Biology subjects

Meseguer, A.

Publications and source records attributed to Meseguer, A..

10 recordsLinked to original sources

bioRxiv2026

ModCRE-NN: Interpretable Deep Learning Harnesses Structural and Evolutionary Synergy to Predict Transcription Factor Binding Specificity

We present ModCRE-NN, a machine-learning framework and server for predicting transcription-factor (TF) DNA-binding motifs through the integration of structural and evolutionary information. The method combines structure-derived Position Weight Matrices (PWMs) together with PWMs of homologous spanning multiple evolutionary sequence-identity intervals, which are integrated into a unified 20-channel tensor representation. Benchmark datasets were constructed on experimental databases of TF motifs, showing DNA binding specificity, while redundancy reduction and strict train/test partitioning minimized homology leakage. Prediction quality was evaluated on an independent separated set of TFs using the similarity analysis of profiles. Three complementary architectures were implemented and evaluated: an interpretable regression-based model, a convolutional neural network (CNN), and a Transformer-based architecture using self-attention mechanisms. The regression model achieved strong performance in high-homology regimes dominated by closely related PWMs, whereas CNN and Transformer architectures showed superior robustness under low evolutionary similarity and increased structural uncertainty. Importantly, AI-generated motifs consistently improved the similarity-scores while reducing prediction variance relative to the original structural and evolutionary input motifs, indicating that the models effectively denoise heterogeneous motif assemblies and reconstruct stable consensus DNA-binding representations rather than simply transferring PWMs from the nearest homolog. The CNN model exhibited the most balanced attribution profile, suggesting enhanced ability to combine weak structural and evolutionary signals into coherent motif representations. Additionally, we implemented a prediction-reliability framework combining Random Forest regression, exponential interpolation, and hybrid residual-corrected modeling to estimate the quality and uncertainty of the PWMs as functions of evolutionary similarity, motif-cluster consistency, and TF-family context. Overall, our results demonstrate that integrating structural information with deep learning provides a robust framework for large-scale TF-binding specificity prediction under conditions of substantial evolutionary divergence and motif uncertainty.

bioinformatics↗

bioRxiv2025

TMEM9 and SEC22B interact with ClC-5 to shape renal proximal tubule function and Dent's Disease type I pathogenesis

Cl-/H+ antiporter ClC-5 is a key regulator of renal proximal tubule function, primarily by controlling endosomal acidification. Loss-of-function mutations in ClC-5 cause Dents Disease type 1 (DD1), a rare renal tubulopathy that progresses to kidney failure with varying severity. To understand the specific mechanisms linking ClC-5 loss-of-function with DD1 phenotypic heterogeneity, three ClC-5 pathogenic mutations (I524K, E527D and V523{Delta}) were investigated using renal proximal tubule epithelial cell lines. We have identified distinct intracellular retention patterns of these ClC-5 mutants, all leading to altered endolysosomal pH and disrupted secretory pathway organization. Through an interactome analysis, we have uncovered several ClC-5 partners including TMEM9, which interacted with all ClC-5 forms. TMEM9 knockdown (KD) recapitulated key DD1 characteristics, like defective endocytosis and epithelial dedifferentiation, but paradoxically enhanced endosomal acidification. The secretory pathway was also altered in cells lacking TMEM9 (e.g. enlarged endosomes, and fragmented Golgi apparatus). A similar phenotype was observed in cells depleted of SEC22B; an R-SNARE that we have found to specifically interact with wild-type ClC-5, but not the mutants. Notably, its deletion impaired ClC-5 trafficking, causing its retention at the Golgi and endosomes. Altogether, our findings highlight the relevance of TMEM9 and SEC22B in ClC-5 function, suggesting them as DD1 pathophysiology modifiers.

cell biology↗

bioRxiv2025

sKL/mKL Transcript Ratio and Protein Localization Define a Species- and Region-Specific Klotho Signature in the CNS and AD Progression

