A5061824149- RNA modifications and cancer
- Advanced Proteomics Techniques and Applications
- Immunotherapy and Immune Responses
- Lung Cancer Treatments and Mutations
- Epigenetics and DNA Methylation
- HER2/EGFR in Cancer Research
- Protease and Inhibitor Mechanisms
- Cancer, Lipids, and Metabolism
- vaccines and immunoinformatics approaches
- RNA Research and Splicing
- RNA Interference and Gene Delivery
- Cancer-related gene regulation
- Immune Cell Function and Interaction
- Monoclonal and Polyclonal Antibodies Research
- Genomics and Chromatin Dynamics
- Ferroptosis and cancer prognosis
- Gene expression and cancer classification
- Nanoparticle-Based Drug Delivery
- Genomics and Phylogenetic Studies
- Glycosylation and Glycoproteins Research
- MicroRNA in disease regulation
- Birth, Development, and Health
- Lung Cancer Diagnosis and Treatment
- Algal biology and biofuel production
- Nutrition, Genetics, and Disease
Fred Hutch Cancer Center
2009-2023
Jackson Laboratory
2017-2023
Lawrence Berkeley National Laboratory
2013-2018
Joint Genome Institute
2015-2018
Cancer Research Center
2011-2014
Cape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa
2011-2014
The University of Texas Southwestern Medical Center
2014
Stanford University
2012
University of Washington
2012
The University of Texas MD Anderson Cancer Center
2011
No plasma biomarkers are associated with the response of acute graft-versus-host disease (GVHD) to therapy after allogeneic hematopoietic stem-cell transplantation.We compared 12 in obtained a median 16 days initiation from 10 patients complete by day 28 and progressive GVHD during therapy. The lead biomarker, suppression tumorigenicity 2 (ST2), was measured at beginning treatment for 381 first month transplantation three independent sets totaling 673 determine association this biomarker...
Abstract Epithelial-to-mesenchymal transition (EMT) is a key process associated with tumor progression and metastasis. To define molecular features EMT states, we undertook an integrative approach combining mRNA, miRNA, DNA methylation, proteomic profiles of 38 cell populations representative the genomic heterogeneity in lung adenocarcinoma. The resulting data were integrated functional consisting invasiveness, adhesion, motility. A subset lines that readily defined as epithelial or...
In many studies, particularly in the field of systems biology, it is essential that identical protein sets are precisely quantified multiple samples such as those representing differentially perturbed cell states. The high degree reproducibility required for experiments has not been achieved by classical mass spectrometry-based proteomics methods. this study we describe implementation a targeted quantitative approach which predetermined first identified and subsequently at sensitivity...
The microRNA-200 (miR-200) family restricts epithelial-mesenchymal transition (EMT) and metastasis in tumor cell lines derived from mice that develop metastatic lung adenocarcinoma. To determine the mechanisms responsible for EMT regulated by this microRNA, we conducted a global liquid chromatography/tandem mass spectrometry analysis to compare nonmetastatic murine adenocarcinoma cells which had undergone because of loss miR-200. An syngeneic tumors generated these identified multiple novel...
Significance Phytochromes are photosensory signaling proteins widely distributed in unicellular organisms and multicellular land plants. Best known for their global regulatory roles photomorphogenesis, plant phytochromes often assumed to have arisen via gene transfer from the cyanobacterial endosymbiont that gave rise photosynthetic chloroplast organelles. Our analyses support scenario were acquired prior diversification of Archaeplastida, possibly before endosymbiosis event. We show...
Prasinophytes are widespread marine green algae that related to plants. Cellular abundance of the prasinophyte Micromonas has reportedly increased in Arctic due climate-induced changes. Thus, studies these unicellular eukaryotes important for ecology and understanding Viridiplantae evolution diversification. We generated evidence-based gene models using proteomics RNA-Seq improve genomic resources. First, sequences four chromosomes 22 Mb pusilla (CCMP1545) genome were finished. Comparison...
