Biology subjects

Nault, R.

Publications and source records attributed to Nault, R..

13 recordsLinked to original sources

bioRxiv2026

Automating scientific annotations for open transcriptomic profiles via multi-stage agents

Public transcriptomic repositories contain millions of samples, yet their large-scale reuse is hindered by heterogeneous and inconsistently reported metadata. In the Gene Expression Omnibus (GEO), key biological information is often distributed across study- and sample-level records, requiring context-dependent interpretation. Here we present GEOMeta, a large language model (LLM)-based multi-stage workflow with task-specialized agents for automated GEO metadata curation. The pipeline separates metadata retrieval, task-specific information extraction, field standardization, ontology mapping and quality control. Using GEOMeta, we generated standardized annotations for approximately 600,000 human bulk RNA-seq samples. To demonstrate its utility, we benchmarked transcriptome representation models for predicting sex, age, tissue and disease from transcriptome embeddings. We further prospectively annotated newly submitted GEO studies and evaluated 22 frontier LLMs. Recent open-source Flash models achieved annotation quality comparable to leading reasoning models while reducing costs by an order of magnitude. GEOMeta provides a scalable resource and reproducible framework for metadata curation.

bioinformatics↗

bioRxiv2025

Isomer-specific distribution of perfluorooctane sulfonate (PFOS) in hepatic zonation in mouse

Per- and polyfluoroalkyl substances (PFAS) are a class of emerging contaminants that are widely distributed and persistent in the environment, accumulated in biological organisms and associated with adverse health outcomes. Evidence has shown a wide existence of branched PFAS isomers from source to applications. Notably, linear and branched isomeric PFAS structures are associated with differential toxicity outcomes and health effects. Herein, we investigated distribution of perfluorooctane sulfonate (PFOS) isomers in mouse liver tissue after exposure using matrix-assisted laser desorption/ionization-trapped ion mobility spectrometry-mass spectrometry imaging (MALDI-TIMS-MSI). Mice were treated with vehicle control or commercially sourced PFOS, a mixture of linear and branched isomers, at concentrations to achieve doses of 0.1 and 1 mg/kg/day for 84 days. Liver tissues were collected, followed by sample preparation and MALDI-TIMS-MSI analysis. Using a TIMS ramp time of 150 ms, we successfully separated linear and branched isomers on-tissue. Coupling with post-MALDI immunofluorescence imaging of canonical zonation markers, we discovered hepatic zonation-specific distribution for linear isomer but more homogenous distribution of branched PFOS. Dual-polarity MSI was performed on the same tissue for hepatic metabolites and lipids, and results showed concomitant alteration of liver lipid zonation upon PFOS exposure. With MALDI-TIMS-MSI, our results for the first time demonstrated on-tissue differentiation of PFOS isomers. Multi-modal imaging revealed isomer-specific PFOS distribution and spatial lipidomic changes, both mapped to canonical hepatic zonation markers, to reveal zone-selective PFOS toxicokinetics/toxicodynamics. Together our results demonstrate the critical need for further investigating isomer-specific PFAS toxicity.

pharmacology and toxicology↗

bioRxiv2025

Omega-3 Fatty Acid Synergy with Glucocorticoid in Lupus Macrophages: Targeting Pathogenic Pathways to Reduce Steroid Dependence