-Klotho is a multifunctional protein widely recognized for its anti-aging and neuroprotective properties. This study investigates the expression and localization of the secreted Klotho (s-KL) isoform in the human brain and its potential role in Alzheimers disease. Using RT-qPCR, we observed that the s-KL transcript predominates over the membrane-bound KL (m-KL) in multiple brain regions, a pattern consistent in macaques and lemurs. Immunohistochemistry and immunoprecipitation assays confirmed the presence of the s-KL protein in human and mouse brain parenchyma, revealing species-specific cellular localization. In human cerebrospinal fluid (CSF), s-KL constitutes [~]28% of total KL, with levels significantly reduced in mild dementia-AD patients. These findings underscore s-KLs potential neuroprotective role and highlight its differential regulation and expression during AD progression.

neuroscience↗

bioRxiv2023

Renal Cl-/H+ antiporter ClC-5 regulates collagen production and release in Dent Disease models

Mutations in the Cl-/H+ antiporter ClC-5 cause Dents Disease 1 (DD1), a rare primary tubulopathy that eventually progresses to renal failure. In fact, even with normal kidney function, DD1 patients present renal tubulointerstitial fibrosis. However, the link between ClC-5 loss-of-function and renal fibrosis remains unclear. Here, we have shown that DD1 mice models lacking ClC-5 present higher renal collagen deposition and fibrosis. Accordingly, deletion of ClC-5 in human renal proximal tubule epithelial cells (CLCN5 KD) recapitulates this effect. We have demonstrated that CLCN5 KD causes an increase of collagen I (Col I) and IV (Col IV) intracellular levels by promoting their transcription through {beta}-catenin pathway and impairing their lysosomal-mediated degradation. In addition, CLCN5 KD cells release more Col I and IV at the extracellular space that form fibres with altered properties and resistance to removal compared to control cells. Altogether, we describe a new regulatory mechanism for collagens production and release by ClC-5, which is altered in DD1 and provides a better understanding of disease progression to renal fibrosis. SIGNIFICANCE STATEMENTRenal fibrosis is a common pathologic process occurring as consequence of chronic kidney injury and leading to renal dysfunction. Dents Disease is a rare renal pathology that progresses to chronic kidney disease and tubulointerstitial fibrosis. Interestingly, it is caused by mutations in a single gene called CLCN5, therefore it can help understanding the cellular mechanisms of renal fibrosis. Using cellular and mice models of the disease, we describe a mechanism linking CLCN5 function, cell differentiation and regulation of collagen levels, major component of extracellular matrix and important player for renal fibrosis development. In conclusion, our results provide a link between CLCN5 and altered collagen deposition, which could be relevant for other renal Fanconi syndrome related diseases also progressing to fibrosis.

cell biology↗

bioRxiv2022

Cross regulation between the molecular clock and kidney inflammatory, metabolic and fibrotic responses

Chronic kidney disease is a highly prevalent condition that remains a major clinical and biomedical challenge. Tubulo-interstitial fibrosis is the common pathological substrate for many causes that lead to chronic kidney disease. It is characterized by profound derangements in metabolic and inflammatory responses, whereby functional tissue is replaced with extracellular matrix, leading to the suppression of renal function. Perturbations in the circadian rhythm have been associated with many human pathologies, including renal disease. However, the role of the molecular clock in the instauration of fibrosis remains incompletely understood. We investigated the relationship between the molecular clock and renal damage in experimental models of injury and fibrosis (UUO, FAN and adenine toxicity), employing genetically-modified mice with selective deficiencies of the clock components Bmal1, Clock and Cry. We found that UUO induced a marked increase in the expression of Bmal1. In human tubular epithelial cells, the pro-fibrotic mediator, TGF-{beta}, significantly altered the expression of core clock components. We further observed that the absence of Cry drastically aggravated kidney fibrosis, while both Cry and Clock played a role in the neutrophil and macrophage mediated inflammatory response, respectively. Suppression of Cry1/2 was associated with a major shift in the expression of metabolism-related genes, underscoring the importance of metabolic dysfunction in fibrosis. These results support a reciprocal interaction between the circadian clock and the response to kidney injury. Translational statementChronic kidney disease (CKD) is a highly prevalent clinical syndrome that still poses major clinical challenges. Kidney fibrosis underlies many cases of CKD and therapies against it are of very limited efficacy. Alterations in circadian rhythms (CR) are relevant in patients with CKD, but very little is known about the relationship between CKD and CR. Our study shows that disruption of the molecular clock can impact kidney inflammation and fibrosis and that, reciprocally, kidney fibrosis can alter the expression of clock components. A better understanding of this crosstalk could open new therapeutic avenues for the prevention and treatment of CR-related CKD.

