Star Protocols: Protocol to benchmark gene expression signature scoring techniques for single-cell RNA sequencing data in cancer (Zheng Lab)

January 4, 2023

 Nighat Noureen123 Xiaojing Wang12 Siyuan Zheng124 • Protocol for benchmarking signature scoring techniques in scRNAseq data analysis • Comparing single-cell and bulk-based approaches in sensitivity and specificity • Using down sampling to simulate the impact of dropouts on signature scoring techniques Summary Scoring gene signatures are common for bulk and single-cell RNA sequencing (scRNAseq) data. [...]

Molecular Cancer Theraputics: Sensitization to Ionizing Radiation by MEK Inhibition Is Dependent on SNAI2 in Fusion-Negative Rhabdomyosarcoma (Ignatius, Vaseva, Houghton Labs)

January 3, 2023

 Nicole R. Hensch, Kathryn Bondra, Long Wang, Prethish Sreenivas, Xiang R. Zhao, Paulomi Modi, Angelina V. Vaseva, Peter J. Houghton, Myron S. Ignatius Abstract In fusion-negative rhabdomyosarcoma (FN-RMS), a pediatric malignancy with skeletal muscle characteristics, >90% of high-risk patients have mutations that activate the RAS/MEK signaling pathway. We recently discovered that SNAI2, in addition to [...]

Genes & Cancer: Slit2 signaling stimulates Ewing sarcoma growth (Shiio Lab)

December 19, 2022

 Kruthi Suvarna1, Panneerselvam Jayabal1, Xiuye Ma1 and Yuzuru Shiio1,2,3 1 Greehey Children’s Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA 2 Cancer Therapy and Research Center, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA 3 Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, [...]

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. [...]