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)

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Approaches targeting factors that simultaneously promote tumor growth and progression, induce therapy resistance, and inhibit anti-tumor immunity offer clear benefits over therapies targeting only one of these tumor-promoting processes. Through comprehensive loss-of-function genomic screening, we identified SCUBE3 as a pivotal factor that supports survival and therapy resistance and also orchestrates an immunosuppressive tumor microenvironment. Secretory SCUBE3 supported oncogenic activity through interactions with key oncogenic cell surface receptor proteins, including EGFR, mutant CALR, and TGFβRI/II. These interactions activated the transcription factors FOXR2 and c-Myc, promoting cancer cell proliferation and therapy resistance by enhancing DNA damage repair. Additionally, the SCUBE3-FOXR2 axis created an immunosuppressive tumor microenvironment by facilitating recruitment of the DNMT1 epigenetic repressor complex to the transcription regulator IRF1, thereby inhibiting the expression of MHC-I and MHC-II genes. A first-in-class neutralizing antibody targeting SCUBE3, developed using a sophisticated antibody discovery platform and engineered with specific mutations in the heavy chain to enhance specificity and efficacy, demonstrated profound therapeutic potential across various cancer types in preclinical models, including breast and ovarian cancer patient-derived xenografts. This discovery advances efforts to develop a targeted therapy for cancers characterized by hyperactive SCUBE3-associated signaling pathways.

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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

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Approaches targeting factors that simultaneously promote tumor growth and progression, induce therapy resistance, and inhibit anti-tumor immunity offer clear benefits over therapies targeting only one of these tumor-promoting processes. Through comprehensive loss-of-function genomic screening, we identified SCUBE3 as a pivotal factor that supports survival and therapy resistance and also orchestrates an immunosuppressive tumor microenvironment. Secretory SCUBE3 supported oncogenic activity through interactions with key oncogenic cell surface receptor proteins, including EGFR, mutant CALR, and TGFβRI/II. These interactions activated the transcription factors FOXR2 and c-Myc, promoting cancer cell proliferation and therapy resistance by enhancing DNA damage repair. Additionally, the SCUBE3-FOXR2 axis created an immunosuppressive tumor microenvironment by facilitating recruitment of the DNMT1 epigenetic repressor complex to the transcription regulator IRF1, thereby inhibiting the expression of MHC-I and MHC-II genes. A first-in-class neutralizing antibody targeting SCUBE3, developed using a sophisticated antibody discovery platform and engineered with specific mutations in the heavy chain to enhance specificity and efficacy, demonstrated profound therapeutic potential across various cancer types in preclinical models, including breast and ovarian cancer patient-derived xenografts. This discovery advances efforts to develop a targeted therapy for cancers characterized by hyperactive SCUBE3-associated signaling pathways.

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NGS User Group Holiday Gathering

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Dear NGS Community,

The Greehey Children’s Cancer Research Institute (CCRI) Genome Sequencing Facility (GSF), the Next Generation Sequencing Shared Resource of the Mays Cancer Center, warmly invites you to our 2025 NGS User Group Holiday Party:

📅 Wednesday, December 3, 2025
📍 Greehey CCRI Dining Area
⏰ Breakfast begins at 8:30 AM | Event: 9:00 AM – 11:00 AM
☕ Breakfast, coffee, holiday treats & gift giveaways included!

This annual celebration is our way of thanking you for your trust, collaboration, and continued support. The event provides a casual, festive space to:

  • Hear updates on new assays, equipment (including 10x Genomics Xenium), and GSF pilot grants (50% off for new Visium HD & Xenium users)
  • Learn about BD Biosciences single-cell workflows and other genomic technologies
  • Engage with field application scientists, specialists, and local reps from our vendors, including Illumina, 10x Genomics, and BD Biosciences.
  • Share your needs and feedback on future directions, such as spatial biology and multi-omics
  • Network with colleagues, collaborators, and fellow NGS users

For questions, please get in touch with Brian Phillips (PhillipsB@uthscsa.edu) or Zhao Lai (laiz@uthscsa.edu)

We look forward to celebrating with you, sharing exciting technology updates, and welcoming the holiday season together.

Wishing everyone a Merry Christmas and a wonderful New Year ahead!