physiology↗

bioRxiv2022

ModCRE: a structure homology-modeling approach to predict TF binding in cis-regulatory elements

Transcription factor (TF) binding is a key component of genomic regulation. There are numerous high-throughput experimental methods to characterize TF-DNA binding specificities. Their application, however, is both laborious and expensive, which makes profiling all TFs challenging. For instance, the binding preferences of ~25% human TFs remain unknown; they neither have been determined experimentally nor inferred computationally. We introduce a structure-based learning approach to predict the binding preferences of TFs and the automated modelling of TF regulatory complexes. We show the advantage of using our approach over the state-of-art nearest-neighbor prediction in the limits of remote homology. Starting from a TF sequence or structure, we predict binding preferences in the form of motifs that are then used to scan a DNA sequence for occurrences. The best matches are either profiled with a binding score or collected for their subsequent modeling into a higher-order regulatory complex with DNA. Cooperativity is modelled by: i) the co-localization of TFs; and ii) the structural modeling of protein-protein interactions between TFs and with co-factors. As case examples, we apply our approach to automatically model the interferon-{beta} enhanceosome and the pioneering complex of OCT4, SOX2 and SOX11 with a nucleosome, which are compared with the experimentally known structures.

bioinformatics↗

bioRxiv2021

Temporal and sex-dependent gene expression patterns in a renal ischemia-reperfusion injury and recovery pig model

Men are more prone to acute kidney injury (AKI) and chronic kidney disease (CKD), progressing to end-stage renal disease (ESRD) than women. Severity and capacity to regenerate after AKI are important determinants of CKD progression, and of patient morbidity and mortality in the hospital setting. To determine sex differences during injury and recovery we have generated a female and male renal ischemia/reperfusion injury (IRI) pig model, which represents a major cause of AKI. Although no differences were found in blood urea nitrogen (BUN) and serum creatinine (SCr) levels between both sexes, females exhibited higher mononuclear infiltrates at basal and recovery, while males showed more tubular damage at injury. Global transcriptomic analyses of kidney biopsies from our IRI pig model revealed a sexual dimorphism in the temporal regulation of genes and pathways relevant for kidney injury and repair, which was also detected in human samples. Enrichment analysis of gene sets revealed five temporal and four sexual patterns governing renal IRI and recovery. Overall, this study constitutes an extensive characterization of the time and sex differences occurring during renal IRI and recovery at gene expression level and offers a template of translational value for further study of sexual dimorphism in kidney diseases. AUTHOR SUMMARYKidneys correct functioning is essential for optimal body homeostasis, being their basic functions blood filtration and excretion of wastes and toxins. Inherited or acquired conditions can cause renal dysfunction requiring renal replacement therapy, which will affect patients life quality and survival. A major cause of kidney failure is the renal ischemia/reperfusion injury (IRI), which occurs in many clinical situations like kidney transplantation or aortic aneurysm surgery. Interestingly, men are more susceptible to IRI than women, being women more protected against kidney injury. However, the genetics regulating these sex differences in injury and renal repair remained unknown. Here, we provide a novel porcine model to study renal injury and recovery in both males and females. Using this model, we have identified the gene sets involved in renal injury and recovery processes. Moreover, global genetic analyses allowed us to discover the temporal and sex-dependent patterns that regulate those gene sets and, finally, kidney damage and repair. A relevant finding of our study is that males develop a feminized genetic profile during recovery, which may represent a survival mechanism to diminish the androgenic pro-damage effects on kidney cells. To sum up, our results provide novel sex-dependent targets to prevent renal injury and promote kidney recovery.

genomics↗

bioRxiv2020

Global gene-expression analysis reveals the molecular processes underlying ClC-5 loss-of-function in novel Dent Disease 1 cellular models

