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Biology subjects

Ramos, O. H. P.

Publications and source records attributed to Ramos, O. H. P..

2 recordsLinked to original sources

Optimized quantitative bacterial two-hybrid (qB2H) for protein-protein interaction assessment

Characterizing mutation effects on protein-protein interactions (PPIs) is crucial for elucidating protein structure and function. Massively parallel PPI variant analyses such as deep mutational scanning (DMS) enable interface identification and generate datasets for machine learning. In cellulo strategies such as two-hybrid systems provide straightforward access to such data, but reliability depends on quantitative properties. Here, we show that existing bacterial two-hybrid (B2H) systems have limitations constraining accurate dataset generation. We engineered and benchmarked optimized quantitative B2H (qB2H) alternatives, enabling strain-independent assays, improved metrics, and generation of high-quality datasets. We demonstrate qB2H utility through interface mapping and binder optimization. Perturbation analysis of single-site variants accurately recovered known ASF1 complex contact positions, matching crystallographic data. Integration of generative AI-based design yielded an ASF1-binding peptide with a 70-fold increase in affinity. qB2H offers to R&D scientists a robust, reusable platform for quantitative PPI analysis, enabling both rational protein engineering and data-driven discovery.

synthetic biology↗

A low-dose immunotherapy targeting Fc-gamma Receptors and Heparan Sulfate Proteoglycan to impact myeloid cells and control tumor growth in cancers with varying immunosuppressive profiles

BackgroundMyeloid cells play a central role in cancer-associated immunosuppression. Indeed, their accumulation and functional reprogramming attenuate effective immune responses and may facilitate tumor progression. To modulate the activity of the myeloid subsets, we chose to target Fc{gamma} receptors (Fc{gamma}Rs), since all myeloid cell populations variably express Fc{gamma}Rs. As Fc{gamma}RIIb provides an inhibitory signaling that might alter efficacy, we developed an immunotherapy, active at a low dose to limit binding via this low-affinity receptor while still interacting with higher-affinity Fc{gamma}Rs. We engineered a Fc-based fusion protein whose activity is potentiated by its ability to engage both Fc{gamma}Rs and a coreceptor, Heparan Sulfate Proteoglycan (HSPGs). We designed and fused a HSPG-ligand, named T54, to a human IgG1-Fc molecule to produce the Fc-T54 fusion protein. MethodsFc-T54 was produced using recombinant technologies. Binding characteristics were assessed using ELISA and flow-cytometric assays. Immune activity was investigated using cell-culture assays. Ability to affect tumor growth was investigated using four syngeneic tumor models with deserted to inflamed characteristics that differ in their sensitivity to immune checkpoint inhibitors (ICIs). Tumor microenvironment (TME) was analysed by flow cytometry. ResultsCompared to Fc, Fc-T54 demonstrates superior binding to low-affinity Fc{gamma}Rs and interacts more effectively with human leukocytes, including neutrophils, and B lymphocytes, as well as with monocytes and dendritic cells (DCs) within peripheral blood mononuclear cells. In activation assays Fc-T54 increases the number of monocytes/macrophages and B-lymphocytes, decreases neutrophil abundance, and enhances DC activation. Fc-T54 also demonstrates enhanced interaction with murine DCs accompanied by increased activation. Subcutaneous administration of low dose Fc-T54 - or its murine surrogate - significantly inhibits tumor growth in immune-deserted and immune-excluded mouse models, and synergizes with anti-PD-1 therapy in the immune-inflamed model. TME analysis in the MB49 bladder cancer model reveals that the immunotherapy decreases the proportion of granulocytic myeloid-derived suppressor cells while increasing CD8+ T-cells and natural killer cells, promoting a microenvironment more prone to tumor control. ConclusionsThis new Fc{gamma}R/HSPG-engaging immunotherapy, administered via subcutaneous route, offers a novel approach to modulate the myeloid compartment and expand therapeutic options for ICI-resistant, deserted/excluded tumors, and for inflamed tumors when used in combination regimens.

cancer biology↗