Biology subjects

Ou, C.

Publications and source records attributed to Ou, C..

7 recordsLinked to original sources

bioRxiv2026

Integrating activation-induced costimulation and cytokine signals enhance TCR-based cell therapies

TCR-based cell therapies offer broad targeting of tumor antigens with high sensitivity but often low durability due to insufficient costimulation (signal 2) and cytokine (signal 3) support. To address this, we developed a dual stimulatory receptor (DSR) consisting of the 4-1BBL ectodomain fused to the thrombopoietin receptor (cMPL) endodomain. DSR engages 4-1BB that is transiently upregulated upon TCR stimulation eliciting signal 2 and simultaneously activates cMPL-driven STAT3/5 phosphorylation providing signal 3. DSR increases the expansion of T cells, preserving their effector function and an effector-associated transcriptional profile upon repeated antigen stimulation. DSR arming significantly improves in vivo antitumor activity of T cells redirected to cancer through engineered TCRs or soluble T-cell engagers in diverse xenograft tumor models by enhancing T cell expansion and persistence post-infusion. These results demonstrate broad utility and establish DSR as a modular receptor for the effective and synchronized delivery of signals 2 and 3 to support TCR-based immunotherapies.

immunology↗

bioRxiv2026

Engineering CAR-Vδ2 T cells to boost persistence and anti-tumor function

Chimeric antigen receptor (CAR)-modified V{delta}2 T cells are an attractive therapeutic cell platform for cancer immunotherapy. However, their clinical efficacy is limited by short in vivo persistence due to insufficient cytokine support and high susceptibility to activation-induced cell death (AICD). Through comparison of membrane-bound (mb) cytokines, we identified mbIL-18 to support superior anti-tumor activity of CAR-V{delta}2 T cells in vitro and in vivo. To reduce constitutive surface exposure of IL-18 and enable antigen-driven signal 3, we fused MyD88 - the key IL-18R signaling mediator - to an extracellular domain of Fas (Fas88). Antigen stimulation-induced FasL engagement of Fas88 triggered IL-18 signaling while simultaneously protecting V{delta}2 T cells from AICD. Fas88-armed human CAR-V{delta}2 T cells produced superior yet stimulation-dependent in vivo expansion and functional persistence in xenograft models of hematologic and solid malignancies. Together, these findings highlight the importance of IL-18 signaling and AICD resistance for CAR-V{delta}2 T cell activity, enabling a single-transgene modification to limit inflammatory risk and facilitate clinical translation.

synthetic biology↗

bioRxiv2025

Protein Diffusion Models as Statistical Potentials

Machine learning has driven rapid progress in protein structure prediction and design, but key challenges remain such as predicting protein structures when evolutionary information is unavailable, modeling full conformational landscapes, and capturing the thermodynamics of mutations and conformational changes. To address these problems we developed ProteinEBM, an Energy-Based Model of protein conformational space. ProteinEBMs energies can be used to rank protein structure correctness, predict the energetic effects of mutations, sample from protein conformational landscapes, predict protein structures, and simulate protein folding pathways. Across all of these tasks, ProteinEBM shows performance competitive with or exceeding previous machine learning and physics-based methods, including state-of-the-art performance at predicting the effects of mutations on protein stability.

biophysics↗

bioRxiv2025

OriGene: A Self-Evolving Virtual Disease Biologist Automating Therapeutic Target Discovery

Here, we present OriGene, a self-evolving multi-agent system that functions as a virtual disease biologist, systematically identifying original and mechanistically grounded therapeutic targets at scale. OriGenes architecture integrates over 600 specialized tools through a Model Context Protocol (MCP), enabling it to reason across diverse data modalities including genomics, protein networks, pharmacology, clinical records and literature evidence, to generate and prioritize target discovery hypotheses. We implemented a strategy combining a knowledge graph-based Tool RAG with an advanced agent selection mechanism to enable dynamic, context-aware tool deployment. Through a self-evolving framework, OriGene continuously integrates human and experimental feedback to iteratively refine its core thinking templates, tool composition, and analytical protocols, thereby enhancing both accuracy and adaptability over time. To comprehensively evaluate its performance, we established TRQA, an original benchmark comprising over 1,900 expert-level question-answer pairs spanning a wide range of diseases and target classes. OriGene consistently outperforms human experts, leading research agents, and state-of-the-art large language models in accuracy, recall, and robustness, particularly under conditions of data sparsity or noise. Critically, OriGene nominated previously underexplored therapeutic targets for liver (GPR160) and colorectal cancer (ARG2), which demonstrated significant anti-tumor activity in patient-derived organoid and tumor fragment models mirroring human clinical exposures. These findings demonstrate OriGenes potential as a scalable and adaptive platform for AI-driven discovery of mechanistically grounded therapeutic targets, offering a new paradigm to accelerate drug development.

