Michelina Plateroti Abstract Colorectal cancers (CRCs) are highly h …

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

April 29, 2024

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 formatio …

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

April 23, 2024

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 mode …

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)

April 8, 2024

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 amyo …

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

March 27, 2024

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 ribonucleopr …

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

February 20, 2024

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 compou …

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

February 15, 2024

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 •Impaire …

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

February 13, 2024

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 th …

Nature Communications: Reconstitution of human PDAC using primary cells reveals oncogenic transcriptomic features at tumor onset (Chen, Zheng)

February 8, 2024

Yi Xu, Michael H. Nipper, Angel A. Dominguez, Zhenqing Ye, Naoki Akanuma, Kevin Lopez, Janice J. Deng, Destiny Arenas, Ava Sanchez, Francis E. Sharkey, Colin M. Court, Aatur D. Singhi, Huamin Wang, Martin E. Fernandez-Zapico, Lu-Zhe Sun, Siyuan Zheng, …

Cancers: The Versatile Attributes of MGMT: Its Repair Mechanism, Crosstalk with Other DNA Repair Pathways, and Its Role in Cancer (Sung Lab)

February 5, 2024

by  Qingming Fang Simple Summary This review offers a thorough examination of the potential role and structural properties of MGMT, the progression in targeting MGMT, and the interactions between MGMT and DNA repair pathways involved in processing DNA …

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