A5019556057- Cancer, Hypoxia, and Metabolism
- Radiomics and Machine Learning in Medical Imaging
- Cancer Research and Treatments
- Colorectal Cancer Treatments and Studies
- RNA modifications and cancer
- Cancer Immunotherapy and Biomarkers
- Cancer Genomics and Diagnostics
- Lung Cancer Treatments and Mutations
- Melanoma and MAPK Pathways
- Cancer-related Molecular Pathways
- Cancer Cells and Metastasis
- Cancer-related molecular mechanisms research
- Microtubule and mitosis dynamics
- Cancer-related gene regulation
- Pancreatic and Hepatic Oncology Research
- Epigenetics and DNA Methylation
- Fibroblast Growth Factor Research
- Wnt/β-catenin signaling in development and cancer
- MicroRNA in disease regulation
- Cutaneous Melanoma Detection and Management
- CAR-T cell therapy research
- Thyroid Cancer Diagnosis and Treatment
- Cancer Mechanisms and Therapy
- Immunotherapy and Immune Responses
- Computational Drug Discovery Methods
Huntsman Cancer Institute
2023-2025
University of Utah
2023-2025
Canisius-Wilhelmina Ziekenhuis
2006-2025
Singapore General Hospital
2025
Nepean Hospital
2024
Moffitt Cancer Center
2019-2023
University of Colorado Anschutz Medical Campus
2014-2023
University of Colorado Denver
2013-2023
University of Colorado Cancer Center
2013-2023
Cancer Research Center
2010-2023
Abstract Summary: We report the creation of Drug Signatures Database (DSigDB), a new gene set resource that relates drugs/compounds and their target genes, for enrichment analysis (GSEA). DSigDB currently holds 22 527 sets, consists 17 389 unique compounds covering 19 531 genes. also developed an online allows users to search, view download sets. sets provide seamless integration GSEA software linking expressions with drug repurposing translational research. Availability implementation: is...
Abstract Purpose: To define the genetic landscape of advanced differentiated and anaplastic thyroid cancer (ATC) identify alterations potential diagnostic, prognostic, therapeutic significance. Experimental Design: The profiles 583 196 ATCs generated with targeted next-generation sequencing cancer-associated gene panels MSK-IMPACT FoundationOne were analyzed. Results: ATC had more per tumor, pediatric papillary fewer tumor when compared other types. DNA mismatch repair deficit activity...
Most of the studies characterizing DNA methylation patterns have been restricted to particular genomic loci in a limited number human samples and pathological conditions. Herein, we present compromise between an extremely comprehensive study sample population with intermediate level resolution CpGs at level. We obtained fingerprint 1628 which interrogated 1505 CpG sites. The revealed show this epigenetic mark be critical tissue-type definition stemness, particularly around transcription...
Various studies have shown that cancer tissue samples can be successfully detected and classified by their gene expression patterns using machine learning approaches. One of the challenges in applying these techniques for classifying data is to extract accurate, readily interpretable rules providing biological insight as how classification performed. Current methods generate classifiers are accurate but difficult interpret. This trade-off between credibility comprehensibility classifiers....
Abstract Purpose: Anaplastic lymphoma kinase (ALK) rearrangements, associated with sensitivity to an experimental ALK/MET inhibitor, occur in 3% 5% of non–small cell lung cancers. Intratumoral fluorescence situ hybridization (FISH) heterogeneity has been reported. We explored the basis, requirements for accurately determining ALK FISH positivity, and effect enriching tested population using clinical molecular factors. Experimental Design: Lung cancer patients were screened by MET EGFR KRAS...
Despite initial and often dramatic responses of epidermal growth factor receptor (EGFR)-addicted lung tumors to the EGFR-specific tyrosine kinase inhibitors (TKIs), gefitinib erlotinib, nearly all develop resistance relapse. To explore novel mechanisms mediating acquired resistance, we employed non-small-cell cancer (NSCLC) cell lines bearing activating mutations in EGFR rendered them resistant TKIs through chronic adaptation tissue culture. In addition previously observed including...
Purpose: Radiotherapy (RT) can transform the immune landscape and render poorly immunogenic tumors sensitive to PD-L1 inhibition. Here, we established that response combined RT inhibition is transient investigated mechanisms of resistance.Experimental Design: Mechanisms resistance blockade were in orthotopic murine head neck squamous cell carcinoma (HNSCC) using mass cytometry whole-genome sequencing. Mice treated with anti-PD-L1 or anti-TIM-3 alone combination without RT. Tumor growth...
Abstract Purpose: Antiendocrine therapy remains the most effective treatment for estrogen receptor–positive (ER+) breast cancer, but development of resistance is a major clinical complication. Effective targeting mechanisms that control loss ER dependency in cancer elusive. We analyzed cancer–associated fibroblasts (CAF), largest component tumor microenvironment, as factor contributing to expression levels and antiendocrine resistance. Experimental Design: Tissues from patients with ER+ were...
Abstract Motivation Gene Set Enrichment Analysis (GSEA) is routinely used to analyze and interpret coordinate pathway-level changes in transcriptomics experiments. For an experiment where less than seven samples per condition are compared, GSEA employs a competitive null hypothesis test significance. A gene set enrichment score tested against distribution of scores generated from permuted sets, genes randomly selected the input experiment. Looking across variety biological conditions,...
Abstract Purpose: Thyroid cancer cell lines are valuable models but have been neglected in pancancer genomic studies. Moreover, their misidentification has a significant problem. We aim to provide validated dataset for thyroid researchers. Experimental Design: performed next-generation sequencing (NGS) and analyzed the transcriptome of 60 authenticated compared our findings with known defects human cancers. Results: Unsupervised transcriptomic analysis showed that 94% clustered distinctly...
Significance The nucleotide-binding domain, leucine-rich containing family, pyrin domain-containing-3 (NLRP3) inflammasome, an intracellular complex that regulates maturation and release of interleukin (IL)-1β, is active in biopsies metastatic melanoma. Here, we demonstrate NLRP3 activation melanoma cells drives tumor progression mice. Subsequent to cells, IL-1β induces melanoma-associated inflammation, resulting immunosuppression. Oral administration a single inhibitor (OLT1177) reduces...
The goal of this study was to evaluate prospectively the engraftment rate, factors influencing engraftment, and predictability clinical outcome low-passage xenografts from patients with resectable pancreatic ductal adenocarcinoma (PDA) establish a bank PDA xenografts.Patients scheduled for resection at Johns Hopkins Hospital were eligible. Representative pieces tumor implanted in nude mice. status SMAD4 gene content tumor-generating cells determined by immunohistochemistry. Gene expression...
The current "gold-standard" for Parkinson's disease (PD) diagnosis is based primarily on subjective clinical rating scales related with motor features. Molecular biomarkers that are objective and quantifiable remain attractive as tools to detect PD prior its onsets.Here, we aimed identify, develop, validate plasma-based circulating microRNA (miRNAs) PD.Global miRNA expressions were acquired from a discovery set of 32 PD/32 controls using microarrays. k-Top Scoring Pairs (k-TSP) algorithm...
Transplantation of exogenous dopaminergic neuron (DA neurons) is a promising approach for treating Parkinson's disease (PD). However, major stumbling block has been the lack reliable source donor DA neurons. Here we show that combination five transcriptional factors Mash1, Ngn2, Sox2, Nurr1, and Pitx3 can directly effectively reprogram human fibroblasts into neuron-like cells. The reprogrammed cells stained positive various markers They also showed characteristic uptake production...