Biology subjects

Torres, J. M.

Publications and source records attributed to Torres, J. M..

15 recordsLinked to original sources

bioRxiv2026

Evaluation of ivermectin effectiveness under contrasting anthelmintic resistance scenarios in beef cattle: a comparative study in Italy and Argentina

Beef cattle farming plays a crucial role in the livestock-related economies of both Italy and Argentina. Although both countries have grazing systems of meat production, the heterogeneity of those systems leads to different parasitological scenarios regarding epidemiology and the presence of resistance to commonly used anthelmintic drugs. Considering ivermectin (IVM) is the most widely used anthelmintic for treating gastrointestinal nematode (GIN) infections in cattle, the current studies evaluated the efficacy of ivermectin (IVM) given subcutaneously (SC) to both young calves and adult cows in ten (10) commercial cattle farms from Italy (A to E) and Argentina (F to J). The work was complemented with the assessment of the IVM plasma exposure and disposition kinetics both in young and adult animals. While adult cows and young calves were included in the study performed in Italy (Campania region), only calves aged 8-14 months old were selected to perform the efficacy trials in Argentina (central area of the Buenos Aires province). Fifteen (15) calves/cows naturally infected with GINs were treated with IVM (0.2 mg/kg) in each of the Farms. The therapeutic response (efficacy) was determined at 14 days after treatment by the faecal egg count reduction test. Six (6) adult cows and eight (8) young calves treated with IVM were randomly selected to perform the pharmacokinetic (PK) study with blood samples being taken 2 h and 21 days post-treatment. Drug concentrations were measured by HPLC. Similar IVM PK trends were obtained for both adult and young cattle. The IVM systemic exposure (expressed as AUC) obtained for adult cattle (380{+/-}158 ng.d/mL) was similar to that observed in calves group (313{+/-}85.5 ng.d/mL). No statistical differences between animals from both ages were observed for the most representative PK parameters (P>0.05). Surprisingly, while in Argentina IVM resistance was present in all the farms evaluated (90% CI = 0%-95%), in Italy a fully susceptible nematode population was presented in three farms (90% CI = 96%-100%) and only a very low level of IVM resistance was detected in the rest of the farms (90% CI = 92%-98%). Whereas Cooperia spp. and Haemonchus spp. were identified as the principal genera exhibiting resistance to IVM in Argentina, Cooperia spp., Ostertagia spp., and Oesophagostomum spp. were reported to display low levels of resistance under the Italian field scenario. In conclusion, IVM can be safely and effectively used in both young and adult cattle with similar disposition kinetic patterns. While its therapeutic response is failing under the conditions investigated in the Argentinian farms, its efficacy remains notably high in the Italian region under study. However, the use of IVM, as well any other active antiparasitic principle, should always be preceded by a diagnostic assessment of the nematode populations resistance status.

pharmacology and toxicology↗

bioRxiv2024

Clostridioides difficile binary toxin CDT induces biofilm-like persisting microcolonies

Clinical symptoms of Clostridioides difficile infection (CDI) range from diarrhea to pseudomembranous colitis. A major challenge in managing CDI is the high rate of relapse. Several studies correlate production of CDT binary toxin by clinical strains of Clostridioides difficile with higher relapse rates. Although the mechanism of action of CDT on host cells is known, its exact contribution to CDI is still unclear. To understand the physiological role of CDT during CDI, we established two hypoxic relevant intestinal models, Transwell and Microfluidic Intestine-on-Chip systems. Both were challenged with the epidemic strain UK1 CDT+ and its isogenic CDT- mutant. We report that CDT binary toxin induces mucin-associated microcolonies that increase C. difficile colonization and display biofilm-like properties by enhancing C. difficile resistance to vancomycin but not to fidaxomicin, a biofilm disrupting antibiotic. Importantly, biofilm- like CDT-dependent microcolonies were also observed in the caecum and colon of infected mice. Hence, our study shows that CDT toxin induces biofilm-like microcolonies, increasing C. difficile colonization and persistence.

