A5048320821- Ubiquitin and proteasome pathways
- Cancer, Hypoxia, and Metabolism
- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Genetic Neurodegenerative Diseases
- RNA modifications and cancer
- Protein Degradation and Inhibitors
- Metabolomics and Mass Spectrometry Studies
- RNA Research and Splicing
- Mitochondrial Function and Pathology
- Neuroblastoma Research and Treatments
- Autophagy in Disease and Therapy
- Muscle Physiology and Disorders
- Epigenetics and DNA Methylation
- Acute Lymphoblastic Leukemia research
- Genetics and Neurodevelopmental Disorders
- Genomics and Chromatin Dynamics
- Cancer-related gene regulation
- Bioinformatics and Genomic Networks
- Genetics, Aging, and Longevity in Model Organisms
- Sarcoma Diagnosis and Treatment
- T-cell and B-cell Immunology
- Endoplasmic Reticulum Stress and Disease
- RNA and protein synthesis mechanisms
- Renal and related cancers
St. Jude Children's Research Hospital
2016-2025
Abbott (Sweden)
2024
University of Tennessee at Knoxville
2006
University of Idaho
2002
Ubiquitin-conjugating enzymes (E2s) are key for protein turnover and quality control via ubiquitination. Some E2s also physically interact with the proteasome, but it remains undetermined which maintain proteostasis during aging. Here, we find that have diverse roles in handling a model aggregation-prone (huntingtin-polyQ) Drosophila retina: while some mediate aggregate assembly, UBE2D/effete (eff) other required huntingtin-polyQ degradation. UBE2D/eff is skeletal muscle: eff levels decline...
Isobaric labeling quantification by mass spectrometry (MS) has emerged as a powerful technology for multiplexed large-scale protein profiling, but measurement accuracy in complex mixtures is confounded the interference from coisolated ions, resulting ratio compression. Here we report that compression can be essentially resolved combination of pre-MS peptide fractionation, MS2-based detection, and post-MS computational correction. To recapitulate complexity biological samples, pooled tandem...
Abstract Ubiquitination is a post-translational modification initiated by the E1 enzyme UBA1, which transfers ubiquitin to ~35 E2 ubiquitin-conjugating enzymes. While UBA1 loss cell lethal, it remains unknown how partial reduction in activity endured. Here, we utilize deep-coverage mass spectrometry define E1-E2 interactome and determine proteins that are modulated knockdown of each human cells. These analyses UBA1/E2-sensitive proteome specificity protein modulation. Interestingly, profound...
Skeletal muscle cell (myofiber) atrophy is a detrimental component of aging and cancer that primarily results from protein degradation via the proteasome ubiquitin ligases. Transcriptional upregulation some ligases contributes to myofiber atrophy, but little known about role most other play in this process. To address question, we have used RNAi screening Drosophila identify function > 320 evolutionarily conserved size regulation vivo. We find whereas for induces loss others (including N-end...
Abstract High throughput omics approaches provide an unprecedented opportunity for dissecting molecular mechanisms in cancer biology. Here we present deep profiling of whole proteome, phosphoproteome and transcriptome two high-grade glioma (HGG) mouse models driven by mutated RTK oncogenes, PDGFRA NTRK1 , analyzing 13,860 proteins 30,431 phosphosites mass spectrometry. Systems biology identify numerous master regulators, including 41 kinases 23 transcription factors. Pathway activity...
Abstract Sarcopenia is a degenerative condition that consists in age-induced atrophy and functional decline of skeletal muscle cells (myofibers). A common hypothesis inducing myofiber hypertrophy should also reinstate contractile function but such model has not been extensively tested. Here, we find the levels ubiquitin ligase UBR4 increase with aging, increases proteolytic activity proteasome. Importantly, muscle-specific loss rescues age-associated mice. However, reduces specific force...
Skeletal muscle atrophy is a debilitating condition that occurs with aging and disease, but the underlying mechanisms are incompletely understood. Previous work determined common transcriptional changes occur in during induced by different stimuli. However, whether this holds true at proteome level remains largely unexplored. Here, we find that, contrary to earlier model, distinct atrophic stimuli (corticosteroids, cancer cachexia, aging) induce mRNA protein mice. Moreover, there widespread...
