A5047260313- Glycosylation and Glycoproteins Research
- RNA and protein synthesis mechanisms
- Advanced Proteomics Techniques and Applications
- Biotin and Related Studies
- Click Chemistry and Applications
- Ubiquitin and proteasome pathways
- Mass Spectrometry Techniques and Applications
- CRISPR and Genetic Engineering
- RNA modifications and cancer
- Carbohydrate Chemistry and Synthesis
- RNA Research and Splicing
- Advanced biosensing and bioanalysis techniques
- Acute Myeloid Leukemia Research
- Protein Degradation and Inhibitors
- Genetics and Neurodevelopmental Disorders
- Galectins and Cancer Biology
- Chromosomal and Genetic Variations
- Epigenetics and DNA Methylation
- Erythrocyte Function and Pathophysiology
- Pluripotent Stem Cells Research
- Genomics and Chromatin Dynamics
- Immune Cell Function and Interaction
- Prostate Cancer Treatment and Research
- Cytokine Signaling Pathways and Interactions
- Peptidase Inhibition and Analysis
La Jolla Institute for Immunology
2021-2025
University of California, San Diego
2023-2025
Duke University
2025
University of Bologna
2024
Italian Institute of Technology
2023-2024
Dublin City University
2024
GNA University
2024
National Research Council
2024
Broad Institute
2017-2023
Massachusetts Institute of Technology
2020-2023
Increasing energy costs and environmental concerns have motivated engineering microbes for the production of "second generation" biofuels that better properties than ethanol.Saccharomyces cerevisiae was engineered with an n-butanol biosynthetic pathway, in which isozymes from a number different organisms (S. cerevisiae, Escherichia coli, Clostridium beijerinckii, Ralstonia eutropha) were substituted Clostridial enzymes their effect on compared. By choosing appropriate isozymes, we able to...
Much attention has focussed on the conversion of human pluripotent stem cells (PSCs) to a more naïve developmental status. Here we provide method for resetting via transient histone deacetylase inhibition. The protocol is effective across multiple PSC lines and can proceed without karyotype change. Reset be expanded feeders with doubling time around 24 h. WNT inhibition stabilises process. transcriptome reset diverges markedly from that primed PSCs shares features inner cell mass (ICM)....
The monosaccharide addition of an N -acetylglucosamine to serine and threonine residues nuclear cytosolic proteins ( O -GlcNAc) is a posttranslational modification emerging as general regulator many cellular processes, including signal transduction, cell division, transcription. sole mouse -GlcNAc transferase (OGT) essential for embryonic development. To understand the role OGT in development better, we mapped sites -GlcNAcylation stem cells (ESCs). Here, unambiguously identify over 60...
Significance The biogenesis, processing, function, and degradation of cellular RNAs depend critically on their protein interaction partners. Systematic analysis the interactome specific interest inside living cells can therefore enable a better understanding many biological processes. We developed two complementary methods for tagging endogenous proteins in vicinity RNAs, subsequent identification by mass spectrometry. When applied to human telomerase RNA, our recovered known partners as...
Proteomic profiling describes the molecular landscape of proteins in cells immediately available to sense, transduce, and enact appropriate responses extracellular queues. Transcriptional has proven invaluable our understanding cellular responses; however, insights may be lost as mounting evidence suggests transcript levels only moderately correlate with protein steady state cells. Mass spectrometry-based quantitative proteomics is a well-suited widely used analytical tool for studying...
Abstract Metastasis causes most cancer-related deaths, and one poorly understood aspect of metastatic cancer is the adaptability cells from a primary tumor to create new niches survive in multiple, different secondary sites. We used quantitative mass spectrometry analyze extracellular matrix (ECM), critical component niches, metastases brain, lungs, liver, bone marrow, all derived parental MDA-MB-231 triple-negative breast cells. Tumor stromal cooperated forming niches; produced...
Abstract Proximity labeling (PL) with genetically-targeted promiscuous enzymes has emerged as a powerful tool for unbiased proteome discovery. By combining the spatiotemporal specificity of PL methods functional protein enrichment, we show that it is possible to map specific subclasses within distinct compartments living cells. In particular, develop method enrich subcompartment-specific RNA binding proteins (RBPs) by peroxidase-catalyzed organic-aqueous phase separation crosslinked...
