Biology subjects

Rojo, C.

Publications and source records attributed to Rojo, C..

3 recordsLinked to original sources

bioRxiv2026

A guide for establishing patient-derived organoids from bile samples obtained during endoscopic procedures and performing gene expression knockdown

Bile represents a clinically accessible biological fluid that can mitigates major limitations associated with tissue-based sampling for the generation of organoid models to study hepatobiliary disease, including biliary tract cancers where tissue availability is often limited. Importantly, bile can also enable the generation of non-malignant cholangiocyte organoids that are otherwise difficult to obtain. Here, we describe an operator-oriented, step-by-step protocol to generate organoids from fresh bile collected during endoscopic retrograde cholangiopancreatography (ERCP), together with two complementary workflows for siRNA delivery in 3D cultures. We detail critical control points that are often under-reported, yet considerably influence success and reproducibility. The protocol was optimized and applied in a real-world cohort of 21 patients undergoing ERCP, including benign biliary obstruction due to choledocholithiasis (n=5) and malignant strictures (n=16: cholangiocarcinoma n=13, gallbladder adenocarcinoma n=1, ampullary tumors n=2). Expandable organoids were established in 17/21 cases (81%), with establishment rates of 60% for choledocholithiasis and 85-100% across malignant entities. Anticipated results include organoid outgrowth within [~]2-3 weeks and morphological heterogeneity in cultures derived from malignant strictures, where normal-like and tumor-like populations may initially coexist and can drift toward a cystic phenotype under routine expansion, motivating optional manual handpicking when tumor-enriched lines are required. As downstream readouts, we show feasibility of DNA-based profiling in selected paired bile-organoid samples (targeted sequencing and ULP-WGS copy-number analysis) and demonstrate proof-of-concept gene silencing via siRNA in both dissociated cells prior to re-embedding, and intact fully formed organoids while preserving 3D architecture. Collectively, this workflow provides a practical and reproducible framework to establish, expand, characterize and functionally perturb bile-derived organoids from routine clinical procedures, facilitating standardized implementation across laboratories.

cancer biology↗

bioRxiv2025

Demonstration of SLU7 as a new pan-cancer target

Cancer treatment remains challenging due to heterogeneous responses to immunotherapy across patients and tumor types. Innovative strategies are required to overcome immune evasion. We have identified the splicing factor SLU7 as essential for the survival of cancer cells from diverse origins. SLU7 knockdown induces R-loop accumulation, transcription-dependent genomic instability, DNA damage, and replication catastrophe, together with aberrant splicing and inhibition of nonsense-mediated mRNA decay (NMD) and/or DNA methylation. These alterations lead to the expression of neoantigens, interferon B1, endogenous retroviruses, and cancer-testis antigens, which would enhance tumor immunogenicity. Therefore, we propose SLU7 targeting as a dual-action therapy, combining direct tumor suppression with immune activation. Using various murine cancer models, including orthotopic liver tumors, and multiple molecular strategies--such as inducible CRISPR/Cas9, systemic delivery of chimeric siSLU7-nucleolin aptamers (APTASLU), and intratumoral injection of siSLU7-loaded nanoparticles--we show that distinct siSLU7 sequences and delivery platforms effectively inhibit tumor growth. Furthermore, SLU7 silencing synergizes with immune checkpoint inhibitors, amplifying anti-tumor responses. Our in vivo data demonstrate that SLU7 is a promising, versatile target for diverse cancers. Its multimodal mechanism offers potential to overcome tumor heterogeneity, reverse immune tolerance, and enhance immunotherapy efficacy.

cancer biology↗

bioRxiv2021

Metacommunities from bacteria to birds: stronger environmental effects in Mediterranean than in tropical ponds.

The metacommunity concept provides a theoretical framework that aims at explaining organism distributions by a combination of environmental filtering, dispersal and drift. With the development of statistical tools to quantify and partially isolate the role of each of these processes, empirical metacommunity studies have multiplied worldwide. However, few works attempt a multi-taxon approach and even fewer compare two distant biogeographical regions using the same methodology. Under this framework, we tested the expectation that temperate (mediterranean-climate) pond metacommunities would be more influenced by environmental and spatial processes than tropical ones, because of stronger environmental gradients and greater isolation of waterbodies. We surveyed 30 tropical and 32 mediterranean temporary ponds from Costa Rica and Spain, respectively, and obtained data on 49 environmental variables (including limnological, hydrogeomorphological, biotic, climatic, and landscape variables). We characterized the biological communities of Bacteria and Archaea (from both the water column and the sediments), phytoplankton, zooplankton, benthic invertebrates, amphibians and birds, and estimated the relative role of space and environment on metacommunity organization for each group and region, by means of variation partitioning using Generalized Additive Models (GAMs). Environmental selection was important in both tropical and mediterranean ponds, but markedly stronger in the latter, probably due to their larger limnological heterogeneity. Spatialized environment and pure spatial effects were greater in the tropics, related to higher climatic heterogeneity and dispersal processes (e.g. restriction, surplus) acting at different scales. The variability between taxonomic groups in spatial and environmental contributions was very wide. Effects on passive and active dispersers were similar within regions but different across regions, with higher environmental effects in mediterranean active dispersers. The residual (unexplained) variation was larger in tropical pond metacommunities, suggesting a higher role for stochastic processes and/or effects of biotic interactions in the tropics. Overall, these results provide support, for a wide variety of organisms related to aquatic habitats, for the classical view of stronger abiotic niche constraints in temperate areas compared to the tropics.

ecology↗