Sincerely,

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

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  • 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 a ribosomal protein (RP) that is encoded as a fusion protein with ubiquitin (Ub). In yeast, each Ub-RP fusion requires processing by deubiquitylating enzymes (DUBs) to generate ribosome-assembly-competent RPs and to contribute to the cellular Ub pool. However, the mechanism by which DUBs in human cells process Ub-RP fusions remains unclear. Here, we discovered that Ub-RPs are substrates of the Ub-fusion degradation (UFD) pathway in human cells via lysine 29 and 48 (K29/K48)-specific ubiquitylation and proteasomal degradation. We identified a pool of DUBs that catalytically process Ub-RPs, as well as DUBs that physically occlude the interaction of Ub-RPs with UFD pathway Ub E3 ligases to prevent their degradation in a non-catalytic manner. Our results suggest that DUBs both process and stabilize Ub-RPs, whereas the UFD pathway regulates levels of Ub-RPs that cannot be fully processed by DUBs to fine-tune protein homeostasis.

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

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Abstract

B cells express many protein ligands, yet their regulatory functions are incompletely understood. We profiled ligand expression across murine B sublineage cells, including those activated by defined receptor signals, and assessed their regulatory capacities and specificities through in silico analysis of ligand-receptor interactions. Consequently, we identified a B cell subset that expressed cytokine interleukin-27 (IL-27) and chemokine CXCL10. Through the IL-27–IL-27 receptor interaction, these IL-27/CXCL10-producing B cells targeted CD40-activated B cells in vitro and, upon induction by immunization and viral infection, optimized antibody responses and antiviral immunity in vivo. Also present in breast cancer tumors and retained there through CXCL10-CXCR3 interaction–mediated self-targeting, these cells promoted B cell PD-L1 expression and immune evasion. Mechanistically, Il27 and Cxcl10 transcription was induced by synergizing Toll-like receptor (TLR) and CD40 signals and driven by coinduced transcription factor BATF3, which directly targeted these genes. By applying a discovery framework focusing on regulatory cells, our findings expand the recognized scope of B cell regulatory functions.
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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)

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  • 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 for the development of a SARS-CoV-2 main protease (MPro) inhibitor. Compound 6a displayed submicromolar biochemical potency in the ultrasensitive assay developed by Drag and co-workers. Through an iterative structure–activity relationship campaign, we discovered an unexpected improvement in both biochemical and cellular potency through the incorporation of an ortho substituent within the P3 benzamide. X-ray crystallography revealed that incorporation of the ortho substituent caused a subtle but important binding enhancement of the P1 glutamate group within the MPro S1 pocket. While incorporation of the ortho substituent improved the potency, the off-target selectivity against a panel of cysteine proteases and cell activity remained suboptimal. Further scanning of the P2 core revealed that incorporation of the 3.1.0 proline could address these issues and afford compound 22e, a highly potent and cellularly active MPro inhibitor.

Keywords

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

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Abstract

Background

Treatment for patients with malignant peripheral nerve sheath tumors (MPNST) is an unmet clinical need. Loss of NF1 in MPNST leads to hyperactivation of RAS; however, little is known about relevant downstream oncogenic signaling through RAF paralogs, and effective targeted therapies in MPNST are still lacking.

Methods

Conditional gene expression, CRISPR-CAS9, and shRNA-mediated knockdown were used to perform gain/loss-of-function experiments to explore the effect of reconstituting the GTPase-activating protein-related domain of NF1 or knockdown of A/B/CRAF kinases on ERK signaling output and MPNST cell growth. Colony formation, cell proliferation, and live cells imaging assays were performed to assess cell growth in response to genetic manipulations or drug treatments. Pathway enrichment analysis on RNA sequencing following drug perturbation, efficacy studies in cell-line-derived and patient-derived xenograft models, and immunoblotting/immunohistochemistry were conducted to assess tumor growth and ERK pathway activity in cells or in pharmacodynamic analyses of tumor xenografts.