Dent disease 1 (DD1) is a rare X-linked renal proximal tubulopathy characterized by low molecular weight proteinuria (LMWP) and variable degree of hypercalciuria, nephrocalcinosis and/or nephrolithiasis with progression to chronic kidney disease (CKD). Although loss-of-function mutations in the gene CLCN5 encoding the electrogenic Cl-/H+ antiporter ClC-5, which impair endocytic uptake in proximal tubule cells, cause the disease, there is poor genotype-phenotype correlation and their contribution to proximal tubule dysfunction remains unclear. Here, in order to discover the mechanisms leading to proximal tubule dysfunction due to ClC-5 loss-of-function, we have generated and characterized new human cellular models of DD1 by silencing CLCN5 and introducing the ClC-5 pathogenic mutants V523del, E527D and I524K into the human proximal tubule-derived cell line RPTEC/TERT1. Depletion of CLCN5 or expression of mutant ClC-5 impairs albumin endocytosis, increases substrate adhesion and decreases collective migration, which correlates with a less differentiated epithelial phenotype. Interestingly, although all conditions compromised the endocytic capacity in a similar way, their impact on gene expression profiles was different. Our DNA microarray studies show that ClC-5 silencing or mutant re-introduction alter pathways related to nephron development, anion homeostasis, organic acid transport, extracellular matrix organization and cell migration, compared to control cells. Cells carrying the V523del ClC-5 mutation show the largest differences in gene expression vs WT cells, which is in agreement with the more aggressive clinical phenotype observed in some DD1 patients. Overall, this work emphasizes the use of human proximal tubule derived cell models to identify the molecular processes underlying ClC-5 deficiency.

pathology↗

bioRxiv2019

On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF.

Cis2-His2 zinc finger (C2H2-ZF) proteins are the largest family of transcription factors in human and higher metazoans. However, the DNA-binding preferences of many members of this family remain unknown. We have developed a computational method to predict these DNA-binding preferences. We combine information from crystal structures composed by C2H2-ZF domains and from bacterial one-hybrid experiments to compute scores for protein-DNA binding based on statistical potentials. We apply the scores to compute theoretical position weight matrices (PWMs) of proteins with a DNA-binding domain composed by C2H2-ZF domains, with the only requirement of an input structure (experimentally determined or modelled). We have tested the capacity to predict PWMs of zinc finger domains, successfully predicting 3-2 nucleotides of a trinucleotide binding site for about 70% variants of single zinc-finger domains of Zif268. We have also tested the capacity to predict the PWMs of proteins composed by three C2H2-ZF domains, successfully matching between 60% and 90% of the binding-site motif according to the JASPAR database. The tests are used as a proof of the capacity to scan a DNA fragment and find the potential binding sites of transcription-factors formed by C2H2-ZF domains. As an example, we have tested the approach to predict the DNA-binding preferences of the human chromatin binding factor CTCF.

bioinformatics↗

bioRxiv2018

Cyclophilins A and B Oppositely Regulate Renal Tubular Epithelial Phenotype

Cyclophilins (Cyp) are peptidil-prolyl-isomerases and the intracellular receptors for the immunosuppressant Cyclosporine-A (CsA), which produces epithelial-mesenchymal-transition (EMT) and renal tubule-interstitial fibrosis. Since CsA inhibits Cyp enzymatic activity, we hypothesized that Cyp could be involved in EMT and fibrosis. Here, we demonstrate that CypB is a critical regulator of tubule epithelial cell plasticity on the basis that: i) CypB silencing caused epithelial differentiation in proximal tubule-derived HK-2 cells, ii) CypB silencing prevented TGF{beta}-induced EMT in HK-2, and iii) CypB knockdown mice exhibited reduced UUO-induced inflammation and kidney fibrosis. By contrast, silencing of CypA induces a more undifferentiated phenotype and favors TGF{beta} effects. EMT mediators Slug and Snail were up-regulated in CypA-silenced cells, while in CypB silencing, Slug, but not Snail, was down-regulated; thus, reinforcing the role of Slug in kidney fibrosis. CypA regulates Slug through its PPIase activity whereas CypB depends on its ER location, where interacts with calreticulin, a calcium modulator which is involved in TGF{beta} signaling. In conclusion, this work uncovers new roles for CypA and CypB in modulating proximal tubular cell plasticity.

molecular biology↗