A5009988063- Advanced Proteomics Techniques and Applications
- Single-cell and spatial transcriptomics
- Molecular Biology Techniques and Applications
- Cell Image Analysis Techniques
- Advanced Biosensing Techniques and Applications
- RNA modifications and cancer
- Ferroptosis and cancer prognosis
- Immune cells in cancer
- Advanced biosensing and bioanalysis techniques
- Cancer Genomics and Diagnostics
- RNA Research and Splicing
- interferon and immune responses
- Gene expression and cancer classification
- Glycosylation and Glycoproteins Research
- Metabolomics and Mass Spectrometry Studies
- Genomics and Phylogenetic Studies
- Biosensors and Analytical Detection
- Cancer Research and Treatments
- Cancer, Hypoxia, and Metabolism
- Genomics and Chromatin Dynamics
- Cancer, Lipids, and Metabolism
- RNA and protein synthesis mechanisms
- Advanced Fluorescence Microscopy Techniques
- Genetics, Bioinformatics, and Biomedical Research
- Immune Cell Function and Interaction
Presage Biosciences (United States)
2025
Nanostring Technologies (United States)
2015-2024
North Seattle College
2019
Seattle University
2008-2015
University of Washington
2000-2008
University College London
2008
The University of Queensland
2008
University of Washington Medical Center
2004-2006
Armed Forces Institute of Pathology
2002
Colorado State University
1994-1997
The four intrinsic subtypes of breast cancer, defined by differential expression 50 genes (PAM50), have been shown to be predictive risk recurrence and benefit hormonal therapy chemotherapy. Here we describe the development Prosigna™, a PAM50-based subtype classifier model on NanoString nCounter Dx Analysis System intended for decentralized testing in clinical laboratories. 514 formalin-fixed, paraffin-embedded (FFPE) cancer patient samples were used train prototypical centroids each...
Abstract Metastatic prostate cancer (mPC) comprises a spectrum of diverse phenotypes. However, the extent inter- and intra-tumor heterogeneity is not established. Here we use digital spatial profiling (DSP) technology to quantitate transcript protein abundance in spatially-distinct regions mPCs. By assessing multiple discrete areas across metastases, find high level intra-patient homogeneity with respect tumor phenotype. there are notable exceptions including tumors comprised low androgen...
Building predictive models of the cell requires systematically mapping how perturbations reshape each cell's state, function, and behavior. Here, we present Tahoe-100M, a giga-scale single-cell atlas 100 million transcriptomic profiles measuring 1,100 small-molecule impact cells across 50 cancer lines. Our high-throughput Mosaic platform, composed highly diverse optimally balanced 'cell village', reduces batch effects enables parallel profiling thousands conditions at resolution an...
The NS1 protein of influenza A virus contributes to viral pathogenesis, primarily by enabling the disarm host cell type IFN defense system. We examined downstream effects expression during infection on global cellular mRNA levels measuring over 13,000 genes in response with wild-type and mutant viruses human lung epithelial cells. Influenza A/PR/8/34 resulted a significant induction involved pathway. Deletion gene increased number magnitude implicated IFN, NF-κB, other antiviral pathways....
Double-stranded (ds) RNA, a common component of virus-infected cells, is potent inducer the type I interferon and other cellular genes. For identifying full repertoire human dsRNA-regulated genes, cDNA microarray hybridization screening was conducted using mRNA from dsRNA-treated GRE cells. Because these cells lack all possibility gene induction by autocrine actions eliminated. Our screen identified 175 dsRNA-stimulated genes (DSG) 95 dsRNA-repressed A subset DSGs also induced different...
We assessed NanoString's nCounter Analysis System for its ability to quantify gene expression of forty-eight genes in a single reaction with 100 ng total RNA or an equivalent amount tissue lysate. In the System, multiplexed target levels are directly detected, without enzymatic reactions, via two sequence-specific probes. The individual mRNA is captured one capture probe that used post-hybridization affinity purification procedure. second specific-sequence and fluorescent-labeled colored...
Acute promyelocytic leukemia (APL) is characterized by the t(15;17) chromosomal translocation, which results in fusion of retinoic acid receptor alpha (RARA) gene to another gene, most commonly (PML). The resulting protein, PML-RARA, initiates APL, a subtype (M3) acute myeloid (AML). In this report, we identify expression signature that specific M3 samples; it was not found other AML subtypes and did simply represent normal pattern primary promyelocytes. To validate for large number genes,...