microbiology↗

bioRxiv2024

Prefrontal 5α-reductase 2 mediates male-specific acute stress response

A key response to acute stress is the increased brain synthesis of the neurosteroid allopregnanolone (AP). While the rate-limiting step of this reaction is catalyzed by 5-reductase (5R), the role of its two primary isoenzymes, 5R1 and 5R2, in stress reactivity remains unclear. Here, we found that acute stress led to increased levels of 5R2, but not 5R1, in the medial prefrontal cortex (mPFC) of male, but not female, rats. Downregulation of 5R2 in the mPFC significantly reduced stress response in males, and similar sexual dimorphic effects were observed in a novel line of 5R2 knockout rats. Notably, 5R1 regulated baseline AP synthesis, while 5R2 enabled AP production under stress. Acute AP administration restored stress response in 5R2 knockdown rats. Single-nucleus transcriptomics showed that 5R2 enabled stress-induced protein translation in neurons and glia. These results highlight the crucial role of 5R2 in mediating sex-specific differences in acute stress reactivity.

neuroscience↗

bioRxiv2022

Inferring causal genes at type 2 diabetes GWAS loci through chromosome interactions in islet cells

Resolving causal genes for type 2 diabetes at loci implicated by genome-wide association studies (GWAS) requires integrating functional genomic data from relevant cell types. Chromatin features in endocrine cells of the pancreatic islet are particularly informative and recent studies leveraging chromosome conformation capture (3C) with Hi-C based methods have elucidated regulatory mechanisms in human islets. However, these genome-wide approaches are less sensitive and afford lower resolution than methods that target specific loci. To gauge the extent to which targeted 3C further resolves chromatin-mediated regulatory mechanisms at GWAS loci, we generated interaction profiles at 23 loci using next-generation (NG) Capture-C in a human beta cell model (EndoC-{beta}H1) and contrasted these maps with Hi-C maps in EndoC-{beta}H1 cells and human islets and a promoter capture Hi-C map in human islets. We found improvements in assay sensitivity of up to 33-fold and resolved 4.8X more chromatin interactions. At a subset of 18 loci with 25 co-localised GWAS and eQTL signals, NG Capture-C interactions implicated effector transcripts at five additional genetic signals relative to promoter capture Hi-C through physical contact with gene promoters. Therefore, high resolution chromatin interaction profiles at selectively targeted loci can complement genome- and promoter-wide maps.

genetics↗

bioRxiv2022

Loss of RREB1 in pancreatic beta cells reduces cellular insulin content and affects endocrine cell gene expression

Aims/hypothesisGenome-wide studies have uncovered multiple independent signals at the RREB1 locus associated with altered type 2 diabetes risk and related glycemic traits. However, little is known about the function of the zinc finger transcription factor RREB1 in glucose homeostasis or how changes in its expression and/or function influence diabetes risk. MethodsA zebrafish model lacking rreb1a and rreb1b was used to study the effect of RREB1 loss in vivo. Using transcriptomic and cellular phenotyping of a human beta cell model (EndoC-{beta}H1) and human induced pluripotent stem cell (hiPSC)-derived beta-like cells, we investigated how loss of RREB1 expression and activity affects pancreatic endocrine cell development and function. Ex vivo measurements of human islet function were performed in donor islets from carriers of RREB1 T2D-risk alleles. ResultsCRISPR-Cas9-mediated loss of rreb1a and rreb1b function in zebrafish supports an in vivo role for the transcription factor in beta cell mass, beta cell insulin expression, and glucose levels. Loss of RREB1 reduced insulin gene expression and cellular insulin content in EndoC-{beta}H1 cells, and impaired insulin secretion under prolonged stimulation. Transcriptomic analysis of RREB1 knockdown and knockout EndoC-{beta}H1 cells supports RREB1 as a novel regulator of genes involved in insulin secretion. In vitro differentiation of RREB1KO/KO hiPSCs revealed a dysregulation of pro-endocrine cell genes, including RFX family members, suggesting that RREB1 also regulates genes involved in endocrine cell development. Human donor islets from carriers of T2D-risk alleles in RREB1 have altered glucose-stimulated insulin secretion ex vivo, consistent with RREB1 regulating islet cell function. Conclusions/interpretationTogether, our results indicate that RREB1 regulates beta cell function by transcriptionally regulating the expression of genes involved in beta cell development and function. Research in contextO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LIHuman genetic variation in RREB1 is associated with altered diabetes risk, variation in glycemic, and anthropometric traits C_LIO_LIRREB1 is a transcription factor that binds to Ras-responsive elements and is expressed in multiple diabetes relevant tissues, including pancreatic islets C_LI What is the key question?O_LIHow does altered expression or function of RREB1 influence diabetes risk? C_LI What are the new findings?O_LIKnockdown and knockout of RREB1 in mature human EndoC-{beta}H1 cells reduces expression of insulin transcript and cellular content, as well as insulin secretion under prolonged stress C_LIO_LICarriers of the T2D-risk RREB1 coding allele trend towards reduced insulin content, but have improved glucose-stimulated insulin secretion C_LIO_LIA loss-of-function zebrafish model suggests that RREB1 is required for insulin expression C_LI How might this impact on clinical practice in the foreseeable future?O_LIRREB1 controls beta cell function and whole-body glucose homeostasis by transcriptionally regulating the development and function of pancreatic beta cells C_LI

