Lopez-Aladid, R. | bioRxiv Science

bioRxiv2025

Enhanced Kidney Targeting and Distribution of Tubuloids During Normothermic Perfusion

Tubuloids have become a promising tool for kidney disease model and regeneration, although their ability for integration and regeneration in vivo is not well documented. Here we establish, characterize and compare human tubuloids using two optimized protocols, which added a prior isolation of tubular cells (Crude tubuloids) and proximal tubular cells (F4 tubuloids). Secondly, using this protocol, healthy rat-derived tubuloids were established. Finally, we compared two strategies to deliver GFP tubuloids in a kidney host: 1) subcapsular/intracortical injection and 2) tubuloid infusion during normothermic preservation in a rat transplantation model and a human discarded kidney. F4 tubuloids achieved a more differentiation state compared to Crude tubuloids. When analyzing tubuloid delivery to the kidney, normothermic perfusion was more efficient compared to in vivo injection, observing fully-developed tubules in the host parenchyma after 1 week and 1 month. Normothermic perfusion also successfully delivered kidney tubuloids to a discarded human kidney for transplantation. These results suggest that tubuloids administered during normothermic perfusion represent a potential strategy to enhance the translatability of kidney regenerative therapies to the clinical practice to condition kidney grafts and to treat kidney diseases.

bioengineering↗

bioRxiv2022

Brewpitopes: a pipeline to refine B-cell epitope predictions during public health emergencies

The application of B-cell epitope identification for the development of therapeutic antibodies is well established but consuming in terms of time and resources. For this reason, in the last few years, the immunoinformatic community has developed several computational predictive tools. While relatively successful, most of these tools only use a few properties of the candidate region to determine their likelihood of being a true B-cell epitope. However, this likelihood is influenced by a wide variety of protein features, including the presence of glycosylated residues in the neighbourhood of the candidate epitope, the subcellular location of the protein region or the three-dimensional information about their surface accessibility in the parental protein. In this study we created Brewpitopes, an integrative pipeline to curate computational predictions of B-cell epitopes by accounting for all the aforementioned features. To this end, we implemented a set of rational filters to mimic the conditions for the in vivo antibody recognition to enrich the B-cell epitope predictions in actionable candidates. To validate Brewpitopes, we analyzed the SARS-CoV-2 proteome. In the S protein, Brewpitopes enriched the initial predictions in 5-fold on epitopes with neutralizing potential (p-value < 2e-4). Other than S protein, 4 out of 16 proteins in the proteome contain curated B-cell epitopes and hence, have also potential interest for viral neutralization, since mutational escape mainly affects the S protein. Our results demonstrate that Brewpitopes is a powerful pipeline for the rapid prediction of refined B-cell epitopes during public health emergencies. Statement of significanceWe have created Brewpitopes, a new pipeline that integrates additional important features such as glycosylation or structural accessibility, to curate B-cell epitope more likely to be functional in vivo. We have also validated Brewpitopes against SARS-CoV-2 not only for S protein but also for the entire viral proteome demonstrating that is a rapid and reliable epitope predictive tool to be implemented in present or future public health emergencies. Brewpitopes has identified 7 SARS-CoV-2 epitopes in S and epitopes allocated in 4 other proteins. Overall, offering an accurate selection of epitopes that might be scaled up to the production of new antibodies.

bioinformatics↗