Biology subjects

Choi, H. Y.

Publications and source records attributed to Choi, H. Y..

3 recordsLinked to original sources

bioRxiv2024

Associations Between Prenatal Vitamin D and Placental Gene Expression

BackgroundVitamin D is a hormone regulating gene transcription. Prenatal vitamin D has been linked to immune and vascular function in the placenta, a key organ of pregnancy. To date, studies of vitamin D and placental gene expression have focused on a limited number of candidate genes. Transcriptome-wide RNA sequencing can provide a more complete representation of the placental effects of vitamin D. ObjectiveWe investigated the association between prenatal vitamin D levels and placental gene expression in a large, prospective pregnancy cohort. MethodsParticipants were recruited in Shelby County, Tennessee in the Conditions Affecting Neurocognitive Development and Learning in Early childhood (CANDLE) study. Vitamin D level (plasma total 25-hydroxyvitatmin D, [25(OH)D]) was measured at mid-pregnancy (16-28 weeks gestation) and delivery. Placenta samples were collected at birth. RNA was isolated and sequenced. We identified differentially expressed genes (DEGs) using adjusted linear regression models. We also conducted weighted gene co-expression network analysis (WGCNA). ResultsThe median 25(OH)D of participants was 21.8 ng/mL at mid-pregnancy (N=774, IQR: 15.4-26.5 ng/mL) and 23.6 ng/mL at delivery (N=753, IQR: 16.8-29.1 ng/mL). Placental expression of 25 DEGs was associated with 25(OH)D at mid-pregnancy, but no DEG was associated with 25(OH)D at delivery. DEGs were related to energy metabolism, cytoskeletal function, and RNA transcription. Using WGCNA, we identified 2 gene modules whose expression was associated with 25(OH)D at mid-pregnancy and 1 module associated with 25(OH)D at delivery. These modules were enriched for genes related to mitochondrial and cytoskeletal function, and were regulated by transcription factors including ARNT2, BHLHE40, FOSL2, JUND, and NFKB1. ConclusionsOur results indicate that 25(OH)D during mid-pregnancy, but not at delivery, is associated with placental gene expression at birth. Future research is needed to investigate a potential role of vitamin D in programming placental mitochondrial metabolism, intracellular transport, and transcriptional regulation during pregnancy.

developmental biology↗

bioRxiv2023

Matrix Linear Models for connecting metabolite composition to individual characteristics

AO_SCPLOWBSTRACTC_SCPLOWHigh-throughput metabolomics data provide a detailed molecular window into biological processes. We consider the problem of assessing how the association of metabolite levels with individual (sample) characteristics such as sex or treatment may depend on metabolite characteristics such as pathway. Typically this is one in a two-step process: In the first step we assess the association of each metabolite with individual characteristics. In the second step an enrichment analysis is performed by metabolite characteristics among significant associations. We combine the two steps using a bilinear model based on the matrix linear model (MLM) framework we have previously developed for high-throughput genetic screens. Our framework can estimate relationships in metabolites sharing known characteristics, whether categorical (such as type of lipid or pathway) or numerical (such as number of double bonds in triglycerides). We demonstrate how MLM offers flexibility and interpretability by applying our method to three metabolomic studies. We show that our approach can separate the contribution of the overlapping triglycerides characteristics, such as the number of double bonds and the number of carbon atoms. The proposed method have been implemented in the open-source Julia package, MatrixLM. Data analysis scripts with example data analyses are also available.

bioinformatics↗

bioRxiv2020

Inhibition of lysyl oxidase-like 2 ameliorates folic acid-induced renal tubulointerstitial fibrosis

Tubulointerstitial fibrosis is characterized by accumulation of the extracellular matrix in the interstitium. Lysyl oxidase-like 2 (LOXL2), a member of the lysyl oxidase family, is known for promoting cancer metastasis, invasion, and stromal fibrosis in various organs. Our previous study demonstrated expression of LOXL2 in kidney podocytes and tubular epithelial cells, and the association between elevated LOXL2 and tubulointerstitial fibrosis. The present study evaluated the effect of LOXL2 inhibition using an inhibitory monoclonal antibody (AB0023) on tubulointerstitial fibrosis in a folic acid-induced tubulointerstitial fibrosis mouse model. We also evaluated the association of LOXL2 with epithelial-mesenchymal transformation related molecules in vitro using HK-2 cells. Our data demonstrate that AB0023 prevented the progression of tubulointerstitial fibrosis significantly, as determined by trichrome and picro-sirius red staining, as well as the total collagen assay. The mean expression of phosphorylated Smad2 and Smad4 was lower in the AB0023-treated group although it was not statistically significant. Following transforming growth factor-{beta} (TGF-{beta}) challenge, LOXL2-deficient HK-2 cells exhibited significantly lower expression of the mesenchymal markers vimentin and fibronectin than control HK-2 cells. In conclusion, LOXL2 inhibition ameliorates renal fibrosis through the TGF-{beta}/Smad signalling pathway.

pathology↗