Biology subjects

Searles, R.

Publications and source records attributed to Searles, R..

3 recordsLinked to original sources

bioRxiv2025

In vitro evidence for bisphenol A as a human liver carcinogen: Environmentally relevant doses inhibit cancer protective ESR1 signaling in a human liver cell line

I.Several environmentally ubiquitous endocrine disrupting chemicals (EDCs) are suspected carcinogens, but their mechanism(s) of action are unknown. In this study, we test the potential for a model EDC, bisphenol A (BPA), to both initiate (via oxidative mutagenesis) and promote (via endocrine disruption) liver carcinogenesis. This study is motivated by our prior finding that developmental BPA exposure caused hepatocellular carcinoma (HCC) in mice. Here, we provide in vitro evidence supporting a mechanism for BPA as a non-genotoxic carcinogen. Using a highly sensitive, error-corrected sequencing method, we demonstrate that human population-relevant doses of BPA cause mutations that are consistent with oxidative DNA damage; however, overall mutation frequency does not differ substantially from controls. In contrast, we show that BPA inhibits cancer-protective, estrogen-induced transcription of estrogen receptor 1 (ESR1) target genes in the presence of pre-pubertal, but not post-pubertal, levels of estradiol. These results constitute strong initial evidence supporting BPA as a liver cancer promoting agent. This mechanism may be generalizable to a wide range of environmental EDCs that are weak agonists for ESR1. This finding is critically important to prevention of HCC, which is prevalent, lethal, and poorly responsive to therapy.

pharmacology and toxicology↗

bioRxiv2024

Metabolomic and transcriptomic remodeling of bone marrow myeloid cells in response to maternal obesity

Maternal obesity puts the offspring at high risk of developing obesity and cardio-metabolic diseases in adulthood. Here, using a mouse model of maternal high-fat diet (HFD)-induced obesity, we show that whole body fat content of the offspring of HFD-fed mothers (Off-HFD) increases significantly from very early age when compared to the offspring regular diet-fed mothers (Off-RD). We have previously shown significant metabolic and immune perturbations in the bone marrow of newly-weaned offspring of obese mothers. Therefore, we hypothesized that lipid metabolism is altered in the bone marrow Off-HFD in newly-weaned offspring of obese mothers when compared to the Off-RD. To test this hypothesis, we investigated the lipidomic profile of bone marrow cells collected from three-week-old offspring of regular and high fat diet-fed mothers. Diacylgycerols (DAGs), triacylglycerols (TAGs), sphingolipids and phospholipids, including plasmalogen, and lysophospholipids were remarkably different between the groups, independent of fetal sex. Levels of cholesteryl esters were significantly decreased in offspring of obese mothers, suggesting reduced delivery of cholesterol to bone marrow cells. This was accompanied by age-dependent progression of mitochondrial dysfunction in bone marrow cells. We subsequently isolated CD11b+ myeloid cells from three-week-old mice and conducted metabolomics, lipidomics, and transcriptomics analyses. The lipidomic profiles of these bone marrow myeloid cells were largely similar to that seen in bone marrow cells and included increases in DAGs and phospholipids alongside decreased TAGs, except for long-chain TAGs, which were significantly increased. Our data also revealed significant sex-dependent changes in amino acids and metabolites related to energy metabolism. Transcriptomic analysis revealed altered expression of genes related to major immune pathways including macrophage alternative activation, B-cell receptor signaling, TGF{beta} signaling, and communication between the innate and adaptive immune systems. All told, this study revealed lipidomic, metabolomic, and gene expression abnormalities in bone marrow cells broadly, and in bone marrow myeloid cells particularly, in the newly-weaned offspring of obese mothers, which might at least partially explain the progression of metabolic and cardiovascular diseases in their adulthood.

molecular biology↗

bioRxiv2020

Accelerating Prediction of Chemical Shift of Protein Structures on GPUs

Experimental chemical shifts (CS) from solution and solid state magic-angle-spinning nuclear magnetic resonance spectra provide atomic level information for each amino acid within a protein or protein complex. However, structure determination of large complexes and assemblies based on NMR data alone remains challenging due the complexity of the calculations. Here, we present a hardware accelerated strategy for the estimation of NMR chemical-shifts of large macromolecular complexes based on the previously published PPM_One software. The original code was not viable for computing large complexes, with our largest dataset taking approximately 14 hours to complete. Our results show that the code refactoring and acceleration brought down the time taken of the software running on an NVIDIA V100 GPU to 46.71 seconds for our largest dataset of 11.3M atoms. We use OpenACC, a directive-based programming model for porting the application to a heterogeneous system consisting of x86 processors and NVIDIA GPUs. Finally, we demonstrate the feasibility of our approach in systems of increasing complexity ranging from 100K to 11.3M atoms. Author summary

biophysics↗