A5090077283- Neonatal Respiratory Health Research
- Congenital Diaphragmatic Hernia Studies
- Single-cell and spatial transcriptomics
- Renal and related cancers
- Preterm Birth and Chorioamnionitis
- Infant Nutrition and Health
- Cancer Genomics and Diagnostics
- Innovations in Medical Education
- Gut microbiota and health
- RNA modifications and cancer
- Biomedical Text Mining and Ontologies
- Machine Learning in Bioinformatics
- Biological Research and Disease Studies
- Cell Image Analysis Techniques
- Child and Adolescent Health
- Lung Cancer Diagnosis and Treatment
- Bioinformatics and Genomic Networks
- Extracellular vesicles in disease
- Erythrocyte Function and Pathophysiology
- Congenital Anomalies and Fetal Surgery
- ATP Synthase and ATPases Research
- Respiratory viral infections research
- Health Sciences Research and Education
- Tuberous Sclerosis Complex Research
- Medical Education and Admissions
Cincinnati Children's Hospital Medical Center
2015-2023
University of Cincinnati
2014-2018
Idiopathic pulmonary fibrosis (IPF) is a lethal interstitial lung disease characterized by airway remodeling, inflammation, alveolar destruction, and fibrosis. We utilized single-cell RNA sequencing (scRNA-seq) to identify epithelial cell types associated biological processes involved in the pathogenesis of IPF. Transcriptomic analysis normal human cells defined gene expression patterns with highly differentiated type 2 (AT2) cells, indicated enrichment RNAs critical for surfactant...
The respiratory system undergoes a diversity of structural, biochemical, and functional changes necessary for adaptation to air breathing at birth. To identify the heterogeneity pulmonary cell types dynamic in gene expression mediating respiration, here we perform single RNA analyses mouse lung on postnatal day 1. Using an iterative type identification strategy unbiasedly murine types. We distinct populations epithelial, endothelial, mesenchymal, immune cells, each containing subpopulations....
The human lung plays vital roles in respiration, host defense, and basic physiology. Recent technological advancements such as single-cell RNA sequencing genetic lineage tracing have revealed novel cell types enriched functional properties of existing lung. time has come to take a new census. Initiated by members the NHLBI-funded LungMAP Consortium aided experts biology community, we synthesized current data into comprehensive practical cellular census Identities normal are captured...
Abstract Accurate cell type identification is a key and rate-limiting step in single-cell data analysis. Single-cell references with comprehensive types, reproducible functionally validated identities, common nomenclatures are much needed by the research community for automated annotation, integration, sharing. Here, we develop computational pipeline utilizing LungMAP CellCards as dictionary to consolidate transcriptomic datasets of 104 human lungs 17 mouse lung samples construct reference...
‘LungGENS’, our previously developed web tool for mapping single-cell gene expression in the developing lung, has been well received by pulmonary research community. With continued support from ‘LungMAP’ consortium, we extended scope of LungGENS database to accommodate transcriptomics data tissues and cells human mouse at different stages lung development. Lung Gene Expression Analysis (LGEA) portal is an version useful analysis, display interpretation patterns obtained single cells, sorted...
Although modern clinical practices such as cesarean sections and perinatal antibiotics have improved infant survival, treatment with broad-spectrum alters intestinal microbiota causes dysbiosis. Infants exposed to an increased likelihood of life-threatening infections, including pneumonia. Here, we investigated how the gut sculpt pulmonary immune responses, promoting recovery resolution infection in newborn rhesus macaques. Early-life antibiotic exposure interrupted maturation commensal...
Abstract Cell type-resolved proteome analyses of the brain, heart and liver have been reported, however a similar effort on lipidome is currently lacking. Here we applied liquid chromatography-tandem mass spectrometry to characterize major lung cell types isolated from human donors, representing first map any organ. We coupled this with proteomics same samples (available at Lungmap.net). Complementary substantiated functional identity cells. Lipidomics showed significant variations in across...
An improved understanding of the human lung necessitates advanced systems models informed by an ever-increasing repertoire molecular omics, cellular imaging, and pathological datasets. To centralize standardize information across broad research efforts, we expanded LungMAP.net website into a new gateway portal. This portal connects spectrum networks, bulk single-cell multiomics data, diverse collection image data that span mammalian development disease. The are standardized species...