IntroductionSystemic lupus erythematosus (SLE) is a complex autoimmune disorder characterized by aberrant inflammation, type I IFN-stimulated gene (ISG) expression, and autoantibody production. Glucocorticoids (GCs) like dexamethasone (DEX) are standard long-term SLE treatments but cause significant side effects, highlighting the need for safer steroid-sparing options. Preclinical and clinical studies suggest that dietary supplementation with omega-3 fatty acids (O3FAs), particularly docosahexaenoic acid (DHA), suppress inflammation and autoimmunity associated with SLE disease progression. We explored the steroid-sparing potential of DHA to influence suppressive effects of DEX on pathogenic gene expression. MethodsMacrophages from SLE-prone NZBWF1 mice were first subjected to DHA (5, 10, or 25 {micro}M), DEX (1, 10, 100, or 1000 nM), or DHA+DEX cotreatment. Following pretreatment, cells were exposed to lipopolysaccharide (LPS; 20 ng/mL) to model SLE hyperinflammation. Effects on gene expression were analyzed by qRT-PCR and RNA-seq. ResultsqRT-PCR indicated that subinhibitory concentrations of DHA (5-10 {micro}M) potentiated the efficacy of low-dose DEX (1-100 nM) in suppressing LPS-induced ISG expression (e.g., Irf7, Oasl1, Rsad2), amplifying the effects of DEX monotherapy by 10- to 100-fold. SynergyFinder analysis confirmed that DHA and DEX interacted synergistically in suppressing ISG expression, with significant inhibition observed at concentrations as low as 1 nM DEX and 5 {micro}M DHA. RNA-seq revealed that combining suboptimal DHA (10 M) and DEX (100 nM) induced 247 differentially expressed genes (DEGs) at 4 hr and 347 DEGs at 8 hr post-LPS, dramatically surpassing the effects of each treatment alone. Functional enrichment analysis indicated that DHA+DEX cotreatment robustly suppressed immune and inflammatory pathways while promoting proliferative and metabolic processes, reflecting a shift from inflammatory (M1) to pro-resolving (M2) macrophage phenotypes. DHA and DEX countered LPS effects by i) downregulating common transcription factors (TFs) canonically associated with inflammation (e.g., NF-{kappa}B, AP-1, STATs, and IRF1), ii) upregulating shared regulatory factors involved in inflammation resolution (e.g., YBX1, EGR1, and BCL6), and iii) selectively influencing other regulatory factors. DiscussionAltogether, DHA and DEX synergistically suppress inflammation by targeting common and unique molecular pathways in SLE macrophages, favoring the pro-resolving M2 phenotype. O3FA-GC cotreatment might facilitate reducing requisite steroid dosages for SLE management.

immunology↗

bioRxiv2025

Single-nucleus analysis of thoracic perivascular adipose tissue reveals critical changes in cell composition, communication, and gene regulatory networks induced by a high fat hypertensive diet

Perivascular adipose tissue (PVAT), an intriguing layer of fat surrounding blood vessels, regulates vascular tone and mediates vascular dysfunction through mechanisms that are not well understood. Here we show with single nucleus RNA-sequencing of thoracic aortic PVAT from Dahl SS rats that a high-fat (HF) hypertensive diet induces coordinated changes in gene expression across the diverse cell types within PVAT. HF diet produced sex-specific alterations in cell-type proportions and genes related to remodeling of extracellular matrix dynamics and vascular integrity and stiffness, as well as changes in cell-cell communication pathways involved in angiogenesis, vascular remodeling, and mechanotransduction. Gene regulatory network analysis with virtual transcription factor knockout in adipocytes identified specific nuclear receptors that could be targeted for suppression or potential reversal of HF diet-induced changes. Interestingly, generative deep learning models were able to predict cross-cell-type perturbations in gene expression, indicating a hypertensive disease signature that characterizes HF-diet-induced perturbations in PVAT.

bioinformatics↗

bioRxiv2024

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) elicited dose-dependent shifts in the murine urinary metabolome associated with hepatic AHR-mediated differential gene expression

Epidemiological evidence suggests an association between dioxin and dioxin-like compound (DLC) exposure and human liver disease. The prototypical DLC, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), has been shown to induce the progression of reversible hepatic steatosis to steatohepatitis with periportal fibrosis and biliary hyperplasia in mice. Although the effects of TCDD toxicity are mediated by aryl hydrocarbon receptor (AHR) activation, the underlying mechanisms of TCDD-induced hepatotoxicity are unresolved. In the present study, male C57BL/6NCrl mice were gavaged every 4 days for 28 days with 0.03 - 30 g/kg TCDD and evaluated for liver histopathology and gene expression as well as complementary 1-dimensional proton magnetic resonance (1D-1H NMR) urinary metabolic profiling. Urinary trimethylamine (TMA), trimethylamine N-oxide (TMAO), and 1-methylnicotinamide (1MN) levels were altered by TCDD at doses [≤] 3 g/kg; other urinary metabolites, like glycolate, urocanate, and 3-hydroxyisovalerate, were only altered at doses that induced moderate to severe steatohepatitis. Bulk liver RNA-seq data suggested altered urinary metabolites correlated with hepatic differential gene expression corresponding to specific metabolic pathways. In addition to evaluating whether altered urinary metabolites were liver-dependent, published single-nuclear RNA-seq (snRNA-seq), AHR ChIP-seq, and AHR knockout gene expression datasets provide further support for hepatic cell-type and AHR-regulated dependency, respectively. Overall, TCDD-induced liver effects were preceded by and occurred with changes in urinary metabolite levels due to AHR-mediated changes in hepatic gene expression.

