A5028087995- Immune cells in cancer
- Neuroinflammation and Neurodegeneration Mechanisms
- Cancer Immunotherapy and Biomarkers
- Chemokine receptors and signaling
- Tryptophan and brain disorders
- Immune Cell Function and Interaction
- Glioma Diagnosis and Treatment
- CAR-T cell therapy research
- Single-cell and spatial transcriptomics
- Virus-based gene therapy research
- Birth, Development, and Health
- Neonatal Respiratory Health Research
- Pregnancy and preeclampsia studies
- Immunotherapy and Immune Responses
- Preterm Birth and Chorioamnionitis
- Gestational Diabetes Research and Management
- Opioid Use Disorder Treatment
- RNA Interference and Gene Delivery
- Cancer, Hypoxia, and Metabolism
- Neonatal and fetal brain pathology
- Cell Image Analysis Techniques
- Cancer Genomics and Diagnostics
- Heme Oxygenase-1 and Carbon Monoxide
- Alzheimer's disease research and treatments
- Substance Abuse Treatment and Outcomes
Stanford University
2020-2025
Stanford Medicine
2020-2025
Washington University in St. Louis
2024
Palo Alto University
2024
Stony Brook Medicine
2023
Tufts University
2023
University of Oulu
2022
University of Jyväskylä
2022
Tempus Labs (United States)
2019
Northwestern University
2016-2019
Abstract Purpose: Glioblastoma (GBM) is the most common form of malignant glioma in adults. Although protected by both blood–brain and blood–tumor barriers, GBMs are actively infiltrated T cells. Previous work has shown that IDO, CTLA-4, PD-L1 dominant molecular participants suppression GBM immunity. This includes IDO-mediated regulatory T-cell (Treg; CD4+CD25+FoxP3+) accumulation, interaction T-cell–expressed, with dendritic cell-expressed, CD80, as well tumor- and/or macrophage-expressed,...
Abstract Purpose: Glioblastoma multiforme (GBM) is an aggressive adult brain tumor with a poor prognosis. One hallmark of GBM the accumulation immunosuppressive and tumor-promoting CD4+FoxP3+GITR+ regulatory T cells (Tregs). Here, we investigated role indoleamine 2,3 dioxygenase (IDO) in tumors impact on Treg recruitment. Experimental Design: To determine clinical relevance IDO expression tumors, first correlated patient survival to level from resected glioma specimens. We also used novel...
The mechanisms by which regulatory T cells (Tregs) migrate to and function within the hypoxic tumor microenvironment are unclear. Our studies indicate that specific ablation of hypoxia-inducible factor 1α (HIF-1α) in Tregs results enhanced CD8+ cell suppression versus wild-type under hypoxia, due increased pyruvate import into mitochondria. Importantly, HIF-1α-deficient minimally affected inhibition lipid oxidation, a fuel is critical for Treg metabolism tumors. Under HIF-1α directs glucose...
We developed and clinically validated a hybrid capture next generation sequencing assay to detect somatic alterations microsatellite instability in solid tumors hematologic malignancies. This targeted oncology utilizes tumor-normal matched samples for highly accurate alteration calling whole transcriptome RNA unbiased identification of gene fusion events. The was with combination clinical specimens cell lines, recorded sensitivity 99.1% single nucleotide variants, 98.1% indels, 99.9%...
The phosphodiesterase A1 protein of Acetobacter xylinum, AxPDEA1, is a key regulator bacterial cellulose synthesis. This linearizes cyclic bis(3'→5')diguanylic acid, an allosteric activator the synthase, to ineffectual pGpG. Here we show that AxPDEA1 contains heme and regulated by reversible binding O2 heme. Apo-AxPDEA1 has less than 2% activity holo-AxPDEA1, reconstitution with hemin restores full activity. regulation due deoxyheme being better oxyheme. homologous Escherichia coli direct...
