A5017694538- Cancer Genomics and Diagnostics
- Radiomics and Machine Learning in Medical Imaging
- Cancer Research and Treatments
- Nanoplatforms for cancer theranostics
- interferon and immune responses
- Nanoparticle-Based Drug Delivery
- Chemical Reactions and Isotopes
- Immune cells in cancer
- Cell Image Analysis Techniques
- Computational Drug Discovery Methods
- Biosimilars and Bioanalytical Methods
- Advanced Biosensing Techniques and Applications
- Cancer, Hypoxia, and Metabolism
- Ferroptosis and cancer prognosis
- Cancer Immunotherapy and Biomarkers
- Monoclonal and Polyclonal Antibodies Research
- Cytokine Signaling Pathways and Interactions
- Single-cell and spatial transcriptomics
- Metabolomics and Mass Spectrometry Studies
- Medical Imaging Techniques and Applications
- Tuberculosis Research and Epidemiology
- Immunotherapy and Immune Responses
- RNA modifications and cancer
- Ubiquitin and proteasome pathways
- Physiological and biochemical adaptations
Nanostring Technologies (United States)
2021-2024
Bruker (United States)
2024
Seattle University
2023
University of Washington
2018-2021
University of California, Berkeley
2015-2016
Abstract Ulcerative colitis and Crohn’s disease are chronic inflammatory intestinal diseases with perplexing heterogeneity in manifestation response to treatment. While the molecular basis for this remains uncharacterized, single-cell technologies allow us explore transcriptional states within tissues at an unprecedented resolution which could further understanding of these complex diseases. Here, we apply RNA-sequencing human inflamed intestine show that largest differences among patients...
Abstract High-grade serous ovarian carcinoma (HGSOC) is genetically unstable and characterised by the presence of subclones with distinct genotypes. Intratumoural heterogeneity linked to recurrence, chemotherapy resistance, poor prognosis. Here, we use spatial transcriptomics identify HGSOC study their association infiltrating cell populations. Visium reveals multiple tumour different copy number alterations present within individual sections. These differentially express various ligands...
Abstract Marine populations of the threespine stickleback (Gasterosteus aculeatus) have repeatedly colonized and rapidly adapted to freshwater habitats, providing a powerful system map genetic architecture evolved traits. Here, we developed applied binned genotyping-by-sequencing (GBS) method build dense genome-wide linkage maps sticklebacks using two large marine by F2 crosses more than 350 fish each. The resulting significantly improve genome assembly anchoring 78 new scaffolds...
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...
Cancer drug development is currently limited by a paradigm of preclinical evaluation that does not adequately recapitulate the complexity intact human tumor microenvironment (TME). To overcome this, we combined trackable intratumor microdosing (CIVO) with spatial biology readouts to directly assess effects in patient tumors situ.In first-of-its-kind phase 0 clinical trial, explored an investigational stage SUMOylation-activating enzyme (SAE) inhibitor, subasumstat (TAK-981) 12 patients head...
The extent to which convergent adaptation similar ecological niches occurs by a predictable genetic basis remains fundamental question in biology. Threespine stickleback fish have undergone an adaptive radiation ancestral oceanic populations repeatedly colonized and adapted freshwater habitats. In multiple lakes British Columbia, two different ecotypes evolved: deep-bodied benthic form forage near the lake substrate, narrow-bodied limnetic open water. Here, we use genome-wide linkage mapping...
Melanoma clinical outcomes emerge from incompletely understood genetic mechanisms operating within the tumor and its microenvironment. Here, we used single-cell RNA-based spatial molecular imaging (RNA-SMI) in patient-derived archival tumors to reveal clinically relevant markers of malignancy progression prognosis. We examined gene expression 203,472 cells inside benign malignant melanocytic neoplasms, including nevi primary invasive metastatic melanomas. Algorithmic cell clustering paired...
ABSTRACT Ulcerative colitis (UC) and Crohn’s disease (CD) are chronic inflammatory intestinal diseases that show a perplexing heterogeneity in manifestations response to treatment. The molecular basis for this remains uncharacterized. We applied single-cell RNA sequencing CosMx™ Spatial Molecular Imaging human colon found the highest diversity cellular composition myeloid compartment of UC CD patients. Besides resident macrophage subsets (M0 M2), patients showed variety activated macrophages...
Abstract Ancestrally marine threespine stickleback fish ( Gasterosteus aculeatus ) have undergone an adaptive radiation into freshwater environments throughout the Northern Hemisphere, creating excellent model system for studying molecular adaptation and speciation. Ecological behavioral factors been suggested to underlie reproductive isolation incipient speciation, but proteins mediating gamete recognition during fertilization so far remained unexplored. To begin investigate contribution of...
Abstract Residual cancer burden (RCB) based on pathologic characteristics is the most powerful prognostic factor in breast (BC) which received neoadjuvant chemotherapy (NAC) followed by surgery. According to RCB classification, class III predicted short survival duration regardless of BC subtypes according hormone receptor (HR) and human epidermal growth receptor-2 (HER-2) state. However, up 20-40% BCs with did not experience recurrence had long term without disease recurrence. In our study,...
<p>Subasumstatinduces IFNβ in immune cells.</p>
<p>UMAP Cluster Analysis for Patients 7 and 8</p>
<p>Subasumstat induces interferon-response genes in a dose responsive fashion</p>
<p>Expression of IFNB1 and ISG15 as a function subasumstat exposure.</p>
<p>Subasumstat initiates cell death and cytotoxic T activity</p>
<p>FOV placement for SMI Analysis Patients 7 and 8 showing variation between sampled regions of the tumor</p>
<p>Subasumstat induces IFN response genes in CIVO micro-injected tumors</p>
<p>Correlation of MKI67 gene expression levels to Percent MIL113 Positivity for Tumors 7 and 8</p>