Biology subjects

Barutcu, R.

Publications and source records attributed to Barutcu, R..

3 recordsLinked to original sources

bioRxiv2024

Investigating the mode of action for liver toxicity and wasting-like responses produced by high dose exposures to longer chain perfluoroacid substances (PFAS) using high throughput transcriptomics

Single doses of perfluoro-n-decanoic acid (PFDA) cause wasting, a progressive loss of 30 to 50% body weight, increasing liver/body weight ratios, and death within several weeks (Olson and Andersen, 1983). Repeat high doses of perfluorooctane sulfonate (PFOS) produce a subset of these responses in rats and monkeys. The mode of action (MOA) of these wasting-like syndromes is not clear, nor is it understood if these responses are limited to a subset of perfluoroacid substances (PFAS) or a common response to high dose exposure with a larger number of PFAS. To identify pathway perturbations in liver caused by PFAS, we analyzed published in vitro gene expression studies from human primary liver spheroids treated with various PFAS for treatment times up to 14 days (Rowan-Carroll et al., 2021). With treatment times of 10 to 14 days, longer-chain PFAS compounds, specifically PFOS, perfluorodecane sulfonate (PFDS) and higher doses of perfluorooctanoic acid (PFOA), downregulated large numbers of genes in pathways for steroid metabolism, fatty acid metabolism and biological oxidations. Shorter chain PFAS compounds upregulated genes in pathways for fatty acid metabolism. Although PFDA was more toxic and could only be examined at 1-day of treatment, it also downregulated genes for lipid metabolism, steroid metabolism, and biological oxidations. Shorter chain PFAS, both carboxylic and sulfonic acids, did not lead to downregulation of pathways for fatty acid or steroid metabolism. TCDD is also known to cause wasting responses in rodents and humans. In intact rats, high dose responses of longer chain PFAS produce downregulation of batteries of genes associated with fatty acid oxidation and lipogenesis similar to those seen with TCDD. Based on our results, when combined with other literature, we propose that the longer-chain PFAS impair lipogenic pathways through inhibitory interactions between PPAR{beta}, PPAR and PPAR{gamma}.

pharmacology and toxicology↗

bioRxiv2024

Investigating the mode of action for wasting produced by tetrachlorodibenzo-p-dioxin (TCDD) in rats using transcriptomics: Evidence for roles of AHR and ARNT in circadian cycling

Single, high doses of TCDD in rats caused wasting, a progressive loss of 30 to 50% body weight and death within several weeks. To identify pathway perturbations at or near doses causing wasting, we examined differentially gene expression (DGE) and pathway enrichment in centrilobular (CL) and periportal (PP) regions of female rat livers following 6 dose levels of TCDD - 0, 3, 22, 100, 300, and 1000 ng/kg/day, 5 days/week for 4 weeks. At the higher doses, rats lost weight, had increased liver/body weight ratios and nearly complete cessation of liver cell proliferation, signs consistent with wasting. DGE curves were left shifted for the CL versus the PP regions. Canonical Phase I and Phase II genes were maximally increased at lower doses and remained elevated at all doses. At lower doses, < 22 ng/kg/day in the CL and < 100 ng/kg/day, upregulated genes showed transcription factor (TF) enrichment for AHR and ARNT. At the mid- and hi-dose doses, there was a large number of downregulated genes and pathway enrichment for DEGs showed downregulation of many cellular metabolism processes including those for steroids, fatty acid metabolism, pyruvate metabolism and citric acid cycle. There was significant TF enrichment of the hi-dose downregulated genes for RXR, ESR1, LXR, PPARalpha. At the highest dose, there was also pathway enrichment with upregulated genes for extracellular matrix organization, collagen formation, hemostasis and innate immune system. TCDD demonstrates most of its effects through binding the aryl hydrocarbon receptor (AHR) while the downregulation of metabolism genes at higher TCDD doses is known to be independent of AHR binding to DREs. Based on our results with DEG, we provide a hypothesis for wasting in which high doses of TCDD shifts circadian processes away from the resting state leading to greatly reduced synthesis of steroids and complex lipids needed for cell growth and producing gene expression signals consistent with an epithelial-to-mesenchymal transition in hepatocytes.

pharmacology and toxicology↗

bioRxiv2023

Impact of gene selection criteria on transcriptomic ontology-based point of departure estimates

Apical effects are typically associated with changes in gene expression, which allows for the use of short- term in life transcriptomic studies to derive biologically relevant points of departure (POD). These methods offer cost savings over conventional toxicology assessments and can derive data from very short-term studies where apical effects may not yet be present. When there is limited or insufficient data for a conventional POD assessment, a transcriptomic screen could provide valuable data for deriving a cellular bioactivity POD for chemical screening and hazard assessment. We used existing transcriptomic data from published 5-day rat in vivo kidney and liver exposures to examine the effect of differential gene expression metrics for the selection of genes used for ontology pathway-based POD derivation. Williams Trend Test (WTT) indicate no gene expression dose-response in 6 instances and ANOVA in one, while DESeq2 detected differentially expressed genes in all instances. The three statistical metrics produced consistent POD values. One chemical (PFOA in liver) showed ontology enrichment indicative of a cytotoxic response at the highest dose, emphasizing the effect which too high a dose can have on the derivation of POD values if such response is not accounted for. Whether the choice of a gene selection metric combining both a statistical significance criterion as well as a minimum magnitude of change threshold affects the sensitivity of POD values depends on the specifics of the dose- response. Existing alternative and complementary analyses could be utilized with existing analyses pipelines to better inform analytical decisions when using transcriptomics and BMD for point of departure determinations.

pharmacology and toxicology↗