<h3>Importance</h3> Worldwide, preterm birth (PTB) is the single largest cause of deaths in perinatal and neonatal period associated with increased morbidity young children. The PTB multifactorial, development generalizable biological models may enable early detection guide therapeutic studies. <h3>Objective</h3> To investigate ability transcriptomics proteomics profiling plasma metabolomics analysis urine to identify measurements PTB. <h3>Design, Setting, Participants</h3> This...
Although prematurity is the single largest cause of death in children under 5 years age, current definition prematurity, based on gestational lacks precision needed for guiding care decisions. Here, we propose a longitudinal risk assessment adverse neonatal outcomes newborns deep learning model that uses electronic health records (EHRs) to predict wide range over period starting shortly before conception and ending months after birth. By linking EHRs Lucile Packard Children’s Hospital...
Preeclampsia is a complex disease of pregnancy whose physiopathology remains unclear. We developed machine-learning models for early prediction preeclampsia (first 16 weeks pregnancy) and over gestation by analyzing six omics datasets from longitudinal cohort pregnant women. For pregnancy, model using nine urine metabolites had the highest accuracy was validated on an independent (area under receiver-operating characteristic curve [AUC] = 0.88, 95% confidence interval [CI] [0.76, 0.99]...
Abstract Advanced measurement and data storage technologies have enabled high-dimensional profiling of complex biological systems. For this, modern multiomics studies regularly produce datasets with hundreds thousands measurements per sample, enabling a new era precision medicine. Correlation analysis is an important first step to gain deeper insights into the coordination underlying processes such However, construction large correlation networks in remains major computational challenge...
Preterm birth (PTB) is the leading cause of death in children under five, yet comprehensive studies are hindered by its multiple complex etiologies. Epidemiological associations between PTB and maternal characteristics have been previously described. This work used multiomic profiling multivariate modeling to investigate biological signatures these characteristics. Maternal covariates were collected during pregnancy from 13,841 pregnant women across five sites. Plasma samples 231...
Abstract Dendritic cells (DCs) are professional APCs that traditionally divided into two distinct subsets, myeloid DC (mDCs) and plasmacytoid (pDCs). pDCs known for their ability to secrete large amounts of IFN-α. Apart from IFN-α production, can also process Ag induce T cell immunity or tolerance. In several solid tumors, have been shown play a critical role in promoting tumor immunosuppression. We investigated the glioma progression syngeneic murine model glioma. show glioma-infiltrating...
Abstract High-throughput single-cell analysis technologies produce an abundance of data that is critical for profiling the heterogeneity cellular systems. We introduce VoPo ( https://github.com/stanleyn/VoPo ), a machine learning algorithm predictive modeling and comprehensive visualization captured in large datasets. In three mass cytometry datasets, with largest measuring hundreds millions cells over samples, defines phenotypically functionally homogeneous cell populations. further...
Abstract Preterm birth (PTB) is the leading cause of infant mortality globally. Research has focused on developing predictive models for PTB without prioritizing cost-effective interventions. Physical activity and sleep present unique opportunities interventions in low- middle-income populations (LMICs). However, objective measurement physical remains challenging self-reported metrics suffer from low-resolution accuracy. In this study, we use data collected using a wearable device comprising...
Abstract Assay for Transposase Accessible Chromatin by sequencing (ATAC-seq) accurately depicts the chromatin regulatory state and altered mechanisms guiding gene expression in disease. However, bulk entangles information from different cell types obscures cellular heterogeneity. To address this, we developed Cellformer, a deep learning method that deconvolutes ATAC-seq into type-specific across whole genome. Cellformer enables cost-effective open profiling large cohorts. Applied to 191...
Prescription opioid misuse is a growing problem in the United States. There are limited data to illuminate nature of this issue. The Internet seems be novel approach surveying populations users. An Internet-based survey nonmedical users visiting informational drug websites was used measure rates use and characterize users.The prescription module Addiction Severity Index Multimedia Version Connect adapted include variables such as favorite opioid. Links were posted on an website. Nonmedical...