Biology subjects

Loch-Caruso, R.

Publications and source records attributed to Loch-Caruso, R..

5 recordsLinked to original sources

bioRxiv2024

Placental and Immune Cell DNA Methylation Reference Panel for Bulk Tissue Cell Composition

To distinguish DNA methylation (DNAm) from cell proportion changes in whole placental tissue research, we developed a robust cell type-specific DNAm reference to estimate cell composition. We collated newly collected and existing cell type DNAm profiles quantified via Illumina EPIC or 450k microarrays. To estimate cell composition, we deconvoluted whole placental samples (n=36) with robust partial correlation based on the top 50 hyper- and hypomethylated sites per cell type. To test deconvolution performance, we evaluated RMSE in predicting principal component one of DNAm variation in 204 external placental samples. We analyzed DNAm profiles (n=368,435 sites) from 12 cell types: cytotrophoblasts (n=18), endothelial cells (n=19), Hofbauer cells (n=26), stromal cells (n=21), syncytiotrophoblasts (n=4), six lymphocyte types (n=36), and nucleated red blood cells (n=11). Median cell composition was consistent with placental biology: 60.4% syncytiotrophoblast, 17.1% stromal, 8.8% endothelial, 4.5% cytotrophoblast, 3.9% Hofbauer, 1.7% nucleated red blood cells, and 1.2% neutrophils. Our expanded reference outperformed an existing reference in predicting DNAm variation (15.4% variance explained, IQR=21.61) with cell composition estimates (RMSE:10.51 vs. 11.43, p-value<0.001). This cell type reference can robustly estimate cell composition from whole placental DNAm data to detect important cell types, reveal biological mechanisms, and improve casual inference.

genomics↗

bioRxiv2023

Placental Cell Conditioned Media Modifies Hematopoietic Stem Cell Transcriptome In Vitro

BackgroundHematopoietic stem cells are cells that differentiate into all blood cell types. Although the placenta secretes hormones, proteins and other factors important for maternal and fetal health, cross-talk between placental cells and hematopoietic stem cells is poorly understood. Moreover, toxicant impacts on placental-hematopoietic stem cell communication is understudied. The goals of this study were to determine if factors secreted from placental cells alter transcriptomic responses in hematopoietic stem cells and if monoethylhexyl phthalate (MEHP), the bioactive metabolite of the pollutant diethylhexyl phthalate, modifies these effects. MethodsWe used K-562 and BeWo cells as in vitro models of hematopoietic stem cells and placental syncytiotrophoblasts, respectively. We treated K-562 cells with medium conditioned by incubation with BeWo cells, medium conditioned with BeWo cells treated with 10 M MEHP for 24 hours, or controls treated with unconditioned medium. We extracted K-562 cell RNA, performed RNA sequencing, then conducted differential gene expression and pathway analysis by treatment group. ResultsRelative to controls, K-562 cells treated with BeWo cell conditioned medium differentially expressed 173 genes (FDR<0.05 and fold-change>2.0), including 2.4 fold upregulatation of TPM4 and 3.3 fold upregulatation of S1PR3. Upregulated genes were enriched for pathways including stem cell maintenance, cell proliferation and immune processes. Downregulated genes were enriched for terms involved in protein translation and transcriptional regulation. MEHP treatment differentially expressed eight genes (FDR<0.05), including genes involved in lipid metabolism (PLIN2, fold-change: 1.4; CPT1A, fold-change: 1.4). ConclusionK-562 cells, a model of hematopoietic stem cells, are responsive to media conditioned by placental cells, potentially impacting pathways like stem cell maintenance and proliferation.

developmental biology↗

bioRxiv2022

The Trichloroethylene Metabolite S-(1,2-dichlorovinyl)-l-cysteine Inhibits Lipopolysaccharide-induced Transcriptomic Inflammation Pathways and Cytokine Secretion in a Macrophage Cell Model

Previous studies have shown that the trichloroethylene metabolite S-(1,2-dichlorovinyl)-l-cysteine (DCVC) inhibits cytokine secretion in pathogen stimulated fetal membrane tissue but little is known about the mechanism for these effects, including which cell types or transcriptomic pathways are impacted. Macrophages play a critical role in the fetal membrane innate immune response during infection. We tested the hypothesis that DCVC inhibits lipopolysaccharide (LPS) stimulated inflammation pathways in differentiated (macrophage-like) THP-1 cells. THP-1 cells were differentiated with phorbol 12-myristate 13-acetone for 24 hours and subsequently treated with 1, 5, or 10 {micro}M DCVC for 24 hours. After an additional 4 hour incubation with lipopolysaccharide (LPS), we collected RNA and cell media. We performed transcriptomic analysis using RNA sequencing analysis for 5{micro}M DCVC treatments and quantified cytokine release (IL-1{beta}, IL-6, and TNF-) into cell media for 1, 5 and 10 {micro}M DCVC treatments. RNAseq analysis revealed 1,399 differentially expressed genes (FDR<0.05 and log2fold change magnitude>2.5) in the cells co-treated with DCVC and LPS compared to LPS alone. For example, TNF was 9-fold downregulated with the addition of DCVC. Major pathways downregulated (adjusted p-value<0.05) in DCVC+LPS treatments versus LPS-only treatments, included: "acute inflammatory response", "production of molecular mediator of immune response" and "phagocytosis". LPS increased IL-1{beta}, IL-6, and TNF- levels in culture media (p<0.001), but this effect which was inhibited by co-treatment with DCVC (p<0.001 for LPS vs. LPS+DCVC treatments). Our results demonstrate that DCVC suppresses inflammatory responses in macrophages.