Abstract The Spatial Molecular Imaging platform (CosMx TM SMI, NanoString Technologies, Seattle, WA) utilizes high-plex in-situ imaging chemistry for both RNA and protein detection. This automated instrument provides 1000’s of plex, at high sensitivity (1 to 2 copies/cell), very low error rate (0.0092 false calls/cell) background (∼0.04 counts/cell). system generates three-dimensional super-resolution localization analytes ∼2 million cells per sample, four samples run. Cell segmentation is...
Pseudomonas aeruginosa is an opportunistic pathogen that plays a major role in lung function deterioration cystic fibrosis patients. To identify critical host responses during infection, we have used high-density DNA microarrays, consisting of 1,506 human cDNA clones, to monitor gene expression the A549 pneumocyte cell line exposure P. . We identified genes are differentially expressed upon several which require interaction with and subunit type IV pili, PilA. Differential involved various...
The expression levels of approximately 4,600 cellular RNA transcripts were assessed in CD4(+)-T-cell lines at different times after infection with human immunodeficiency virus type 1 strain BRU (HIV-1(BRU)) using DNA microarrays. We found that several classes genes inhibited by HIV-1(BRU) infection, consistent the G(2) arrest HIV-1-infected cells induced Vpr. These included involved cell division and transcription, a family DEAD-box proteins (RNA helicases), all translation splicing....
A genome-wide screening study for identification of hypermethylated genes in invasive cervical cancer (ICC) was carried out to augment our previously discovered panel three found be useful detection ICC and its precursor neoplasia. Putatively silenced were reactivated four cell lines by treatment with 5-aza-2'-deoxycytidine trichostatin identified on expression microarrays. Thirty-nine the 235 up-regulated multiple further examined determine methylation status associated CpG islands. The...
ABSTRACT Influenza virus, the causative agent of common flu, is a worldwide health problem with significant economic consequences. Studies influenza virus biology have revealed elaborate mechanisms by which interacts its host cell as it inhibits synthesis cellular proteins, evades innate antiviral response, and facilitates production viral RNAs proteins. With advent DNA array technology now possible to obtain large-scale view how viruses alter environment within cell. In this study, response...
ABSTRACT Alpha/beta interferons (IFN-α/β) induce potent antiviral and antiproliferative responses are used to treat a wide range of human diseases, including chronic hepatitis C virus (HCV) infection. However, for reasons that remain poorly understood, many HCV isolates resistant IFN therapy. To better understand the nature cellular response, we examined effects treatment on global gene expression by using several types cells, HeLa liver cell lines, primary fetal hepatocytes. In response...
ABSTRACT We have developed Digital Spatial Profiling (DSP), a non-destructive method for high-plex spatial profiling of proteins and RNA, using oligonucleotide detection technologies with unlimited multiplexing capability. The key breakthroughs underlying DSP are threefold: (1) multiplexed readout proteins/RNA oligo-tags; (2) oligo-tags attached to affinity reagents (antibodies/RNA probes) through photocleavable (PC) linker; (3) photocleaving light projected onto the tissue sample release...
Abstract Cancer cells produce tumor-specific antigens and neoantigens that can be recognized by T induce their clearance. Single cell profiling of receptors (TCRs) gene expression enables the identification characterization tumor infiltrating have antigen recognition killing capabilities. Existing microfluidic-based single sequencing methods limited sample throughput making it hard to perform longitudinal studies capture changes in TCR repertoire dynamics during progression therapeutic...
Abstract Cytokines, secreted by immune cells, are essential for coordinating responses against pathogens and abnormal such as those found in cancer. Despite their critical role, a comprehensive understanding of how many different types cells respond to individual cytokines remains elusive. To begin address this challenge, we created single cell atlas 90 cytokines, profiling the transcriptomes 10 million PBMCs from 12 donors after 24 hours treatment. We identified 18 types, resulting analysis...
Abstract Single cell analysis is a critical approach to tease out nuanced information in any biological system. Combinatorial barcoding an extremely efficient method for scRNA-seq at scale, achieving both sensitivity gene detection and flexibility sample input. This approach, however, challenging when starting with inputs of less than 100,000 cells. To address this, we have developed modified fixation capture low that compatible the combinatorial approach. allows researchers working fix,...