A5076325815- Pregnancy and preeclampsia studies
- Epigenetics and DNA Methylation
- Genomics and Chromatin Dynamics
- Prenatal Screening and Diagnostics
- Birth, Development, and Health
- Renal and related cancers
- RNA modifications and cancer
- FOXO transcription factor regulation
- Reproductive System and Pregnancy
- Gene expression and cancer classification
- Cancer-related molecular mechanisms research
- Genetic Syndromes and Imprinting
- Genomics and Phylogenetic Studies
- Molecular Biology Techniques and Applications
- Effects and risks of endocrine disrupting chemicals
- Advanced biosensing and bioanalysis techniques
- RNA Interference and Gene Delivery
- Neonatal Respiratory Health Research
- Single-cell and spatial transcriptomics
- Pancreatic function and diabetes
- Kruppel-like factors research
- Adipose Tissue and Metabolism
- RNA Research and Splicing
- Bioinformatics and Genomic Networks
- Connective tissue disorders research
Iowa State University
2015-2024
Stanford University
2011-2015
University of Pennsylvania
2007-2012
Georgia Institute of Technology
2004-2005
RNA-Seq data analysis results in lists of genes that may have a similar function, based on differential gene expression or co-expression network analysis. While tools been developed to identify biological processes are enriched the sets, there remains need for enrichment tissue-specific genes. Therefore, we TissueEnrich, tool calculates an input set. We demonstrated TissueEnrich can assign tissue identities single cell clusters and differentiated embryonic stem cells.The web application is...
The nuclear receptor peroxisome proliferator activator gamma (PPARgamma) is the target of antidiabetic thiazolidinedione drugs, which improve insulin resistance but have side effects that limit widespread use. PPARgamma required for adipocyte differentiation, it also expressed in other cell types, notably macrophages, where influences atherosclerosis, resistance, and inflammation. A central question whether binding macrophages occurs at genomic locations same as or different from those...
The forkhead box proteins A1 and A2 (Foxa1 Foxa2) are transcription factors with critical roles in establishing the developmental competence of foregut endoderm initiating liver specification. Using conditional gene ablation during a later phase development, we show here that deletion both Foxa1 Foxa2 (Foxa1/2) embryonic caused hyperplasia biliary tree. Abnormal bile duct formation Foxa1/2-deficient was due, at least part, to activation IL-6 expression, proliferative signal for...
Placental trophoblast cells are potentially at risk from circulating endocrine-disrupting chemicals, such as bisphenol A (BPA). To understand how BPA and the reputedly more inert S (BPS) affect placenta, C57BL6J mouse dams were fed 200 μg/kg body weight or BPS daily for 2 wk then bred. They continued to receive these chemicals until embryonic day 12.5, whereupon placental samples collected compared with unexposed controls. altered expression of an identical set 13 genes. Both exposures led a...
The assay for transposase-accessible chromatin (ATAC-seq) is a powerful method to examine accessibility. While many studies have reported positive correlation between gene expression and promoter accessibility, few investigated the genes that deviate from this trend. In study, we aimed understand relationship accessibility in multiple cell types while also identifying regulatory networks placenta, an understudied organ critical successful pregnancy.
ChIP-Seq technology, which combines chromatin immunoprecipitation (ChIP) with massively parallel sequencing, is rapidly replacing ChIP-on-chip for the genome-wide identification of transcription factor binding events. Identifying bound regions from large number sequence tags produced by a challenging task. Here, we present GLITR (GLobal Identifier Target Regions), accurately identifies enriched in target data calculating fold-change based on random samples control (input chromatin) data....
We describe a model for early onset preeclampsia (EOPE) that uses induced pluripotent stem cells (iPSCs) generated from umbilical cords of EOPE and control (CTL) pregnancies. These iPSCs were then converted to placental trophoblast (TB) representative pregnancy. Marker gene analysis indicated both sets differentiated at comparable rates. The tested parameters disturbed in EOPE, including invasive potential. Under 5% O 2 , CTL TB lines did not differ, but, under hyperoxia (20% ), invasiveness...