Ubiquitin-like proteins (ub-lps) are conjugated by a conserved enzymatic pathway, involving ATP-dependent activation at the C terminus an activating enzyme (E1) and formation of thiolester intermediate with conjugating (E2) prior to ligation target. Ubc9, E2 for SUMO, synthesizes polymeric chains in presence its E1 MgATP. To better understand conjugation ub-lps, we have performed mutational analysis Saccharomyces cerevisiae Ubc9p, which conjugates SUMO family member Smt3p. We identified...
Abstract Rearrangments in Histone-lysine-N-methyltransferase 2A (KMT2Ar) are associated with pediatric, adult and therapy-induced acute leukemias. Infants KMT2Ar lymphoblastic leukemia (ALL) have a poor prognosis an event-free-survival of 38%. Herein we evaluate 1116 FDA approved compounds primary infant ALL specimens identify sensitivity to proteasome inhibition. Upon exposure this class agents, cells demonstrate depletion histone H2B monoubiquitination (H2Bub1) H3 lysine 79 dimethylation...
Nuclear factor Foxp3 determines regulatory T (Treg) cell fate and function via mechanisms that remain unclear. Here, we investigate the nature of Foxp3-mediated gene regulation in suppressing autoimmunity antitumor immune response. Contrasting with previous models, find Foxp3–chromatin binding is regulated by Treg activation states, tumor microenvironment, antigen cytokine stimulations. Proteomics studies uncover dynamic proteins within proximity upon TCR or IL-2 receptor signaling vitro,...
Chromatin modifiers affect spatiotemporal gene expression programs that underlie organismal development. The Polycomb repressive complex 2 (PRC2) is a crucial chromatin modifier in executing neurodevelopmental programs. Here, we find PRC2 interacts with the nucleic acid-binding protein Ybx1. In mouse embryo vivo, Ybx1 required for forebrain specification and restricting mid-hindbrain growth. neural progenitor cells (NPCs), controls self-renewal neuronal differentiation. Mechanistically,...
Disruption of the circadian clock in skeletal muscle worsens local and systemic health, leading to decreased strength, metabolic dysfunction, aging-like phenotypes. Whole-body knockout mice that lack Bmal1, a key component molecular clock, display premature aging. Here, by using adeno-associated viruses, we rescued Bmal1 expression specifically fibers Bmal1-KO found this engaged output gene contributing extended lifespan. Time course phenotypic analyses mobility, glucose tolerance were...
Intrinsically unstructured proteins (IUPs) represent an important class of primarily involved in cellular signaling and regulation. The aim this study was to develop methodology for the enrichment identification IUPs. We show that heat treatment NIH3T3 mouse fibroblast cell extracts at 98 °C selects majority these IUPs were cytosolic or nuclear These studies first large-scale experimental investigation intrinsically mammalian proteome. Keywords: • disordered proteomics proteome denaturation
The mind bomb 1 (Mib1) ubiquitin ligase is essential for controlling metazoan development by Notch signaling and possibly the Wnt pathway. It also expressed in postmitotic neurons regulates neuronal morphogenesis synaptic activity mechanisms that are largely unknown. We sought to comprehensively characterize Mib1 interactome study its potential function neuron utilizing a novel sequential elution strategy affinity purification, which binding proteins were eluted under different stringency...
Organisms use endogenous clocks to adapt the rhythmicity of environment and synchronize social activities. Although circadian cycle is implicated in aging, it unknown whether natural variation its function contributes differences lifespan between populations clock specific tissues key for longevity. We have sequenced genomes Drosophila melanogaster strains with exceptional longevity that were obtained via multiple rounds selection from a parental strain. Comparison genomic, transcriptomic,...
Abstract Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma of childhood. RMS can be parsed based on clinical outcome into two subtypes, fusion-positive (FP-RMS) or fusion-negative (FN-RMS) presence absence either PAX3-FOXO1 PAX7-FOXO1 gene fusions. In both tumor cells show histology and a expression pattern resembling that developmentally arrested skeletal muscle. Differentiation therapy an attractive approach to embryonal tumors childhood including RMS; however, agents drive...