Computers in Biology and Medicine: Omics-based identification of an NRF2-related auranofin resistance signature in cancer: Insights into drug repurposing (Bishop Lab)

December 12, 2022

 Marcelo Falchettia Marina Delgoboa Helena Zancanaroa Karoline Almeidaa Raquel Nascimentodas Nevesac Barbarados Santosa Natália Marcéli Stefanes Alexander Bishop Maria Cláudia Santos-Silvab AlfeuZanotto-Filhoa Highlights • A 29-gene auranofin resistance signature was obtained from lung cancer datasets. • Auranofin signature is enriched with classical NRF2 target genes. • KEAP1/NRF2 mutations are key features associated with signature upregulation. [...]

Genomics, Proteomics & Bioinformatics: Genome of White-blotched River Stingray Provides Novel Clues for Niche Adaptation and Skeleton Formation (Zheng Lab)

December 8, 2022

 Jingqi Zhoua Ake Liub Funan He Yunbin Zhang Libing Shenef JunYugh XiangZhangi Abstract The white-blotched river stingray (Potamotrygon leopoldi) is a cartilaginous fish native to the Xingu River, a tributary of the Amazon River system. As a rare freshwater-dwelling cartilaginous fish in the Potamotrygonidae family that no member has the genome sequencing information, P. leopoldi [...]

Nature Communications: Genomic disparities between cancers in adolescent and young adults and in older adults (Wang, Langevin, Houghton, & Zheng)

December 6, 2022

 Xiaojing Wang, Anne-Marie Langevin, Peter J. Houghton & Siyuan Zheng Cancers cause significant mortality and morbidity in adolescents and young adults (AYAs), but their biological underpinnings are incompletely understood. Here, we analyze clinical and genomic disparities between AYAs and older adults (OAs) in more than 100,000 cancer patients. We find significant differences in clinical presentation between [...]

Cancers MDPI: Transformer for Gene Expression Modeling (T-GEM): An Interpretable Deep Learning Model for Gene Expression-Based Phenotype Predictions (Chen Lab)

October 14, 2022

 Ting-He Zhang, Md Musaddaqul Hasib, Yu-Chiao Chiu, Zhi-Feng Han,  Yu-Fang Jin, Mario Flores, Yidong Chen and Yufei Huang Simple Summary Cancer is the second leading cause of death worldwide. Predicting phenotype and understanding makers that define the phenotype are important tasks. We propose an interpretable deep learning model called T-GEM that can predict cancer-related phenotype [...]

Hepatology: Melanoma Differentiation Associated Gene-9/Syndecan Binding Protein (MDA-9/SDCBP) Promotes Hepatocellular Carcinoma (HCC) [Lai]

September 22, 2022

 Debashri Manna,Saranya Chidambaranathan Reghupaty,Maria Del Carmen Camarena,Rachel G. Mendoza,Mark A. Subler,Jennifer E. Koblinski,Rebecca Martin,Mikhail G. Dozmorov,Nitai D. Mukhopadhyay,Jinze Liu,Xufeng Qu,Swadesh K. Das,Zhao Lai,Jolene J. Windle,Paul B. Fisher,Devanand Sarkar Abstract The oncogene Melanoma differentiation-associated gene-9/syndecan binding protein (MDA-9/SDCBP) is overexpressed in many cancers promoting aggressive, metastatic disease. However, the role of MDA-9 in regulating hepatocellular carcinoma [...]

NPJ | Precision Oncology: An international working group consensus report for the prioritization of molecular biomarkers for Ewing sarcoma (Bishop)

September 21, 2022

 David S. Shulman, Sarah B. Whittle, Didier Surdez, Kelly M. Bailey, Enrique de Álava, Jason T. Yustein, Adam Shlien, Masanori Hayashi, Alexander J. R. Bishop, Brian D. Crompton, Steven G. DuBois, Neerav Shukla, Patrick J. Leavey, Stephen L. Lessnick, Heinrich Kovar, Olivier Delattre, Thomas G. P. Grünewald, Cristina R. Antonescu, Ryan D. Roberts, Jeffrey A. [...]

Nucleic Acids Research: Exploration and analysis of R-loop mapping data with RLBase (Bishop Lab)

August 30, 2022

 Henry E Miller, Daniel Montemayor, Janet Li, Simon A Levy, Roshan Pawar, Stella Hartono, Kumar Sharma, Bess Frost, Frédéric Chedin, Alexander J R Bishop Abstract R-loops are three-stranded nucleic acid structures formed from the hybridization of RNA and DNA. In 2012, Ginno et al. introduced the first R-loop mapping method. Since that time, dozens of R-loop mapping studies have been conducted, yielding hundreds of publicly available [...]

Molecular Cancer Theraputics: Trastuzumab Deruxtecan, Antibody–Drug Conjugate Targeting HER2, Is Effective in Pediatric Malignancies: A Report by the Pediatric Preclinical Testing Consortium (Houghton, Kurmasheva)

August 3, 2022

 Pooja Hingorani Wendong Zhang; Zhongting Zhang; Zhaohui Xu; Wei-Lien Wang; Michael E. Roth Yifei Wang; Jonathan B. Gill Douglas J. Harrison; Beverly A. Teicher; Stephen W. Erickson Gregory Gatto; Edward A. Kolb Malcolm A. Smith Raushan T. Kurmasheva Peter J. Houghton Richard Gorlick Abstract HER2 is expressed in many pediatric solid tumors and is a [...]

Clinical Cancer Research: Regulation of TORC1 by MAPK Signaling Determines Sensitivity and Acquired Resistance to Trametinib in Pediatric BRAFV600E Brain Tumor Models (Houghton & Kurmasheva)

August 1, 2022

 Fuyang Li; Kathryn M. Bondra; Samson Ghilu; Adam Studebaker; Qianqian Liu Joel E. Michalek Mari Kogiso; Xiao-Nan Li John A. Kalapurakal; C. David James; Sandeep Burma; Raushan T. Kurmasheva Peter J. Houghton Abstract Purpose: We investigated why three patient-derived xenografts (PDX) childhood BRAFV600E-mutant brain tumor models are highly sensitive to trametinib. Mechanisms of acquired resistance [...]