Research Paper Archives - Greehey Children's Cancer

Star Protocols: Transformer and graph variational autoencoder to identify microenvironments: A deep learning protocol for spatial transcriptomics (Chen)

January 6, 2026
Karla Paniagua 1 8, Yufei Huang 2 3 4, Shou-jiang Gao 2 5, Yidong Chen 6 7, Yu-Fang Jin 1, Mario Flores 1 9 Highlights Workflow to build spatial objects linking stitched images with transcriptomics data Steps to apply the transformer and GraphVAE for spatial and contextual tissue modeling Guide to merge gene expression and histology data into one spatial framework. Instructions for clustering and deconvolution to map tumor niches at the single-cell level Summary We present a [...]

Cancer Research: Antibody-Mediated Targeting of Secretory Protein SCUBE3 Suppresses Cancer Progression by Inhibiting Oncogenic Signaling and Inducing Anti-tumor Immunity (Rao, Zhou, Hromas, Sung, Chen, et al)

December 3, 2025
Deepika Singh Benjamin C. Onyeagucha Daisy Medina Panneerdoss Subbarayalu Rahul Mojidra Dongwen Lv Mukund Bhandari Santosh Timilsina Prabhakar Pitta Venkata Jian Yu. Huang Saif Nirzhor Shahad Abdulsahib Jack Yancy. Prochnau Chris TP. Do Subapriya Rajamanickam Yidong Chen Alexander B. Taylor Suryavathi Viswanadhapalli Maria E. Falzone Jean Jiang Patrick Sung Daohong Zhou Abstract Approaches targeting factors [...]

Cancer Research: Antibody-Mediated Targeting of Secretory Protein SCUBE3 Suppresses Cancer Progression by Inhibiting Oncogenic Signaling and Inducing Anti-tumor Immunity (Rao, Zhou, Hromas, Sung, Chen

Molecular Cell: Deubiquitinases cleave ubiquitin-fused ribosomal proteins and physically counteract their targeting to the UFD pathway (Olsen)

December 1, 2025
Stephanie Patchett 1 5, Seyed Arad Moghadasi 1 5, Ankita Shukla 2, Farid El Oualid 3, Beatrix M. Ueberheide 1 4, Shaun K. Olsen 2, Tony T. Huang 1 6 Highlights Cleavage-resistant ubiquitin-fused human ribosomal proteins (RPs) impair ribosome function Unprocessed, Ub-fused RPs are targeted for proteasomal degradation by the UFD pathway DUB activity-based probes for Ub-fused RPs identify Cezanne/OTUD7B and other DUBs Catalytic activity-independent DUB association with Ub-RPs prevents their degradation Summary In eukaryotes, each ribosomal subunit includes [...]

Science Advances: Ligand-receptor interactions induce and mediate regulatory functions of BATF3+ B cells (Chen Lab, Zheng Lab)

November 12, 2025
Hui Yan Rui Wang Suryavathi Viswanadhapalli Christian Cervantes Funan He Shuai Wu Azad Khosh Weiwei Luo Jingwei Wang Maria J. Fernandez Uday P. Pratap Mustafa Khan Karli Hinton Sai Eashan Vankamamidi Dariela Perez Carlos E. Rivera Harshita B. Gupta Fushun Zhang Zhenqing Ye Yidong Chen Xiao-Dong Li Gangadhara R. Sareddy Hong Zan Yue Li Exing Wang Evelien M. Bunnik Guangming Zhong Christopher A. Hunter Ross M. Kedl Zhinan Yin Booki Min Diako Ebrahimi Siyuan Zheng Tyler J. Curiel Yan Xiang Ratna K. Vadlamudi , Paolo Casali and Zhenming Xu [...]

ACS Medicinal Chemistry Letters: Identification and Exploration of a Series of SARS-Cov-2 MPro Cyano-Based Inhibitors Revealing Ortho-Substitution Effects within the P3 Biphenyl Group (Olsen)

November 10, 2025
Emma Clyde-Allen Mikołaj Zmudzinski Mohammad Afsar Ciyana James Anindita Nayak Digant Nayak Priscila dos Santos Bury Dirk Jochmans Johann Neyts Christopher J. Scott Shaun K. Olsen Marcin Drag Rich Williams* Abstract Starting from a simple scaffold hopping exercise based on our previous exploration of cysteine protease inhibitors against legumain, compound 6a was identified as a starting point [...]

Molecular Medicine: Selective inhibition of BRAF and CRAF sensitizes NF1-deficient malignant peripheral nerve sheath tumors to MEK inhibitors (Zheng, Kitagawa Lab)

October 2, 2025
Jiawan Wang, Arnab Sarkar, Natalia Garcia, Lindy Zhang, Ana Calizo, Alla Lisok, Katia Campos, Funan He, Nishanth Punjaala, Teresa Marple, Kai Pollard, Siyuan Zheng, Calixto-Hope G. Lucas, Vesselina G. Cooke, Christine A. Pratilas & Angelina V. Vaseva Abstract Background Treatment for patients with malignant peripheral nerve sheath tumors (MPNST) is an unmet clinical [...]

Nature Structural & Molecular Biology: Cryo-EM structures reveal the molecular mechanism of SUMO E1–E2 thioester transfer (Olsen Lab, Sung Lab)

September 26, 2025
Anindita Nayak, Digant Nayak, Lijia Jia, Eliza A. Ruben, Suryavathi Viswanadhapalli, Priscila dos Santos Bury, Khaled Mohamed Nassar, Corey H. Yu, Anna A. Tumanova, Caleb M. Stratton, Pirouz Ebadi, Dmitri N. Ivanov, Patrick Sung, Ratna K. Vadlamudi, Elizabeth V. Wasmuth & Shaun K. Olsen Abstract Post-translational modification of proteins by SUMO (small ubiquitin-like modifier) regulates fundamental [...]

BioRxiv: Phosphoregulation of RAD51AP1 function in homology-directed repair (Sung Lab)

September 22, 2025
Neelam Sharma, Mollie Uhrig, Youngho Kwon, Patrick Sung, Claudia Wiese ABSTRACT Homology-directed DNA repair (HDR) is critical for genome stability and tumor suppression. HDR is initiated by the RAD51 single-stranded (ss)DNA nucleoprotein filament which conducts the homology search and invades a homologous DNA template, creating a displacement-loop (D-loop). The RAD51 filament is assisted in these processes by several proteins. One [...]

Protein Science: Molecular basis of EWS interdomain self-association and its role in condensate formation (Libich Lab)

September 22, 2025
Erich J. Sohn, Kandarp A. Sojitra, Leticia Rodrigues, Xiaoping Xu, Bess Frost, Jeetain Mittal, David S. Libich Abstract Ewing sarcoma, the second most common pediatric bone and soft tissue cancer, is caused by the aberrant fusion of the RNA-binding protein EWS (EWS) low-complexity domain (EWSLCD) to the DNA-binding domain of the transcription factor friend leukemia integration 1 (FLI1). The resulting fusion, [...]