molecular biology↗

bioRxiv2024

Early life adversity promotes gastrointestinal dysfunction through a sex-dependent phenotypic switch in enteric glia

Irritable bowel syndrome and related disorders of gut-brain interaction (DGBI) are common and exhibit a complex, poorly understood etiology that manifests as abnormal gut motility and pain. Risk factors such as biological sex, stressors during critical periods, and inflammation are thought to influence DGBI vulnerability by reprogramming gut-brain circuits, but the specific cells affected are unclear. Here, we used a model of early life stress to understand cellular mechanisms in the gut that produce DGBIs. Our findings identify enteric glia as a key cellular substrate in which stress and biological sex converge to dictate DGBI susceptibility. Enteric glia exhibit sexual dimorphism in genes and functions related to cellular communication, inflammation, and disease susceptibility. Experiencing early life stress has sex-specific effects on enteric glia that cause a phenotypic switch in male glia toward a phenotype normally observed in females. This phenotypic transformation is followed by physiological changes in the gut, mirroring those observed in DGBI in humans. These effects are mediated, in part, by alterations to glial prostaglandin and endocannabinoid signaling. Together, these data identify enteric glia as a cellular integration site through which DGBI risk factors produce changes in gut physiology and suggest that manipulating glial signaling may represent an attractive target for sex-specific therapeutic strategies in DGBIs.

physiology↗

bioRxiv2023

A Cell Atlas of Thoracic Aortic Perivascular Adipose Tissue: a focus on mechanotransducers

Perivascular adipose tissue (PVAT) is increasingly recognized for its function in mechanotransduction. To examine the cell-specificity of recognized mechanotransducers we used single nuclei RNA sequencing (snRNAseq) of the thoracic aorta PVAT (taPVAT) from male Dahl SS rats compared to subscapular brown adipose tissue (BAT). Approximately 30,000 nuclei from taPVAT and BAT each were characterized by snRNAseq, identifying 8 major cell types expected and one unexpected (nuclei with oligodendrocyte marker genes). Cell-specific differential gene expression analysis between taPVAT and BAT identified up to 511 genes (adipocytes) with many ([≥]20%) being unique to individual cell types. Piezo1 was the most highly, widely expressed mechanotransducer. Presence of PIEZO1 in the PVAT was confirmed by RNAscope(R) and IHC; antagonism of PIEZO1 impaired the PVATs ability to hold tension. Collectively, the cell compositions of taPVAT and BAT are highly similar, and PIEZO1 is likely a mechanotransducer in taPVAT.

molecular biology↗

bioRxiv2022

Dose-dependent disruption of hepatic zonation by 2,3,7,8-tetrachlorodibenzo-p-dioxin in mice: integration of single-nuclei RNA sequencing and spatial transcriptomics.

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) dose-dependently induces the development of hepatic fat accumulation and inflammation with fibrosis in mice initially in the portal region. Conversely, differential gene and protein expression is first detected in the central region. To further investigate cell-specific and spatially resolved dose-dependent changes in gene expression elicited by TCDD, single-nuclei RNA sequencing and spatial transcriptomics were used for livers of male mice gavaged with TCDD every 4 days for 28 days. The proportion of 11 cell (sub)types across 131,613 nuclei dose-dependently changed with 68% of all portal and central hepatocyte nuclei in control mice being overtaken by macrophages following TCDD treatment. We identified 368 (portal fibroblasts) to 1,339 (macrophages) differentially expressed genes. Spatial analyses revealed initial loss of portal identity that eventually spanned the entire liver lobule with increasing dose. Induction of R-spondin 3 (Rspo3) and pericentral Apc, suggested dysregulation of the Wnt/{beta}-catenin signaling cascade in zonally resolved steatosis. Collectively, the integrated results suggest disruption of zonation contributes to the pattern of TCDD-elicited NAFLD pathologies. SYNOPSIS O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY Single-nuclei RNA sequencing (snRNAseq) and spatial transcriptomics were integrated to investigate cell-specific and spatially resolved dose-dependent changes elicited by TCDD. We show that TCDD causes a loss of zonal characteristics that disrupts spatially defined metabolic functions. - Dose-dependent analyses show higher responsiveness of central hepatocytes despite hepatotoxicity occurring initially in the portal region. - Integration of snRNAseq and spatial transcriptomics demonstrates a loss of hepatocytes with portal characteristics. - TCDD disrupted spatially resolved expression of {beta}-catenin signaling members that are critical in maintaining liver zonation. - Spatial transcriptomics and snRNAseq shows induction of R-spondin3 from nonparenchymal cells which serve as cue for the {beta}-catenin pathway.