The SOX2 transcription factor is critical for neural stem cell (NSC) maintenance and brain development. Through chromatin immunoprecipitation (ChIP) interaction analysis (ChIA-PET), we determined genome-wide SOX2-bound regions Pol II-mediated long-range interactions in brain-derived NSCs. DNA was highly enriched distal interacting with promoters carrying epigenetic enhancer marks. Sox2 deletion caused widespread reduction of decreased gene expression. Genes showing reduced expression...
To identify novel tyrosine kinase substrates that have never been implicated in cancer, we studied the phosphoproteomic changes MCF10AT model of breast cancer progression using a combination phosphotyrosyl affinity enrichment, iTRAQ™ technology, and LC-MS/MS. Using complementary MALDI- ESI-based mass spectrometry, 57 unique proteins comprising kinases, phosphatases, other signaling were detected to undergo differential phosphorylation during disease progression. Seven these (SPAG9,...
With the use of breast cancer metastatic model, which comprises four isogenic cell lines, iTRAQ-based ESI-LC/MS/MS proteomics was employed to catalog protein expression changes as cells acquire increasing potential. From more than 1000 proteins detected, 197 proteins, including drug-targetable kinases, phosphatases, proteases and transcription factors, displayed differential when becomes metastatic. Overall, number evenly distributed across mildly (∼30%), moderately (∼40%) aggressively...
Abstract Tumor development relies upon essential contributions from the tumor microenvironment and host immune alterations. These may inform plasma proteome in a manner that could be exploited for cancer diagnosis prognosis. In this study, we employed systems biology approach to characterize response inducible HER2/neu mouse model of breast during induction, progression, regression. Mass spectrometry data derived approximately 1.6 million spectra identified protein networks involved wound...
The T cell Ig and mucin domain 3 (Tim-3) receptor has been implicated as a negative regulator of adaptive immune responses. We have utilized proteomic strategy to identify novel proteins associated with graft versus host disease (GVHD) after allogeneic hematopoietic transplantation (HCT). Mass spectrometry analysis plasma from subjects mid-gut upper-gut GVHD compared those without identified increased levels protein high confidence Tim-3. A follow-up validation study using an immunoassay...
Germline stem cells play an essential role in establishing the fertility of organism. Although extensively characterized, regulatory mechanisms that govern fundamental properties mammalian female germline remain poorly understood. We generate genome-wide profiles histone modifications H3K4me1, H3K27ac, H3K4me3, and H3K27me3, DNA methylation, RNA polymerase II occupancy perform transcriptome analysis mouse cells. Comparison enhancer regions between embryonic identifies lineage-specific...
Complete genome annotation relies on precise identification of transcription units bounded by a initiation site (TIS) and polyadenylation (PAS). To facilitate this process, we developed set two complementary methods, 5′ Long serial analysis gene expression (LS) 3′LS. These analyses are based the original SAGE LS methods coupled with full-length cDNA cloning, enable high-throughput extraction first last 20 bp each transcript. We demonstrate that mapping 5′LS 3′LS tags to allows localization...
Abstract Protein tyrosine kinases (PTKs) play a critical role in the manifestation of cancer cell properties, and respective signaling mechanisms have been studied extensively on immortalized tumor cells. To characterize analyze commonly used lines with regard to variations primary structure all expressed PTKs, we conducted cDNA-based sequence analysis entire kinase transcriptome 254 established lines. The profiles line intrinsic PTK transcript alterations evaluation 155 identified...
Abstract Cancer/testis (CT) antigens are potential immunotherapeutic targets in cancer. However, the expression of particular is limited to a subset tumors given type. Thus, there need identify with complementary patterns for effective therapeutic intervention. In this study, we searched genes that were distinctly expressed at higher level lung tumor tissue and testes compared other nontumor tissues identified members VCX/Y gene family as novel CT antigens. VCX3A, member family, was protein...
Connecting genes to their cis-regulatory elements has been enabled by genome-wide mapping of chromatin interactions using proximity ligation in ChIA-PET, Hi-C, and derivatives. However, these methods require millions input cells for high-quality data thus are unsuitable many studies when only limited available. Conversely, epigenomic profiling via transposase digestion ATAC-seq requires hundreds thousands robustly map open associated with transcription activity, but it cannot directly...