ResultsNF1 loss activates RAS/ERK signaling through B/CRAF, and cell growth and ERK signaling of NF1-MPNST are dependent on B/CRAF, but not ARAF. Genetic or pharmacological inhibition of B/CRAF using a paralog-selective RAF inhibitor (RAFi) significantly potentiates MEK inhibitor (MEKi) treatment through more effective suppression of ERK signaling and proliferation. This is shown in multiple traditional and patient-derived cell lines and xenograft models, including those with acquired resistance to MEKi.

Conclusions

These findings contribute preclinical evidence that the combination of paralog-selective B/CRAFi and MEKi is effective in NF1-MPNST and can overcome resistance to single-agent MEKi.

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

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Abstract

Post-translational modification of proteins by SUMO (small ubiquitin-like modifier) regulates fundamental cellular processes and occurs through the sequential interactions and activities of three enzymes: E1, E2, and E3. SUMO E1 activates SUMO in a two-step process involving adenylation and thioester bond formation, followed by transfer of SUMO to its dedicated E2 enzyme, UBC9. This process is termed E1–E2 thioester transfer (or transthioesterification). Despite its fundamental importance, the molecular basis for SUMO E1–UBC9 thioester transfer and the molecular rules governing SUMO E1–UBC9 specificity are poorly understood. Here we present cryo-EM reconstructions of human SUMO E1 in complex with UBC9, SUMO1 adenylate, and SUMO1 thioester intermediate. Our structures reveal drastic conformational changes that accompany thioester transfer, providing insights into the molecular recognition of UBC9 by SUMO E1 and delineating the rules that govern SUMO E1–UBC9 specificity. Collectively, our structural, biochemical, and cell-based studies elucidate the molecular mechanisms by which SUMOylation exerts its essential biological functions.

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

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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 such protein is RAD51-Associated-Protein 1 (RAD51AP1) which binds DNA and RNA and directly interacts with RAD51. Of note, RAD51AP1 overexpression is associated with poor prognosis in several different cancer types.

Here, we show that RAD51AP1 activity is regulated by phosphorylation. RAD51AP1 bearing S277/282A mutations is more proficient in the stimulation of D-loop formation than wild type RAD51AP1 or phosphomimetic RAD51AP1-S277/282D. In EMSAs, RAD51AP1 with S277/282A mutations more avidly binds ssDNA, double-stranded (ds)DNA, and the nucleosome core particle than wild type RAD51AP1 or RAD51AP1-S277/282D. In cells, RAD51AP1-S277/282A confers no rescue of RAD51AP1 deficiency in toxicity tests and DNA replication assays. In contrast, RAD51AP1-S277/282D fully rescues RAD51AP1 deficiency. We provide evidence that RAD51AP1-S277 is a CDK2 target and propose a model in which RAD51AP1-S277/282 phosphorylation ensures RAD51AP1 flexibility for dynamic engagement in consecutive steps of the HDR reaction. Our results provide new mechanistic insights into RAD51AP1 regulation by a CDK.

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

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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, EWS::FLI1, directly interacts with and engages in a dynamic interplay with EWS that drives tumorigenesis and regulates the function of both proteins. While EWSLCD is known to promote self-association, the role of the RNA-binding domains (RBDs) of EWS, which include arginine–glycine–glycine (RGG) repeat regions and a structured RNA-recognition motif (RRM), remains less well understood. Here, we investigate the interplay between EWSLCD and RBDs using biomolecular condensation assays, microscopy, nuclear magnetic resonance (NMR) spectroscopy, and molecular simulations. Our studies reveal that RBDs differentially influence EWSLCD condensate formation and suggest that electrostatics and polypeptide-chain length likely contribute to this interaction. NMR spectroscopy and molecular dynamics simulations further demonstrate that EWSLCD and the central RNA-binding region, comprising the RRM and RGG2 domains, engage in transient, non-specific interactions that are broadly distributed across both regions and involve diverse residue types. Specifically, tyrosine, polar residues, and proline within EWSLCD preferentially interact with arginine, glycine, and proline residues in the RBD. Atomistic simulations of EWS confirm that the full-length protein exhibits a similar interaction profile with conserved chemical specificity, supporting a model in which a network of weak, distributed interdomain contacts underlies EWS self-association. Together, these findings provide molecular insight into the mechanisms of EWS condensate formation and lay the groundwork for understanding how interdomain interactions regulate EWS and EWS::FLI1 function.

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