Biology subjects

Riudavets Puig, R.

Publications and source records attributed to Riudavets Puig, R..

3 recordsLinked to original sources

bioRxiv2025

Understanding the kinetics of macrophage uptake and the metabolic fate of iron-carbohydrate complexes used for iron deficiency anemia treatment

Iron-carbohydrate complexes (ICCs) are widely used nanomedicines to treat iron deficiency anemia, yet their intracellular fate and the mechanisms of action underlying their differences in treatment outcomes remain poorly understood. Here, we thus performed a comprehensive dynamic characterization of two structurally distinct ICCs - iron sucrose (IS) and ferric carboxymaltose (FCM) - in primary human macrophages, key cells to the iron metabolism. By employing innovative correlative microscopy techniques, elemental analysis, and in vitro pharmacokinetic profiling, we demonstrate that the uptake, intracellular trafficking, and biodegradation of ICCs depend on their physicochemical properties. Specifically, IS is rapidly internalized and processed within endolysosomes, resulting in fast iron release and transient cytotoxicity. Conversely, FCM is sequestered in enlarged endosomes for an extended time before its biodegradation, a phenomenon we term the Hamster Effect, which leads to slower, more sustainable iron release. These results provide unprecedented insights into the metabolic fate of ICCs, enhancing our understanding of their different pharmacokinetic and pharmacodynamic profiles in vivo.

pharmacology and toxicology↗

bioRxiv2025

HiFIseek: gene-specific enrichment of high-impact mutations in associated genomic regions

Transcription is regulated through the sequence-specific binding of transcription factors (TFs) to cis-regulatory regions (CRRs). Although scattered along the genome, multiple CRRs are brought in close spatial proximity to the genes they regulate through the formation of DNA loops. The sequence component of transcriptional regulation suggests that DNA variants in CRRs could disrupt TF-DNA interactions and gene regulatory networks through a cascading effect. To date, only a few cases of recurrent cis-regulatory variants have been described. As an alternative to variant recurrence, some methods utilize genomic annotations that indicate the functional impact (FI) of a variant and the CRRs of each gene to detect the enrichment of high-impact cis-regulatory variants (CRVs). However, the agreement across the different associations and FI scoring methods remains unexplored. This work demonstrates that gene-CRR and FI scoring methods exhibit little consensus, highlighting the impact of the choice of a specific CRR-score combination in a given analysis. In addition, we demonstrate that cancer genes exhibit a higher frequency of FI variants compared to non-cancer genes. Based on this, we developed HiFIseek, a Snakemake pipeline exploring the enrichment of FI variants in associated genomic regions using all region-score combinations and two enrichment detection methods. We apply HiFIseek to detect genes exhibiting high FI CRVs in eight cancer cohorts and a set of breast cancer risk-associated single-nucleotide polymorphisms (SNPs). In the cancer cohorts, we observe a small degree of agreement across CRR-score combinations. Although HiFIseek detected known cancer-related genes with FI CRVs, most of them did not show significant changes in their expression. In the SNPs cohort, HiFIseek found small consensus across CRR-score combinations. However, one of the combinations returned 18 known cancer-related genes, including BRCA1, showing an enrichment of high-impact CRVs.

bioinformatics↗

bioRxiv2020

UniBind: maps of high-confidence direct TF-DNA interactions across nine species

Transcription factors (TFs) bind specifically to TF binding sites (TFBSs) at cis-regulatory regions to control transcription. Hence, it is critical to locate these TF-DNA interactions to understand transcriptional regulation. The availability of datasets generated by chromatin immunoprecipitation followed by sequencing (ChIP-seq) empowers our efforts to predict the specific locations of TFBSs with greater confidence than previously possible by fusing computational and experimental approaches. In this work, we processed ~10,000 public ChIP-seq datasets from nine species to provide high-quality TFBS predictions. After quality control, it culminated with the prediction of ~56 million TFBSs with experimental and computational evidence for direct TF-DNA interactions for 644 TFs in >1,000 cell lines and tissues. These TFBSs were used to predict >198,000 cis-regulatory modules representing clusters of binding events in the corresponding genomes. The high-quality of the TFBSs was reinforced by their evolutionary conservation, enrichment at active cis-regulatory regions, and capacity to predict combinatorial binding of TFs. Further, we confirmed that the cell type and tissue specificity of enhancer activity was correlated with the number of TFs with binding sites predicted in these regions. All the data is provided to the community through the UniBind database that can be accessed through its web-interface (https://unibind.uio.no/), a dedicated RESTful API, and as genomic tracks. Finally, we provide an enrichment tool, available as a web-service and an R package, for users to find TFs with enriched TFBSs in a set of provided genomic regions. UniBind is the first resource of its kind, providing the largest collection of high-confidence direct TF-DNA interactions in nine species.

genomics↗