Research Paper

Structure: Order and disorder bound together in SARS-CoV-2 Nsp1 suppress host translation (Libich Lab)

February 6, 2023

David S Libich 1, Antoine Baudin 2 Abstract In this issue of Structure, Wang et al. investigate the interplay between folded and disordered regions of the SARS-CoV-2 non-structural protein 1 (Nsp1) that promotes the suppression of host protein translation. Their investigation will lead to novel avenues to target critical viral functions necessary for host immune-response suppression therapeutically. Read [...]

Neuro-Oncology: Lysine-specific histone demethylase 1A (KDM1A/LSD1) inhibition attenuates DNA double strand break repair and augments efficacy of temozolomide in glioblastoma (Chen, Lao)

January 23, 2023

Salvador Alejo, Bridgitte E Palacios, Prabhakar Pitta Venkata, Yi He, Wenjing Li, Jessica D Johnson, Chen Yihong, Sridharan Jayamohan, Uday P Pratap, Kyra Clarke, Yi Zou, Yingli Lv, Korri Weldon, Suryavathi Viswanadhapalli, Zhao Lai, Zhenqing Ye, Yidong Chen, Andrea R Gilbert, Takayoshi Suzuki, Rajeshwar R Tekmal, Weixing Zhao, Siyuan Zheng, Ratna K Vadlamudi, Andrew J Brenner, Gangadhara R Sareddy Abstract Efficient DNA repair in response to standard chemo and radiation therapies often contributes to GBM therapy resistance. Understanding the [...]

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

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: Inhibition of LIFR Blocks Adiposity-Driven Endometrioid Endometrial Cancer Growth (Chen, Lai, Zheng)

November 15, 2022

by  Logan Blankenship Uday P. Pratap Xue Yang Zexuan Liu Kristin A. Altwegg Bindu Santhamma Kumaraguruparan Ramasamy Swapna Konda Yidong Chen Zhao Lai Siyuan Zheng Gangadhara R. Sareddy Philip T. Valente Edward R. Kost Hareesh B. Nair Rajeshwar R. Tekmal Ratna K. Vadlamudi and Suryavathi Viswanadhapalli Simple Summary In this study, we utilized global RNA-seq [...]

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 [...]