O -GlcNAc transferase (OGT) modifies serine and threonine residues on nuclear cytosolic proteins with -linked N-acetylglucosamine (GlcNAc). OGT is essential for mammalian cell viability, but the underlying mechanisms are still enigmatic. We performed a genome-wide CRISPR–Cas9 screen in mouse embryonic stem cells (mESCs) to identify candidates whose depletion rescued block proliferation induced by deficiency. show that OGT-deficient stems from mitochondrial dysfunction secondary mTOR...
The development of electron-based, unimolecular dissociation MS, i.e. electron capture and transfer (ECD ETD, respectively), has greatly increased the speed reliability labile PTM site assignment. field intracellular O-GlcNAc (O-linked N-acetylglucosamine) signaling especially advanced with advent ETD MS. Only within last five years have proteomic-scale experiments utilizing allowed assignment hundreds sites cells subcellular structures. Our ability to identify unambiguously assign...
Neuronal activity is an energy-intensive process that largely sustained by instantaneous fuel utilization and ATP synthesis. However, how neurons couple synthesis rate to availability unknown. Here, we demonstrate the metabolic sensor enzyme O-linked N-acetyl glucosamine (O-GlcNAc) transferase regulates neuronal activity-driven mitochondrial bioenergetics in hippocampal cortical neurons. We show upregulates O-GlcNAcylation mitochondria. Mitochondrial promoted glucose consumption, which...
ASXL transcriptional regulator 1 (ASXL1) is one of the three most frequently mutated genes in age-related clonal hematopoiesis (CH), alongside DNA methyltransferase 3 alpha (DNMT3A) and Tet methylcytosine dioxygenase 2 ( TET2) . CH can progress to myeloid malignancies including chronic monomyelocytic leukemia (CMML) also strongly associated with inflammatory cardiovascular disease all-cause mortality humans. DNMT3A TET2 regulate methylation demethylation pathways, respectively,...
Heterozygous coding mutations in TRIO are associated with neurodevelopmental disorders, including autism, schizophrenia, bipolar disorder, and epilepsy, impair TRIO's biochemical activities. To model mutant alleles, we ablated one or both Trio alleles from excitatory neurons the cortex hippocampus of mice. haploinsufficiency increases anxiety impairs social preference motor coordination. loss reduces forebrain size dendritic arborization but spine densities. Cortical synapses...
Antibodies against posttranslational modifications (PTMs) such as lysine acetylation, ubiquitin remnants, or phosphotyrosine have resulted in significant advances our understanding of the fundamental roles these PTMs biology. However, a number remain largely unexplored due to lack robust enrichment reagents. The addition N-acetylglucosamine serine and threonine residues (O-GlcNAc) by O-GlcNAc transferase (OGT) is PTM implicated numerous biological processes disease states but with limited...
Retrons are bacterial retroelements that produce single-stranded, reverse-transcribed DNA (RT-DNA) is a critical part of newly discovered phage defense system. Short retron RT-DNAs produced from larger, structured RNAs via unique 2'-5' initiation and mechanism for precise termination not yet understood. Interestingly, reverse transcriptases (RTs) typically lack an RNase H domain and, therefore, depend on endogenous H1 to remove RNA templates RT-DNA. We find evidence expanded role in the...
Abstract Understanding how small molecules bind to specific protein complexes in living cells is critical understanding their mechanism-of-action. Unbiased chemical biology strategies for direct readout of interactome remodelling by would provide advantages over target-focused approaches, including the ability detect previously unknown ligand targets and complexes. However, there are few current methods unbiased profiling molecule interactomes. To address this, we envisioned a technology...
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Telomere shortening is a prominent hallmark of aging and emerging as characteristic feature Myelodysplastic Syndromes (MDS) Idiopathic Pulmonary Fibrosis (IPF). Optimal telomerase activity prevents progressive telomeres that triggers DNA damage responses. However, the upstream regulation holoenzyme components remains poorly defined. Here, we identify RIOK2, master regulator human blood cell development, critical transcription factor for telomere maintenance. Mechanistically, loss RIOK2 or...
Abstract Background: ASXL1 is one of the three most frequently mutated genes in age-related clonal hematopoiesis (CH), with others being DNMT3A and TET2. CH progresses to myeloid malignancies including chronic monomyelocytic leukemia (CMML), also strongly associated inflammatory cardiovascular disease all-cause mortality humans. TET2 regulate DNA methylation demethylation pathways respectively, loss-of-function mutations both reduce heterochromatin. In contrast, mechanisms that connect...