A5044739877- Cancer Genomics and Diagnostics
- Single-cell and spatial transcriptomics
- Cancer Immunotherapy and Biomarkers
- Immunotherapy and Immune Responses
- Genetic factors in colorectal cancer
- CAR-T cell therapy research
- Inorganic Chemistry and Materials
- CRISPR and Genetic Engineering
- Organometallic Compounds Synthesis and Characterization
- Cancer Cells and Metastasis
- Extraction and Separation Processes
- Ferroptosis and cancer prognosis
- Crystal Structures and Properties
- Monoclonal and Polyclonal Antibodies Research
- Genomics and Phylogenetic Studies
- Colorectal Cancer Treatments and Studies
- Lymphoma Diagnosis and Treatment
- Radiomics and Machine Learning in Medical Imaging
- Radioactive element chemistry and processing
- Inorganic and Organometallic Chemistry
- Molecular Biology Techniques and Applications
- Immune Cell Function and Interaction
- Electrochemical Analysis and Applications
- Immune cells in cancer
- Advanced oxidation water treatment
Stanford University
2016-2025
Stanford Medicine
2018-2025
Stratford University
2024
Palo Alto University
2014-2024
New York Genome Center
2020-2021
Imperial College London
2006-2008
Waste Management (United States)
2006-2008
Brunel University of London
1994-2005
Queen Mary University of London
1996
City, University of London
1982-1992
The tumor microenvironment (TME) consists of a heterogenous cellular milieu that can influence cancer cell behavior. Its characteristics have an impact on treatments such as immunotherapy. These features be revealed with single-cell RNA sequencing (scRNA-seq). We hypothesized scRNA-seq analysis gastric together paired normal tissue and peripheral blood mononuclear cells (PBMC) would identify critical elements deregulation not apparent other approaches.scRNA-seq was conducted seven patients...
Abstract Purpose: The liver is the most frequent metastatic site for colorectal cancer. Its microenvironment modified to provide a niche that conducive cancer cell growth. This study focused on characterizing cellular changes in (mCRC) tumor (TME). Experimental Design: We analyzed series of microsatellite stable (MSS) mCRCs liver, paired normal tissue, and peripheral blood mononuclear cells using single-cell RNA sequencing (scRNA-seq). validated our findings multiplexed spatial imaging bulk...
The Cancer Genome Atlas (TCGA) project has generated genomic data sets covering over 20 malignancies. These provide valuable insights into the underlying genetic and basis of cancer. However, exploring relationship among TCGA results clinical phenotype remains a challenge, particularly for individuals lacking formal bioinformatics training. Overcoming this hurdle is an important step toward wider translation cancer genomic/proteomic implementation precision medicine. Several websites such as...
Abstract Cancer cell lines are not homogeneous nor they static in their genetic state and biological properties. Genetic, transcriptional phenotypic diversity within contributes to the lack of experimental reproducibility frequently observed tissue-culture-based studies. While cancer line heterogeneity has been generally recognized, there no studies which quantify number clones that coexist distinguishing characteristics. We used a single-cell DNA sequencing approach characterize cellular...
Epigenetic characterization of cell-free DNA (cfDNA) is an emerging approach for detecting and characterizing diseases such as cancer. We developed a strategy using nanopore-based single-molecule sequencing to measure cfDNA methylomes. This generated up 200 million reads single sample from cancer patients, order magnitude improvement over existing nanopore methods. classifier determine whether individual originated tumor or immune cells. Leveraging methylomes matched tumors cells, we...
Abstract Microsatellites are multi-allelic and composed of short tandem repeats (STRs) with individual motifs mononucleotides, dinucleotides or higher including hexamers. Next-generation sequencing approaches other STR assays rely on a limited number PCR amplicons, typically in the tens. Here, we demonstrate STR-Seq, next-generation technology that analyses over 2,000 STRs parallel, provides accurate genotyping microsatellites. STR-Seq employs vitro CRISPR–Cas9-targeted fragmentation to...
Abstract Genome sequencing studies have identified numerous cancer mutations across a wide spectrum of tumor types, but determining the phenotypic consequence these remains challenge. Here, we developed high-throughput, multiplexed single-cell technology called TISCC-seq to engineer predesignated in cells using CRISPR base editors, directly delineate their genotype among individual and determine each mutation’s transcriptional phenotype. Long-read target gene’s transcript identifies...
Abstract Purpose: Activating T cell costimulatory receptors is a promising approach for cancer immunotherapy. In preclinical work, adding an OX40 agonist to in situ vaccination (ISV) with SD101, TLR9 agonist, was curative mouse model of lymphoma. We sought test this combination Phase I clinical trial patients low-grade B Patients and Methods: treated 14 low-dose radiation, intratumoral intravenous BMS986178, agonistic anti-OX40 antibody. The primary outcome safety. Secondary outcomes...
491 Background: The Gastric Cancer Registry (GCR) is a comprehensive clinical and genomic data resource focused on gastric cancer (GC) patients individuals with family history of GC or germline CDH1 mutation. As part the GCR’s ongoing enrollment, contribute information, archival tumor samples other biospecimens. undergo extensive molecular cellular analysis that includes sequencing spatial analysis. We have generated robust dataset, publicly accessible online through GCR Genome Explorer...
Introduction Appendiceal mucinous neoplasms (AMN) are rare tumors of the gastrointestinal tract. They metastasize with widespread abdominal dissemination leading to pseudomyxoma peritonei (PMP), a disease poor prognosis. There many unknowns about cellular features origin, differentiation and progression AMN PMP. Methods We characterized AMNs, PMPs matched normal tissues using single-cell RNA-sequencing. validated our findings immunohistochemistry, mass spectrometry on malignant ascites from...
Abstract Gastric cancer precursors demonstrate highly-variable rates of progression toward neoplasia. Certain high-risk precursors, such as gastric intestinal metaplasia with advanced histologic features, may be at up to 30-fold increased risk for compared lower-risk metaplasia. The biological differences between high- and low-risk lesions have been incompletely explored. In this study, we use several clinical cohorts characterize the microenvironment relative using bulk, spatial,...
<p>Supplementary Figure 5. Intratumoral T cell subsets are differentially activated by treatment.</p>
<p>Supplementary Figure 6. Treatment did not alter TGF-beta in tumors.</p>
<p>Supplementary Figure 2. Assay for measuring OX40 saturation; Abundance and expression of T cell subsets.</p>
<p>Supplementary Figure 3. Tumor B cells were identified by phenotypic clustering and restricted light chain expression.</p>
<p>Supplementary Figure 1. Coformulation of SD-101 and BMS-986178 does not alter their properties; Distant target lesions show variable response.</p>
<p>Supplementary Figure 4. Flow cytometry T cell gating and proportion of Tregs.</p>
<div>AbstractPurpose:<p>Activating T-cell costimulatory receptors is a promising approach for cancer immunotherapy. In preclinical work, adding an OX40 agonist to <i>in situ</i> vaccination with SD101, TLR9 agonist, was curative in mouse model of lymphoma. We sought test this combination phase I clinical trial patients low-grade B-cell lymphoma.</p>Patients and Methods:<p>We treated 14 low-dose radiation, intratumoral intravenous BMS986178, agonistic...
<p>Supplementary Figure 7. OX40 expression did not increase after SD101 (CpG) injection in a similar prior trial.</p>