physiology↗

bioRxiv2021

TIGER: The gene expression regulatory variation landscape of human pancreatic islets

GWAS have identified more than 700 genetic signals associated with type 2 diabetes (T2D). To gain insight into the underlying molecular mechanisms, we created the Translational human pancreatic Islet Genotype tissue-Expression Resource (TIGER), aggregating >500 human islet RNA-seq and genotyping datasets. We imputed genotypes using 4 reference panels and meta-analyzed cohorts to improve coverage of expression quantitative trait loci (eQTL) and developed a method to combine allele-specific expression across samples (cASE). We identified >1 million islet eQTLs (56% novel), of which 53 colocalize with T2D signals (60% novel). Among them, a low-frequency allele that reduces T2D risk by half increases CCND2 expression. We identified 8 novel cASE colocalizations, among which an SLC30A8 T2D associated variant. We make all the data available through the open-access TIGER portal (http://tiger.bsc.es), which represents a comprehensive human islet genomic data resource to elucidate how genetic variation affects islet function and translate this into therapeutic insight and precision medicine for T2D.

bioinformatics↗

bioRxiv2020

A multi-omic integrative scheme characterizes tissues of action at loci associated with type 2 diabetes

Resolving the molecular processes that mediate genetic risk remains a challenge as most disease-associated variants are non-coding and functional and bioinformatic characterization of these signals requires knowledge of the specific tissues and cell-types in which they operate. To address this challenge, we developed a framework for integrating tissue-specific gene expression and epigenomic maps (primarily from tissues involved in insulin secretion and action) to obtain tissue-of-action (TOA) scores for each association signal by systematically partitioning posterior probabilities from Bayesian fine-mapping. We applied this scheme to credible set variants for 380 association signals from a recent GWAS meta-analysis of type 2 diabetes (T2D) in Europeans. The resulting tissue profiles underscored a predominant role for pancreatic islets and, to a lesser extent, subcutaneous adipose and liver, that was largely attributable to enhancer elements and transcribed regions, particularly among signals with greater fine-mapping resolution. We incorporated resulting TOA scores into a rule-based classifier, and validated the tissue assignments through comparison with data from cis-eQTL enrichment, functional fine-mapping, RNA co-expression, and patterns of physiological association. In addition to implicating signals with a single tissue-of-action, we also found evidence for signals with shared effects in multiple tissues as well as distinct tissue profiles between independent signals within heterogeneous loci. Lastly, we demonstrated that TOA scores can be directly coupled with eQTL colocalization to further resolve effector transcripts at T2D signals. This framework guides mechanistic inference by directing functional validation studies to the most relevant tissues and can gain power as fine-mapping resolution and cell-specific annotations become richer. This method is generalizable to all complex traits with relevant annotation data and is made available as an R package.

genetics↗

bioRxiv2019

Complementation between pathological prion protein subassemblies to cross existing species barriers