pharmacology and toxicology↗

bioRxiv2021

Placental gene expression-based cell type deconvolution: Cell proportions drive preeclampsia gene expression differences

The placenta mediates adverse pregnancy outcomes, including preeclampsia, which is characterized by gestational hypertension and proteinuria. Placental cell type heterogeneity in preeclampsia is not well-understood and limits mechanistic interpretation of bulk gene expression measures. We generated single-cell RNA-sequencing samples for integration with existing data to create the largest deconvolution reference of 19 fetal and 8 maternal cell types from placental villous tissue at term (n=15,532 cells). We deconvoluted eight published microarray case-control studies of preeclampsia (n=330). Deconvolution revealed excess extravillous trophoblasts and fewer mesenchymal cells. Adjustment for cellular composition reduced preeclampsia-associated differentially expressed genes (FDR<0.05) from 1,224 to 0, whereas pathway alterations exhibiting a metabolic adaptation to hypoxia were robust to cell type adjustment. Cellular composition explained 35.1% of the association between preeclampsia and FLT1 overexpression. Our findings indicate substantial placental cellular heterogeneity in preeclampsia that predicts previously observed bulk gene expression differences. Our deconvolution reference lays the groundwork for cellular heterogeneity-aware investigation into placental dysfunction and adverse birth outcomes.

developmental biology↗

bioRxiv2019

Toxicants Associated with Spontaneous Abortion in the Comparative Toxicogenomics Database (CTD)

BackgroundUp to 70% of all pregnancies result in either implantation failure or spontaneous abortion (SA). Many events occur before women are aware of their pregnancy and we lack a comprehensive understanding of high-risk SA chemicals. In epidemiologic research, failure to account for a toxicants impact on SA can also bias toxicant-birth outcome associations. Our goal was to identify chemicals with a high number of interactions with SA genes, based on known toxicogenomic responses.\n\nMethodsWe used reference SA (MeSH: D000022) and chemical gene lists from the Comparative Toxicogenomics Database in three species (human, mouse, and rat). We prioritized chemicals (n=25) found in maternal blood/urine samples or in groundwater, tap water, or Superfund sites. For chemical-disease gene sets of sufficient size (n=13 chemicals, n=20 comparisons), chi-squared enrichment tests and proportional reporting ratios (PRR) were calculated. We then cross-validated enrichment results. Finally, among the SA genes, we assessed enrichment for gene ontology biological processes and for chemicals associated with SA in humans, we visualized specific gene-chemical interactions.\n\nResultsThe number of unique genes annotated to a chemical ranged from 2 (bromacil) to 5,607 (atrazine), and 121 genes were annotated to SA. In humans, all chemicals tested were highly enriched for SA gene overlap (all p<0.001; parathion PRR=7, cadmium PRR=6.5, lead PRR=3.9, arsenic PRR=3.5, atrazine PRR=2.8). In mice, highest enrichment (p<0.001) was observed for naphthalene (PRR=16.1), cadmium (PRR=12.8), arsenic (PRR=11.6), and carbon tetrachloride (PRR=7.7). In rats, we observed highest enrichment (p<0.001) for cadmium (PRR=8.7), carbon tetrachloride (PRR=8.3), and dieldrin (PRR=5.3). Our findings were robust to 1,000 permutations each of gene sets ranging in size from 100 to 10,000. SA genes were overrepresented in biological processes: inflammatory response (q=0.001), collagen metabolic process (q=1x10-13), cell death (q=0.02), and vascular development (q=0.005).\n\nConclusionWe observed chemical gene sets (parathion, cadmium, naphthalene, carbon tetrachloride, arsenic, lead, dieldrin, and atrazine) were highly enriched for SA genes. Exposures to chemicals linked to SA, thus linked to probability of live birth, may deplete fetuses susceptible to adverse birth outcomes. Our findings have critical public health implications for successful pregnancies as well as the interpretation of environmental pregnancy cohort analyses.

pharmacology and toxicology↗