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bioRxiv2026

A Visually Interpretable Histopathology-Based Immune Model Predicts T-effector Biology and Response to Immune checkpoint inhibition in Clear Cell Renal Cell Carcinoma Clinical Trial and Contemporary Real-World Datasets

Immune checkpoint inhibitors (ICI) are central to the treatment of metastatic clear cell renal cell carcinoma (ccRCC), yet only a subset of patients derive durable benefit, and clinically deployable predictive biomarkers remain an unmet need. RNA-based T-effector signatures capture cytotoxic immune biology and have been associated with ICI response in clinical trial cohorts; however, their clinical implementation is limited by the marked spatial heterogeneity of ccRCC, as well as cost, long turnaround time, sample quality requirements, and limited accessibility. Here, we developed a visually interpretable deep learning (DL) model that predicts a T-cell-enriched immune score directly from hematoxylin and eosin (H&E)-stained whole-slide images. To overcome the inability of H&E morphology alone to distinguish lymphocyte subsets, we trained the model using multimodal spatial supervision from CD8, PAX8, and ERG IHC, which respectively identified cytotoxic T-cell-rich regions, tumor cells, and endothelial cells, thereby constraining immune predictions to relevant tumor microenvironmental niches. The resulting H&E DL Immune score was validated by pathologist review, comparison with held-out CD8 IHC annotations, and independent datasets. The H&E DL Immune score correlated with T-effector RNA scores across independent institutional and IMmotion150 clinical trial cohorts (spearman correlations of 0.726; p=5.90x10-15 and 0.706; p=4.04x10-19). As a proof of principle, the score was used to characterize associations with key biological features across large cohorts, including sarcomatoid differentiation, BAP1 and PBRM1 mutation status, and additional transcriptomic signatures. In IMmotion150 clinical trial cohort, a median-dichotomized H&E DL Immune score, similar to RNA-based T-effector score, was significantly associated with clinical benefit from atezulumab therapy. In contemporary institutional cohorts of patients treated with frontline ipilimumab plus nivolumab or in initial 3 lines of nivolumab monotherapy, patients in the top quartile of H&E DL Immune score had significantly longer progression-free survival. Collectively, these findings support a scalable and interpretable H&E-based biomarker that captures T-effector biology and can help identify patients with ccRCC more likely to benefit from ICIs.

bioinformatics↗

bioRxiv2024

Structure-Based Design of a Highly Immunogenic, Conformationally Stabilized FimH Antigen for a Urinary Tract Infection Vaccine

Adhesion of E. coli to the urinary tract epithelium is a critical step in establishing urinary tract infections. FimH is an adhesin positioned on the fimbrial tip which binds to mannosylated proteins on the urinary tract epithelium via its lectin domain (FimHLD). FimH is of interest as a target of vaccines to prevent urinary tract infections (UTI). Previously, difficulties in obtaining purified recombinant FimH from E. coli along with the poor inherent immunogenicity of FimH have hindered the development of effective FimH vaccine candidates. To overcome these challenges, we have devised a novel production method using mammalian cells to produce high yields of homogeneous FimH protein with comparable biochemical and immunogenic properties to FimH produced in E. coli. Next, to optimize conformational stability and immunogenicity of FimH, we used a computational approach to design improved FimH mutants and evaluated their biophysical and biochemical properties, and murine immunogenicity. This approach identified a highly immunogenic FimH variant (FimH-DSG TM) that is produced at high yields in mammalian cells. By x-ray crystallography, we confirmed that the stabilized structure of the FimHLD in FimH-DSG TM is similar to native FimH on the fimbrial tip. Characterization of monoclonal antibodies elicited by FimH-DSG TM that can block bacterial binding to mannosylated surfaces identified 4 non-overlapping binding sites whose epitopes were mapped via a combinatorial cryogenic electron microscopy approach. Novel inhibitory epitopes in the lectin binding FimH were identified, revealing diverse functional mechanisms of FimH-directed antibodies with relevance to FimH-targeted UTI vaccines. Author summaryEscherichia coli is the primary cause of urinary tract infections. Adherence to uroepithelial surfaces is mediated by the pilus adhesin protein FimH, which is of interest as a vaccine candidate. We developed a method for producing recombinant FimH at bioprocess scale, previously a barrier to commercial development. Structure-based design and screening was used to identify a novel FimH vaccine candidate with improved stability and immunogenicity in mice. Structure of this full-length protein was determined by X-ray crystallography and shown to closely resemble the pilus adhesin present in its native form on the bacterial surface. Binding sites of biologically active FimH monoclonal antibodies were determined by X-ray crystallography or by cryo-electron microscopy, providing insights into mechanisms by which antibodies block binding of the bacteria to urinary tract receptors. One sentence summaryStructure-based design of a conformationally stabilized E. coli FimH vaccine candidate capable of eliciting antibodies to diverse epitopes with the ability to block bacterial binding to bladder epithelial cells.

microbiology↗