Backgroundprion replication results from the autocatalytic templated assisted conversion of the host-encoded prion protein PrPC into misfolded, polydisperse PrPSc conformers. Structurally distinct PrPSc conformers can give rise to multiple prion strains. Within and between prion strains, the biological activity (replicative efficacy and specific infectivity) of PrPSc assemblies is size-dependent and thus reflects an intrinsic structural heterogeneity. The contribution of such PrPSc heterogeneity across species prion adaptation, - which is believed to be based on fit-adjustment between PrPSc template(s) and host PrPC -, has not been explored. Methodsto define the structural-to-fitness PrPSc landscape, we measured the relative capacity of size-fractionated PrPSc assemblies from different prion strains to cross mounting species barriers in transgenic mice expressing foreign PrPc. Resultsin the absence of a transmission barrier, the relative efficacy of the isolated PrPSc assemblies to induce the disease is superimposable to the efficacy observed in the homotypic context. However, in the presence of a transmission barrier, size fractionation overtly delays and even abrogates prion pathogenesis in both neural and extraneural, prion-permissive tissues, for reason independent of the infectivity load of the isolated assemblies. This suggests that a synergy between structurally distinct PrPSc assemblies in the inoculum is requested for crossing the species barrier. We further strengthen this hypothesis by showing that altering, by serial dilution, PrPSc assemblies content of unfractionated inocula reduce their specific infectivity in an aberrant manner, solely in the presence of a transmission barrier. Conclusionsour data support a mechanism whereby overcoming prion species barrier requires complementation between structurally distinct PrPSc assemblies. This work provides key insight into the "quasi-species" concept applied to prions, which would not necessarily rely on prion sub-strains as constituent but on structural PrPSc heterogeneity within prion population.

neuroscience↗

bioRxiv2019

A multi-tissue transcriptome analysis of human metabolites guides the interpretability of associations based on multi-SNP models for gene expression

There is particular interest in transcriptome-wide association studies (TWAS) - gene-level tests based on multi-SNP predictive models of gene expression - for identifying causal genes at loci associated with complex traits. However, interpretation of TWAS associations may be complicated by divergent effects of model SNPs on trait phenotype and gene expression. We developed an iterative modelling scheme for obtaining multi-SNP models of gene expression and applied this framework to generate expression models for 43 human tissues from the Genotype-Tissues Expression (GTEx) Project. We characterized the performance of single- and multi-SNP TWAS models for identifying causal genes in GWAS data for 46 circulating metabolites. We show that: (a) multi-SNP models captured more variation in expression than the top cis-eQTL (median 2 fold improvement); (b) predicted expression based on multi-SNP models was associated (FDR<0.01) with metabolite levels for 826 unique gene-metabolite pairs, but, after step-wise conditional analyses, 90% were dominated by a single eQTL SNP; (c) amongst the 35% of associations where a SNP in the expression model was a significant cis-eQTL and metabolomic-QTL (met-QTL), 92% demonstrated colocalization between these signals, but interpretation was often complicated by incomplete overlap of QTLs in multi-SNP models; (d) using a \"truth\" set of causal genes at 61 met-QTLs, the sensitivity was high (67%), but the positive predictive value was low, as only 8% of TWAS associations at met-QTLs involved true causal genes. These results guide the interpretation of TWAS and highlight the need for corroborative data to provide confident assignment of causality.

genomics↗

bioRxiv2019

Deep learning models predict regulatory variants in pancreatic islets and refine type 2 diabetes association signals

Genome-wide association analyses have uncovered multiple genomic regions associated with T2D, but identification of the causal variants at these remains a challenge. There is growing interest in the potential of deep learning models - which predict epigenome features from DNA sequence - to support inference concerning the regulatory effects of disease-associated variants. Here, we evaluate the advantages of training convolutional neural network (CNN) models on a broad set of epigenomic features collected in a single disease-relevant tissue - pancreatic islets in the case of type 2 diabetes (T2D) - as opposed to models trained on multiple human tissues. We report convergence of CNN-based metrics of regulatory function with conventional approaches to variant prioritization - genetic fine-mapping and regulatory annotation enrichment. We demonstrate that CNN-based analyses can refine association signals at T2D-associated loci and provide experimental validation for one such signal. We anticipate that these approaches will become routine in downstream analyses of GWAS.