Systems biology uses computational approaches to integrate diverse data types understand cell and organ behavior. Data derived from complementary technologies, for example transcriptomic proteomic analyses, are providing new insights into development disease. We compared mRNA protein profiles purified endothelial, epithelial, immune, mesenchymal cells normal human infant lung tissue. Signatures each type were identified at both levels. Cell-specific biological processes pathways predicted by...
Amniotic fluid (AF) is a proximal to the fetus containing higher amounts of cell-free fetal RNA/DNA than maternal serum, thereby making it promising source for identifying novel biomarkers that predict development and organ maturation. Our aim was compare AF transcriptomic profiles at different time points in pregnancy demonstrate unique genetic signatures would serve as potential indicative We isolated RNA from 16 women pregnancy: 4 18 24 weeks, 6 34 36 39 40 weeks. RNA-sequencing performed...
While antenatal glucocorticoids are widely used to enhance lung function in preterm infants, cellular and molecular mechanisms by which glucocorticoid receptor (GR) signaling influences maturation remain poorly understood. Deletion of the gene (Nr3c1) from fetal pulmonary mesenchymal cells phenocopied defects caused global Nr3c1 deletion, while epithelial- or endothelial-specific deletion did not impair at birth. We integrated genome-wide expression profiling, ATAC-seq, single cell RNA-seq...
Perinatal inflammatory stress is associated with early life morbidity and lifelong consequences for pulmonary health. Chorioamnionitis, an condition affecting the placenta fluid surrounding developing fetus, affects 25 to 40% of preterm births. Severe chorioamnionitis birth significantly increased risk disease secondary infections in childhood, suggesting that fetal inflammation may markedly alter development lung. Here, we used intra-amniotic lipopolysaccharide (LPS) challenge induce...
Lymphangioleiomyomatosis (LAM) is a rare lung disease of women, causing cystic remodelling the and progressive respiratory failure. The cellular composition, microenvironment interactions within LAM lesion remain unclear. To facilitate data sharing collaborative research, we performed an integrative analysis single-cell compiled from lung, uterus kidney patients with three research centres developed Cell Atlas (LCA) Web-Portal. LCA offers variety interactive options for investigators to...
ABSTRACT Accurate cell type identification is a key and rate-limiting step in single data analysis. Single references with comprehensive types, reproducible functional validated identities, common nomenclatures are much needed by the research community to optimize automated annotation facilitate integration, sharing, collaboration. In present study, we developed novel computational pipeline utilize LungMAP CellCards as dictionary consolidate single-cell transcriptomic datasets of 104 human...
ABSTRACT An improved understanding of the human lung necessitates advanced systems models informed by an ever-increasing repertoire molecular omics, cellular, imaging and pathological datasets. To centralize standardize information across broad research efforts we expanded LungMAP.net website into a gateway portal. This portal connects broad-spectrum networks, bulk single-cell multi-omics data diverse collection image that span mammalian development disease. The are standardized species...
ABSTRACT Recent advances in single-cell omics and high-resolution imaging have provided unanticipated data resources for the elucidation of genes underlying complex biological processes critical organ formation function. However, processing integrating large amounts presents a major challenge most researchers. There is need ready-to-use computational tools data/knowledge integration visualization. Here we present “Lung-at-a-glance”, an easy-to-use web toolset visualizing interoperating data,...
Abstract Malformations of or injuries to the developing lung are associated with perinatal morbidity and mortality lifelong consequences for subsequent pulmonary health. One fetal exposure linked poor health outcomes is chorioamnionitis, which impacts up 25-40% preterm births. Severe chorioamnionitis prematurity significantly increased risk disease secondary infections in childhood, suggesting that inflammation may alter developmental ontogeny lung. To test this hypothesis, we used...
A portable assessment system, PMEAS, based on the Pediatrics Milestone project, a joint initiative launched by Accreditation Council for Graduate Medical Education (ACGME) and American Board of (ABP) to assess resident physicians, is presented in this paper. Using cutting-edge mobile technology, such as iPad, system platform, simple easy use interface teachers specify competency categories provide evaluation residents immediate feedback their progress learning after daily rounds, enables...