BioRxiv: Intrinsically disordered SERBP1 regulates translation through topology-driven G-quadruplex recognition (Libich Lab)

March 19, 2026

       Antoine Baudin, Hoang H. Dinh, Kira Breunig, Xuifen Lei, Xiaoping Xu, View Luiz O. Penalva, David S. Libich Abstract Serpine mRNA-binding protein 1 (SERBP1) is an intrinsically disordered RNA-binding protein that regulates translation and ribosome biogenesis through interactions with ribosomes and other molecular complexes. Despite its regulatory importance and implication in 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 [...]

Editorial: Efficacy of larotrectinib in pediatric cancers with NTRK gene fusions (Houghton)

December 31, 2025

 Peter J Houghton 1, Mary-Ann Bjornsti 2 PMID: 41502892 PMCID: PMC12771222 DOI: 10.21037/tp-2025-664 No abstract available Figures Figure 1 Signaling pathways downstream of ligand… Figure 2 Schema showing characteristics of fusion… Comment on Elective Discontinuation of Larotrectinib in Pediatric Patients With TRK Fusion Sarcomas and Related Mesenchymal Tumors. Mascarenhas L, DuBois SG, Albert CM, Bielack S, Orbach D, Federman N, Geoerger [...]