Research Paper Archives - Greehey Children's Cancer

iScience: Predicting and interpreting protein and phosphoprotein abundance from pan-cancer and single-cell transcriptomes (Chen Lab)

March 12, 2026
Hui-Mei Tsai1,2,3,12 ∙ Tzu-Hung Hsiao2,4,5,12 ∙ Yu-Chiao Chiu6,7 ∙ Yufei Huang6,7 ∙ Eric Y. Chuang1,8,9,10 chuangey@ntu.edu.tw ∙ Yidong Chen3,11,13 cheny8@uthscsa.edu Highlights • DeepGxP provides a framework to translate transcriptomes into proteomic insight • DeepEnrich links RNA predictors to functional protein pathways and activities • DeepEnrich reveals cancer type-specific EGFR and HER2 phosphorylation patterns • Mutation effects are captured even without mutation data in model training Summary Proteins that impact phenotype and disease are [...]

Chemical Science: Unveiling BCL-xL-specific PROTAC efficiency and dissociation pathways using native mass spectrometry (Olsen, Zhou)

February 24, 2026
Mohamed I. Gadallah, Kailyn L. Nonhof, Digant Nayak, Peiyi Zhang, Olivia Dioli, Guangrong Zheng, Shaun K. Olsen, Daohong Zhou and Jennifer S. Brodbelt Author affiliations Abstract Overexpression of anti-apoptotic proteins such as BCL-xL is a hallmark of various cancers and a major driver of resistance to conventional chemotherapies. While small-molecule BCL-xL inhibitors have shown promising outcomes, [...]

Haematologica: IGF2BP3 inhibition: another home run for RNA-binding protein targeting in hematological malignancies (Penalva)

February 10, 2026
Luiz O.F. Penalva RNA-binding proteins (RBPs) are critical regulators of gene expression, aNecting RNA processing till translation. More than 1,500 proteins have been catalogued as RBPs in the human genome. 1 RBPs are very diverse in respect to structure, characteristic of RNA binding domain and function. In fact, RBPs are notoriously multi-functional with some of [...]

BioRxiv: High-throughput mapping of 6,888 RAD51D variants identifies distinct biochemical functions needed for homologous recombination and olaparib response (Sung)

January 30, 2026
Kristie E. Darrah, Shelby L. Hemker, Yashpal Rawal, Noah J. Goff, Phoebe Parker, Gayatri Ganesan, Caleb M. Stratton, Katherine Oppenheimer, Ella Roberts, Elena Glick, Nicole Banks, Arjun Kumar, Silvia Casadei, Matthew W. Snyder, Katherine Nathanson, Susan M. Domchek, Lea M. Starita, Shaun K. Olsen, Patrick Sung, Jacob O. Kitzman, Kara A. Bernstein Summary The tumor suppressor RAD51D is essential for homologous recombination (HR). Pathogenic variants in RAD51D are associated with breast and ovarian cancers. However, most clinical missense variants are of unknown significance. We performed a multiplex assay of variant effect to test 6,888 RAD51D coding variants for loss-of-function. The resulting variant-to-function [...]

Journal of Biological Chemistry: Phosphoregulation of RAD51AP1 function in homology-directed repair (Sung Lab)

January 16, 2026
Neelam Sharma1 ∙ Mollie E. Uhrig1,2 ∙ Youngho Kwon3 ∙ Patrick Sung3 ∙ Claudia Wiese1 cwiese@colostate.edu 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 a homology search and invades a homologous DNA template, forming a displacement loop (D-loop). The RAD51 filament is assisted in these processes by several proteins. One such protein [...]

BioMolecules: The PELP1 Pathway and Its Importance in Cancer Treatment (Rao Lab)

January 13, 2026
Khaled Mohamed Nassar Panneerdoss Subbarayalu Suryavathi Viswanadhapalli Ratna K. Vadlamudi Abstract Proline-, glutamic acid-, and leucine-rich protein 1 (PELP1) is a proto-oncogene that serves as a nuclear and cytoplasmic scaffolding protein. PELP1 plays a critical role in nuclear receptor signaling, ribosome biogenesis, chromatin modifications, cell cycle progression, non-genomic signaling, and DNA damage response. PELP1 expression [...]

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 [...]