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 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 [...]

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 that Ewing sarcoma harbors two populations of cells, the CD133high population displaying higher growth rate and the CD133low population displaying [...]

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, Yidong Chen, Jun Liu & Pei Wang Animal studies have demonstrated the ability of pancreatic acinar cells [...]

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 lesions. Abstract O6-methylguanine-DNA methyltransferase (MGMT or AGT) is a DNA repair protein with the capability to remove [...]

Genetic Counseling: Families’ experiences accessing care after genomic sequencing in the pediatric cancer context: “It’s just been a big juggle” (Tomlinson)

January 18, 2024

 Blake Vuocolo, Amanda M. Gutierrez, Jill O. Robinson, Alva M. Recinos, Lauren R. Desrosiers, Mary A. Majumder, Juan Carlos Bernini, Jonathan Gill, Timothy Griffin, Gail E. Tomlinson, Kelly Vallance, Amy L. McGuire, D. Williams Parsons, Sharon E. Plon, Sarah Scollon Abstract Access to genomic sequencing (GS) and resulting recommendations have not been well described in pediatric oncology. GS results may provide a cancer predisposition syndrome (CPS) diagnosis that warrants [...]

Cell Reports: The FANCI/FANCD2 complex links DNA damage response to R-loop regulation through SRSF1-mediated mRNA export (Sung & Lab)

January 17, 2024

 Anne Olazabal-Herrero 1 2, Boxue He 3 4, Youngho Kwon 3, Abhishek K. Gupta 2, Arijit Dutta 3, Yuxin Huang 3, Prajwal Boddu 2, Zhuobin Liang 5, Fengshan Liang 1 2, Yaqun Teng 6 7, Li Lan 6 7, Xiaoyong Chen 8, Huadong Pei 9, Manoj M. Pillai 2, Patrick Sung 3, Gary M. Kupfer 1 10 Show more Highlights RSF1 activates the FA pathway by binding and stimulating FANCD2 ubiquitination ANCD2 ubiquitination is crucial for the formation of NXF1-SRSF1 export complex ANCD2 monoubiquitination is critical for NXF1-mediated mRNA export RSF1 cancer mutants fail to bind FANCD2 and NXF1, leading to inefficient mRNA export Summary Fanconi anemia (FA) [...]

Scientific Reports: A CIC-related-epigenetic factors-based model associated with prediction, the tumor microenvironment and drug sensitivity in osteosarcoma (Kitagawa Lab)

January 16, 2024

 Bin Yu, Chengkui Geng, Zhongxiong Wu, Zhongzi Zhang, Aili Zhang, Ze Yang, Jiazheng Huang, Ying Xiong, Huiqin Yang & Zhuoyuan Chen Abstract Osteosarcoma is generally considered a cold tumor and is characterized by epigenetic alterations. Although tumor cells are surrounded by many immune cells such as macrophages, T cells may be suppressed, be inactivated, or not [...]

Cell Reports: TREX2 deficiency suppresses spontaneous and genotoxin-associated mutagenesis (Vaseva Lab, Sung)

January 12, 2024

 Teresa Marple 1 4 8, Mi Young Son 1 2 5 8, Xiaodong Cheng 1 6, Jun Ho Ko 1 7, Patrick Sung 2 3 4, Paul Hasty 1 3 5 9 Highlights The 3′-5′ exonuclease TREX2 causes spontaneous mutations in cells TREX2 causes mutations in cells exposed to a range of genotoxins TREX2 causes spontaneous mutations in MMR-deleted cells Deletion of TREX2 and MMR has a synthetic effect on DNA replication Summary TREX2, a 3′-5′ exonuclease, is a part of the DNA damage tolerance (DDT) [...]

MDPI Cells: Survivin-Sodium Iodide Symporter Reporter as a Non-Invasive Diagnostic Marker to Differentiate Uterine Leiomyosarcoma from Leiomyoma (Bishop Lab)

January 10, 2024

 Natalia Garcia 1,2,†,Mara Ulin 1,3,†,Qiwei Yang 1,4ORCID,Mohamed Ali 1,4,5ORCID,Maarten C. Bosland 6,Weiqiao Zeng 1,Liaohai Chen 1 andAyman Al-Hendy 1,4, Abstract Leiomyosarcoma (LMS) has been challenging to diagnose because of limitations in clinical and radiographic predictors, as well as the lack of reliable serum or urinary biomarkers. Most uterine masses consist of benign leiomyoma (LM). However, [...]