pharmacology and toxicology↗

bioRxiv2021

Benchmarking of a Bayesian single cell RNAseq differential gene expression test for dose-response study designs.

The application of single-cell RNA sequencing (scRNAseq) for the evaluation of chemicals, drugs, and food contaminants presents the opportunity to consider cellular heterogeneity in pharmacological and toxicological responses. Current differential gene expression analysis (DGEA) methods focus primarily on two group comparisons, not multi-group dose-response study designs used in safety assessments. To benchmark DGEA methods for dose-response scRNAseq experiments, we proposed a multiplicity corrected Bayesian testing approach and compare it against 8 other methods including two frequentist fit-for-purpose tests using simulated and experimental data. Our Bayesian test method outperformed all other tests for a broad range of accuracy metrics including control of false positive error rates. Most notable, the fit-for-purpose and standard multiple group DGEA methods were superior to the two group scRNAseq methods for dose-response study designs. Collectively, our benchmarking of DGEA methods demonstrates the importance in considering study design when determining the most appropriate test methods.

genomics↗

bioRxiv2021

Genome-wide ChIPseq analysis of AhR, COUP-TF, and HNF4 enrichment in TCDD-treated mouse liver

The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor known for mediating the toxicity of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and related compounds. Although the canonical mechanism of AhR activation involves heterodimerization with the aryl hydrocarbon receptor nuclear translocator, other transcriptional regulators that interact with AhR have been identified. Enrichment analysis of motifs in AhR-bound genomic regions implicated co-operation with COUP transcription factor (COUP-TF) and hepatocyte nuclear factor 4 (HNF4). The present study investigated AhR, HNF4 and COUP-TFII genomic binding and effects on gene expression associated with liver-specific function and cell differentiation in response to TCDD. Hepatic ChIPseq data from male C57BL/6 mice at 2 hrs after oral gavage with 30 {micro}g/kg TCDD were integrated with bulk RNA-sequencing (RNAseq) time-course (2 - 72 hrs) and dose-response (0.01 - 30 {micro}g/kg) datasets to assess putative AhR, HNF4 and COUP-TFII interactions associated with differential gene expression. TCDD treatment resulted in the genomic enrichment of 23,701, 11,688, and 9,547 binding regions for AhR, COUP-TFII and HNF4, respectively, throughout the genome. Functional enrichment analysis of differentially expressed genes (DEGs) identified differential binding enrichment for AhR, COUP-TFII, and HNF4a to regions within liver-specific genes suggesting intersections associated with the loss of liver-specific functions and hepatocyte differentiation. Analysis found that the repression of liver-specific, HNF4 target and hepatocyte differentiation genes, involved increased AhR and HNF4 binding with decreased COUP-TFII binding. Collectively, these results suggested TCDD-elicited loss of liver-specific functions and markers of hepatocyte differentiation involved interactions between AhR, COUP-TFII and HNF4.

pharmacology and toxicology↗

bioRxiv2021

2,3,7,8-Tetrachlorodibenzo-p-dioxin elicited decreases in cobalamin inhibits methylmalonyl-CoA mutase activity redirecting propionyl-CoA metabolism to the β-oxidation-like pathway resulting in hepatic accumulation of the toxic intermediate acrylyl-CoA