bioinformatics↗

bioRxiv2023

Mechanism and cellular function of direct membrane binding by the ESCRT and ERES-associated Ca2+-sensor ALG-2

Apoptosis Linked Gene-2 (ALG-2) is a multifunctional intracellular Ca2+ sensor and the archetypal member of the penta-EF hand protein family. ALG-2 functions in the repair of damage to both the plasma and lysosome membranes and in COPII-dependent budding at endoplasmic reticulum exit sites (ERES). In the presence of Ca2+, ALG-2 binds to ESCRT-I and ALIX in membrane repair and to SEC31A at ERES. ALG-2 also binds directly to acidic membranes in the presence of Ca2+ by a combination of electrostatic and hydrophobic interactions. By combining GUV-based experiments and molecular dynamics simulations, we show that charge-reversed mutants of ALG-2 at these locations disrupt membrane recruitment. ALG-2 membrane binding mutants have reduced or abrogated ERES localization in response to Thapsigargin-induced Ca2+ release but still localize to lysosomes following lysosomal Ca2+ release. In vitro reconstitution shows that the ALG-2 membrane-binding defect can be rescued by binding to ESCRT-I. These data thus reveal the nature of direct Ca2+-dependent membrane binding and its interplay with Ca2+-dependent protein binding in the cellular functions of ALG-2.

biophysics↗

bioRxiv2023

Mutant Ppbbx24-del gene positively regulates light-induced anthocyanin accumulation in the red pear

Anthocyanins are pigments and nutrients in red pears regulated by BBX family genes. Herein, we characterized a 14-nucleotide deletion mutation in the coding region of the PpBBX24 gene from Red Zaosu pear (Pyrus pyrifolia White Pear Group), named Ppbbx24-del. Genetic and biochemical approaches were used to compare the roles of PpBBX24 and Ppbbx24-del in anthocyanin accumulation. Ppbbx24-del played a positive role in anthocyanin biosynthesis of the Red Zaosu pear peel by light treatment. Functional analyses based on overexpression in tobacco and transient overexpression in pear fruit peels showed that Ppbbx24-del promoted anthocyanin accumulation. Cyanidin and peonidin were major differentially expressed anthocyanins, and transcript levels of some structural genes in the anthocyanin biosynthesis pathway were significantly increased. Protein interaction assays showed that PpBBX24 was located in the nucleus and interacted with PpHY5, whereas Ppbbx24-del was colocalized in the nucleoplasm and did not interact with PpHY5. PpHY5 and Ppbbx24-del had positive regulatory effects on the expression of PpCHS, PpCHI, and PpMYB10 when acting alone, but had cumulative effects on gene activation when acting simultaneously. Alone, PpBBX24 had no significant effect on the expression of PpCHS, PpCHI, or PpMYB10, whereas it inhibited the activation effects of PpHY5 on downstream genes when it existed with PpHY5. Our study demonstrated that mutant Ppbbx24-del positively regulates the anthocyanin accumulation in pear. The results of this study clarify the mechanism and enrich the regulatory network of anthocyanin biosynthesis, which lays a theoretical foundation for Ppbbx24-del use to create red pear cultivars.

molecular biology↗

bioRxiv2022

In vitro reconstitution of calcium-dependent recruitment of the human ESCRT machinery in lysosomal membrane repair

The endosomal sorting complex required for transport (ESCRT) machinery has been shown to be centrally involved in repair of damage to both the plasma and lysosome membranes. ESCRT recruitment to sites of damage occurs on a fast time scale, and Ca2+ has been proposed to play a key signaling role in the process. Here, we show that the Ca2+-binding regulatory protein ALG-2 binds directly to negatively charged membranes in a Ca2+-dependent manner. Next, by monitoring the colocalization of ALIX with ALG-2 on negatively charged membranes, we show that ALG-2 recruits ALIX to the membrane. Furthermore, we show that ALIX recruitment to membrane orchestrates the downstream assembly of late-acting CHMP4B, CHMP3, CHMP2A subunits along with the AAA+ ATPase VPS4B. Finally, we show that ALG-2 can also recruit the ESCRT-III machinery to the membrane via the canonical ESCRT-I/II pathway. Our reconstitution experiments delineate the minimal sets of components needed to assemble the entire membrane repair machinery and open a new avenue for mechanistic understanding of endolysosomal membrane repair. Significance statementOne of the ways by which protein aggregates can propagate and lead to progression of a neurodegenerative disease is by damaging the membrane that is destined to degrade the misfolded, aggregated protein. ESCRT machinery has been implicated in sealing these damaged membranes, and the nature of the membrane recruitment trigger signal for this machinery is a major open question. Here, we show in vitro that ALG-2 can bring ESCRT machinery to membranes in a Ca2+-dependent manner.

cell biology↗