Bisphenol A (BPA), an endocrine-disrupting chemical, is used to produce a wide variety of plastic and common house-hold items. Therefore, there potential continual exposure this compound. BPA has been linked certain placenta-associated obstetric complications such as preeclampsia, fetal growth restriction, miscarriage, preterm birth. However, how results in these disorders remains uncertain. Hence, we have herein summarized the reported impacts on morphology metabolic state placenta proposed...
The winged helix protein FOXA2 and the nuclear receptor peroxisome proliferator-activated receptor-γ (PPARγ) are highly conserved, regionally expressed transcription factors (TFs) that regulate networks of genes controlling complex metabolic functions. Cistrome analysis for Foxa2 in mouse liver PPARγ adipocytes has previously produced consensus-binding sites nearly identical to those used by corresponding TFs human cells. We report here that, despite conservation canonical binding motif,...
The observation that trophoblast (TB) can be generated from primed pluripotent stem cells (PSCs) by exposure to bone morphogenetic protein-4 (BMP4) when FGF2 and ACTIVIN signaling is minimized has recently been challenged with the suggestion procedure instead produces amnion. Here, analyzing transcriptome data multiple sources, including bulk single-cell data, we show BMP4 generates bona fide TB similarities both placental villous cells. analyses also suggest transcriptomic signatures...
The hemochorial placentation site is characterized by a dynamic interplay between trophoblast cells and maternal cells. These cooperate to establish an interface required for nutrient delivery promote fetal growth. In the human, penetrate deep into uterus. This not consistent feature of has hindered establishment suitable animal models. rat represents intriguing model investigating with cell invasion. this study, we used single-cell RNA sequencing characterize transcriptome invasive lineage,...
Genetic studies have identified a core set of transcription factors and target genes that control the development neocortex, region human brain responsible for higher cognition. The specific regulatory interactions between these factors, many key upstream downstream genes, enhancers mediate all remain mostly uncharacterized. We perform p300 ChIP-seq to identify over 6,600 candidate active in dorsal cerebral wall embryonic day 14.5 (E14.5) mice. Over 95% peaks we measure are conserved human....
Abstract Differentiated human embryonic stem cells (hESC) continue to provide a model for studying early trophoblast (TB), but many questions have been raised regarding their true identity. Therefore, we carried out global and unbiased analysis on previously published transcriptomic profiles hESC differentiated TB by means of bone morphogenetic protein-4 inhibitors activin A fibroblast growth factor-2 signaling (BAP treatment). Our results confirm that BAP treated (ESCd) lack mesoderm...
Foxa2 is a critical transcription factor that controls liver development and plays an important role in hepatic gluconeogensis adult mice. Here, we use genome-wide location analysis for to identify its targets the liver. We then show by computational analyses containing cis-regulatory modules are not constructed from random assortment of binding sites other factors expressed liver, but rather their composition depends on strength consensus site present. Genes module with medium or weak much...
The condition of the placenta is a determinant short- and long-term health mother fetus. However, critical processes occurring in early placental development, such as trophoblast invasion establishment metabolism, remain poorly understood. To gain better understanding genes involved regulating these processes, we utilized multiomics approach, incorporating transcriptome, proteome, phosphoproteome data generated from mouse tissue collected at two developmental time points. We found that...
One model to study the emergence of human trophoblast (TB) has been exposure pluripotent stem cells bone morphogenetic protein 4 (BMP4) in presence inhibitors ACTIVIN/TGFB; A 83–01 and FGF2; P D173074 (BAP), which generates a mixture cytotrophoblast, syncytiotrophoblast, with similarities extravillous trophoblast. Here, H1 embryonic were BAP-exposed under two O 2 conditions (20% 5%, respectively). At day 8, single nuclei RNA sequencing was used for transcriptomics analysis, thereby allowing...
ABSTRACT The invasive trophoblast cell lineages in rat and human share crucial responsibilities establishing the uterine-placental interface of hemochorial placenta. These observations have led to becoming an especially useful animal model for studying placentation. However, our understanding similarities or differences between regulatory mechanisms governing populations is limited. In this study, we generated single-nucleus ATAC-seq data from gestation day 15.5 19.5 tissues, integrated with...