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a persistent environmental contaminant which induces diverse biological and toxic effects, including the reprograming of intermediate metabolism, mediated by the aryl hydrocarbon receptor (AHR). Targeted LC-MS analysis of hepatic extracts from mice gavaged with TCDD every 4 days for 28 days detected an increase in S-(2-carboxyethyl)-L-cysteine, a conjugate produced following the spontaneous reaction between the sulfhydryl group of cysteine and highly reactive acrylyl-CoA, an intermediate in the cobalamin (Cbl)-independent {beta}-oxidation-like metabolism of propionyl-CoA. In addition to repressing genes in both the canonical Cbl-dependent carboxylase and the alternate Cbl-independent {beta}-oxidation-like pathways at 30 g/kg TCDD, methylmalonyl-CoA mutase (MUT) activity was inhibited at lower doses. Moreover, TCDD decreased serum Cbl levels and hepatic cobalt levels while eliciting negligible effects on gene expression associated with Cbl absorption, transport, trafficking, or the derivatization to 5-deoxy-adenosylcobalamin (AdoCbl), the required MUT cofactor. In addition to inducing Acod1 that encodes for aconitate decarboxylase 1, the enzyme responsible for the decarboxylation cis-aconitate to itaconate, TCDD also dose-dependently increased itaconate levels in hepatic extracts. MUT inhibition is consistent with itaconate activation to itaconyl-CoA, a MUT suicide inactivator that adducts AdoCbl, that in turn, inhibits MUT activity and reduces Cbl levels. Collectively, these results suggest the decrease in MUT activity is due to Cbl depletion following TCDD treatment that redirected propionyl-CoA metabolism to the alternate Cbl-independent {beta}-oxidation-like pathway. The resulting hepatic accumulation of acrylyl-CoA likely contributes to TCDD-elicited hepatotoxicity and the multi-hit progression of steatosis to steatohepatitis with fibrosis.

pharmacology and toxicology↗

bioRxiv2021

Thioesterase induction by 2,3,7,8-tetrachlorodibenzo-p-dioxin results in a futile cycle that inhibits hepatic β-oxidation

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD), a persistent environmental contaminant, induces steatosis by increasing hepatic uptake of dietary and mobilized peripheral fats, inhibiting lipoprotein export, and repressing {beta}-oxidation. In this study, the mechanism of {beta}-oxidation inhibition was investigated by testing the hypothesis that TCDD dose-dependently repressed straight-chain fatty acid oxidation gene expression in mice following oral gavage every 4 days for 28 days. Untargeted metabolomic analysis revealed a dose-dependent decrease in hepatic acyl-CoA levels, while octenoyl-CoA and dicarboxylic acid levels increased. TCDD also dose-dependently repressed the hepatic gene expression associated with triacylglycerol and cholesterol ester hydrolysis, fatty acid binding proteins, fatty acid activation, and 3-ketoacyl-CoA thiolysis while inducing acyl-CoA hydrolysis. Moreover, octenoyl-CoA blocked the hydration of crotonyl-CoA suggesting short chain enoyl-CoA hydratase (ECHS1) activity was inhibited. Collectively, the integration of metabolomics and RNA-seq data suggested TCDD induced a futile cycle of fatty acid activation and acyl-CoA hydrolysis resulting in incomplete {beta}-oxidation, and the accumulation octenoyl-CoA levels that inhibited the activity of short chain enoyl-CoA hydratase (ECHS1).

pharmacology and toxicology↗

bioRxiv2020

Application of singe nuclei RNA sequencing to assess the hepatic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin

Cell-specific transcriptional responses are lost in the averages of bulk RNA sequencing. We performed single nuclei RNA sequencing (snSeq) on frozen liver samples from male C57BL/6 mice in response to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Approximately 19,907 hepatic genes were detected across 16,015 sequenced nuclei from control and treated samples. Eleven cell-(sub)types were identified including distinct hepatocyte sub-populations, consistent with the cell diversity of the liver. TCDD increased macrophages from 0.5% to 24.7%, while neutrophils were only present in treated samples. The number of differentially expressed genes correlated with the basal expression level of Ahr. In addition to expected functional enrichments within each cell-(sub)type, RAS signaling was enriched in nonparenchymal cells. snSeq also identified a Kupffer cell subtype highly expressing Gpnmb, consistent with a dietary NASH model. Overall, snSeq distinguished cell-specific transcriptional changes and population shifts consistent with the hepatotoxicity of TCDD.

molecular biology↗