bioinformatics↗

bioRxiv2019

Comparative genomics in plant fungal pathogens (Mycosphaerellaceae): variation in mitochondrial composition due to at least five independent intron invasions

Fungi provide new opportunities to study highly differentiated mitochondrial DNA. Mycosphaerellaceae is a highly diverse fungal family containing a variety of pathogens affecting many economically important crops.\n\nMitochondria plays a major role in fungal metabolism and fungicide resistance but up until now only two annotated mitochondrial genomes have been published in this family. We sequenced and annotated mitochondrial genomes of selected Mycosphaerellaceae species that diverged [~]66 MYA. During this time frame, mitochondrial genomes expanded significantly due to at least five independent invasions of introns into different electron transport chain genes. Comparative analysis revealed high variability in size and gene order among mitochondrial genomes even of closely related organisms, truncated extra gene copies and, accessory genes in some species. Gene order variability was common probably due to rearrangements caused by mobile intron invasion. Three three cox1 copies and bicistronic transcription of nad2-nad3 and atp6-atp8 in Pseudocercospora fijiensis were confirmed experimentally. Even though we found variation in mitochondrial genome composition, there was no evidence of hybridization when comparing nuclear and mitochondrial dataset sets for fungal plant pathogens analyzed here. Disentangling the causes of variation in mitochondrial genome composition in plant pathogenic fungal move us closer to understanding the molecular mechanisms responsible for vital functions in fungi ultimately aiding in controlling these diseases.

genomics↗

bioRxiv2019

Interneuron functional diversity in the mouse accessory olfactory bulb

Abstract/SummaryIn the mouse accessory olfactory bulb (AOB), inhibitory interneurons play an essential role in gating behaviors elicited by sensory exposure to social odors. Several morphological classes have been described, but the full complement of interneurons remains incomplete. In order to develop a more comprehensive view of interneuron function in the AOB, we performed targeted patch clamp recordings from partially-overlapping subsets of genetically-labeled and morphologically-defined interneuron types. Gad2 (GAD65), Calb2 (calretinin), and Cort (cortistatin)-cre mouse lines were used to drive selective expression of tdTomato in AOB interneurons. Gad2 and Calb2-labeled interneurons were found in the internal, external, and glomerular layers, whereas Cort-labeled interneurons were enriched within the lateral olfactory tract (LOT) and external cellular layer (ECL). We found that external granule cells (EGCs) from all genetically-labeled subpopulations possessed intrinsic functional differences that allowed them to be readily distinguished from internal granule cells (IGCs). EGCs showed stronger voltage-gated Na+ and non-inactivating voltage-gated K+ currents, decreased IH currents, and robust excitatory synaptic input. These specific intrinsic properties did not correspond to any genetically-labeled type, suggesting that transcriptional heterogeneity among EGCs and IGCs is not correlated with expression of these particular marker genes. Intrinsic heterogeneity was also seen among AOB juxtaglomerular cells (JGCs), with a major subset of Calb2-labeled JGCs exhibiting spontaneous and depolarization-evoked plateau potentials. These data identify specific physiological features of AOB interneurons types that will assist in future studies of AOB function. Significance StatementThe mouse accessory olfactory bulb (AOB) plays a critical role in processing social chemosensory information. Several morphologically-identified types of AOB inhibitory interneurons are thought to refine and restrict information flow from the AOB to its downstream targets in the limbic system. However, little is known about the electrophysiological and transcriptional diversity among AOB interneuron types. We systematically investigated intrinsic electrophysiological diversity across 5 AOB cell populations in three transgenic mouse lines. Analysis of 26 intrinsic physiological features revealed feature combinations associated with identified morphological AOB cell types, but few associated with the transgenic lines we studied. The results provide quantitative information about functional diversity in AOB interneurons and provide an improved foundation for future studies of AOB circuit function.

neuroscience↗

bioRxiv2018

Fine-mapping of an expanded set of type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps

