A5018332268- Protein Tyrosine Phosphatases
- Bioinformatics and Genomic Networks
- Glycosylation and Glycoproteins Research
- Advanced Proteomics Techniques and Applications
- Cancer, Hypoxia, and Metabolism
- Computational Drug Discovery Methods
- Cancer, Lipids, and Metabolism
- 14-3-3 protein interactions
- ATP Synthase and ATPases Research
- Melanoma and MAPK Pathways
- Light effects on plants
- Microtubule and mitosis dynamics
- Photoreceptor and optogenetics research
- Cell Image Analysis Techniques
- Photosynthetic Processes and Mechanisms
- Mitochondrial Function and Pathology
- RNA Research and Splicing
- Machine Learning in Bioinformatics
- Cancer Mechanisms and Therapy
- Biochemical Acid Research Studies
- Cancer-related molecular mechanisms research
- CRISPR and Genetic Engineering
- Genomics, phytochemicals, and oxidative stress
- RNA modifications and cancer
- Cancer-related Molecular Pathways
Massachusetts Institute of Technology
2020-2025
Allen Institute
2020-2024
Precision for Medicine (United States)
2020-2023
National Heart Lung and Blood Institute
2020
National Institutes of Health
2020
Koch Institute for Integrative Cancer Research At MIT
2020
Tyrosine phosphorylation (pTyr) plays a pivotal role in signal transduction and is commonly dysregulated cancer. As result, profiling tumor pTyr levels may reveal therapeutic insights critical to combating disease. Existing discovery targeted mass spectrometry-based methods used monitor networks involve tradeoff between broad coverage of the network, reproducibility target identification across analyses, accurate quantification. To address these limitations, we developed approach, termed...
Engineered allosteric regulation of protein activity provides significant advantages for the development robust and broadly applicable tools. However, application switches in optogenetics has been scarce suffers from critical limitations. Here, we report an optogenetic approach that utilizes engineered Light-Regulated (LightR) switch module to achieve tight spatiotemporal control enzymatic activity. Using tyrosine kinase Src as a model, demonstrate efficient identify temporally distinct...
A major contributor to poor sensitivity anti-cancer kinase inhibitor therapy is drug-induced cellular adaptation, whereby remodeling of signaling and gene regulatory networks permits a drug-tolerant phenotype. Here, we resolve the scale kinetics critical subcellular events following oncogenic inhibition preceding cell cycle re-entry, using mass spectrometry-based phosphoproteomics RNA sequencing capture molecular snapshots within first minutes, hours, days BRAF exposure in human
Long noncoding RNAs (lncRNAs) are intracellular transcripts longer than 200 nucleotides and lack protein-coding information. A subclass of lncRNA known as long intergenic (lincRNAs) transcribed from genomic regions that share no overlap with annotated genes. Increasing evidence has shown some lincRNA do in fact contain open reading frames (ORFs) encoding functional short peptides the cell. Few robust methods for lincRNA-encoded peptide identification have been reported, tissue-specific...
Abstract Coordination of adaptive metabolism through cellular signaling networks and metabolic response is essential for balanced flow energy homeostasis. Post-translational modifications such as phosphorylation offer a rapid, efficient, dynamic mechanism to regulate networks. Although numerous sites have been identified on enzymes, much remains unknown about their contribution enzyme function systemic metabolism. In this study, we stratify enzymes based location with respect functional...
Abstract Dysregulation of intracellular signaling networks underpins cancer. However, a systems-level elucidation how within distinct cell subpopulations drive cancer progression in vivo has been unattainable due to technical limitations. We developed INSIGHT (INvestigating SIGnaling network specific subpopulation Heterogeneous Tissue), new platform technology combining fluorescence-activated sorting with ultra-sensitive mass spectrometry enable phosphoproteomic characterization rare and...
Abstract Tyrosine phosphorylation (pTyr) plays a pivotal role in signal transduction and is commonly dysregulated cancer. As result, profiling tumor pTyr levels may reveal therapeutic insights critical to combating disease. Existing discovery targeted mass spectrometry-based methods used monitor networks involve tradeoff between broad coverage of the network, reproducibility target identification across analyses, accurate quantification. To address these limitations, we developed approach,...
<p>Quantitative dynamics comparison between SureQuant pTyr, PRM, and DDA.</p>
<p>Light to heavy ratios and Z-score normalized pTyr abundances for peptides identified in colon tumors.</p>
<p>Targeted tyrosine phosphorylated peptides, method parameters, and file map of raw data files.</p>
<p>Clinical data for tumor specimens analyzed.</p>
<p>Custom pathway and substrate-kinase libraries for tumor-specific enrichment analyses.</p>
<p>Quantitative reproducibility comparison between SureQuant pTyr and DDA.</p>
<p>Supplementary figures, table legends, and methods.</p>
<p>Tyrosine phosphorylated peptides identified in discovery analyses of colorectal tumors.</p>
<p>Quantitative reproducibility comparison between SureQuant pTyr and DDA.</p>
<p>Clinical data for tumor specimens analyzed.</p>
<p>Targeted tyrosine phosphorylated peptides, method parameters, and file map of raw data files.</p>
<p>Tyrosine phosphorylated peptides identified in discovery analyses of colorectal tumors.</p>
<p>Custom pathway and substrate-kinase libraries for tumor-specific enrichment analyses.</p>
<p>Light to heavy ratios and Z-score normalized pTyr abundances for peptides identified in colon tumors.</p>
<p>Quantitative dynamics comparison between SureQuant pTyr, PRM, and DDA.</p>
<p>Supplementary figures, table legends, and methods.</p>
<div>Abstract<p>Tyrosine phosphorylation (pTyr) plays a pivotal role in signal transduction and is commonly dysregulated cancer. As result, profiling tumor pTyr levels may reveal therapeutic insights critical to combating disease. Existing discovery targeted mass spectrometry–based methods used monitor networks involve tradeoff between broad coverage of the network, reproducibility target identification across analyses, accurate quantification. To address these limitations, we...