We aggregated genome-wide genotyping data from 32 European-descent GWAS (74,124 T2D cases, 824,006 controls) imputed to high-density reference panels of >30,000 sequenced haplotypes. Analysis of {small tilde}27M variants ({small tilde}21M with minor allele frequency [MAF]<5%), identified 243 genome-wide significant loci (p<5x10-8; MAF 0.02%-50%; odds ratio [OR] 1.04-8.05), 135 not previously-implicated in T2D-predisposition. Conditional analyses revealed 160 additional distinct association signals (p<10-5) within the identified loci. The combined set of 403 T2D-risk signals includes 56 low-frequency (0.5%[≤]MAF<5%) and 24 rare (MAF<0.5%) index SNPs at 60 loci, including 14 with estimated allelic OR>2. Forty-one of the signals displayed effect-size heterogeneity between BMI-unadjusted and adjusted analyses. Increased sample size and improved imputation led to substantially more precise localisation of causal variants than previously attained: at 51 signals, the lead variant after fine-mapping accounted for >80% posterior probability of association (PPA) and at 18 of these, PPA exceeded 99%. Integration with islet regulatory annotations enriched for T2D association further reduced median credible set size (from 42 variants to 32) and extended the number of index variants with PPA>80% to 73. Although most signals mapped to regulatory sequence, we identified 18 genes as human validated therapeutic targets through coding variants that are causal for disease. Genome wide chip heritability accounted for 18% of T2D-risk, and individuals in the 2.5% extremes of a polygenic risk score generated from the GWAS data differed >9-fold in risk. Our observations highlight how increases in sample size and variant diversity deliver enhanced discovery and single-variant resolution of causal T2D-risk alleles, and the consequent impact on mechanistic insights and clinical translation.

genomics↗

bioRxiv2017

Integration of human pancreatic islet genomic data refines regulatory mechanisms at Type 2 Diabetes susceptibility loci

Human genetic studies have emphasised the dominant contribution of pancreatic islet dysfunction to development of Type 2 Diabetes (T2D). However, limited annotation of the islet epigenome has constrained efforts to define the molecular mechanisms mediating the, largely regulatory, signals revealed by Genome-Wide Association Studies (GWAS). We characterised patterns of chromatin accessibility (ATAC-seq, n=17) and DNA methylation (whole-genome bisulphite sequencing, n=10) in human islets, generating high-resolution chromatin state maps through integration with established ChIP-seq marks. We found enrichment of GWAS signals for T2D and fasting glucose was concentrated in subsets of islet enhancers characterised by open chromatin and hypomethylation, with the former annotation predominant. At several loci (including CDC123, ADCY5, KLHDC5) the combination of fine-mapping genetic data and chromatin state enrichment maps, supplemented by allelic imbalance in chromatin accessibility pinpointed likely causal variants. The combination of increasingly-precise genetic and islet epigenomic information accelerates definition of causal mechanisms implicated in T2D pathogenesis.

genomics↗

bioRxiv2017

Integrative cross tissue analysis of gene expression identifies novel type 2 diabetes genes

To understand the mechanistic underpinnings of type 2 diabetes (T2D) loci mapped through GWAS, we performed a tissue-specific gene association study in a cohort of over 100K individuals (ncases {approx} 26K,ncontrols {approx} 84K) across 44 human tissues using MetaXcan, a summary statistics extension of PrediXcan. We found that 90 genes significantly (FDR < 0.05) associated with T2D, of which 24 are previously reported T2D genes, 29 are novel in established T2D loci, and 37 are novel genes in novel loci. Of these, 13 reported genes, 15 novel genes in known loci, and 6 genes in novel loci replicated (FDRrep < 0.05) in an independent study (ncases {approx} 10K, ncontrols {approx} 62K). We also found enrichment of significant associations in expected tissues such as liver, pancreas, adipose, and muscle but also in tibial nerve, fibroblasts, and breast. Finally, we found that monogenic diabetes genes are enriched in T2D genes from our analysis suggesting that moderate alterations in monogenic (severe) diabetes genes may promote milder and later onset type 2 diabetes.

genetics↗