A5037898139- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Histone Deacetylase Inhibitors Research
- Ubiquitin and proteasome pathways
- Protein Degradation and Inhibitors
- Single-cell and spatial transcriptomics
- Metabolomics and Mass Spectrometry Studies
- RNA Research and Splicing
- RNA modifications and cancer
- Peptidase Inhibition and Analysis
- Genomics and Chromatin Dynamics
- Neurogenetic and Muscular Disorders Research
- Biosensors and Analytical Detection
- RNA and protein synthesis mechanisms
- Amyotrophic Lateral Sclerosis Research
- Muscle Physiology and Disorders
- Cell Image Analysis Techniques
- Alzheimer's disease research and treatments
- Computational Drug Discovery Methods
- Advanced Biosensing Techniques and Applications
- Genetics, Aging, and Longevity in Model Organisms
- Viral-associated cancers and disorders
- Microtubule and mitosis dynamics
- CRISPR and Genetic Engineering
- Dementia and Cognitive Impairment Research
Biogen (United States)
2020-2024
Boston Children's Hospital
2018-2023
Harvard University
2018-2023
Princeton University
2010-2016
To elucidate the role of Tau isoforms and post-translational modification (PTM) stoichiometry in Alzheimer's disease (AD), we generated a high-resolution quantitative proteomics map 95 PTMs on multiple isolated from postmortem human tissue 49 AD 42 control subjects. Although PTM maps reveal heterogeneity across subjects, subset display high occupancy frequency for AD, suggesting importance disease. Unsupervised analyses indicate that occur an ordered manner, leading to aggregation. The...
Histone deacetylases (HDACs) are a diverse family of essential transcriptional regulatory enzymes, that function through the spatial and temporal recruitment protein complexes. As composition regulation HDAC complexes only partially characterized, we built first global interaction network for all 11 human HDACs in T cells. Integrating fluorescence microscopy, immunoaffinity purifications, quantitative mass spectrometry, bioinformatics, identified over 200 unreported interactions both...
The combination of nanodroplet sample preparation, ultra-low-flow nanoLC, high-field asymmetric ion mobility spectrometry (FAIMS) and latest-generation mass instrumentation provides dramatically improved single-cell proteome profiling.
A limitation of conventional bulk-tissue proteome studies in amyotrophic lateral sclerosis (ALS) is the confounding motor neuron (MN) signals by admixed non-MN proteins. Here, we leverage laser capture microdissection and nanoPOTS single-cell mass spectrometry-based proteomics to query changes protein expression single MNs from postmortem ALS control tissues. In a follow-up analysis, examine impact stratification based on cytoplasmic transactive response DNA-binding 43 (TDP-43)+ inclusion...
Histone deacetylase 5 (HDAC5), a class IIa deacetylase, is prominent regulator of cellular and epigenetic processes that underlie the progression human disease, ranging from cardiac hypertrophy to cancer. Although it established phosphorylation mediates 14-3-3 protein binding provides essential link between HDAC5 nucleo-cytoplasmic shuttling transcriptional repression, thus far only four phospho-acceptor sites have been functionally characterized. Here, using combinatorial proteomics...
Alternative translation initiation and stop codon readthrough in a few well-studied cases have been shown to allow the same transcript generate multiple protein variants. Because brain shows particularly abundant use of alternative splicing, we sought study CNS cells. We show that is widespread regulated across transcripts. In neural cultures, identify on hundreds transcripts, confirm several N-terminal variants, modulation phenomenon by KCl stimulation. also detect cultures differential...
The goal of proteomics is to identify and quantify the complete set proteins in a biological sample. Single-cell specializes identification quantitation for individual cells, often used elucidate cellular heterogeneity. significant reduction ions introduced into mass spectrometer single-cell samples could impact features MS2 fragmentation spectra. As all peptide software tools have been developed on spectra from bulk associated ion-rich spectra, potential spectral change great interest. We...
Class IIa histone deacetylases (HDACs 4/5/7/9) are transcriptional regulators with critical roles in cardiac disease and cancer. HDAC inhibitors promising anticancer agents, although they known to disrupt mitotic progression, the underlying mechanisms of regulation by HDACs not fully understood. Here we provide first identification as substrates Aurora B kinase (AurB). Our study identifies class a novel family AurB targets provides evidence that temporally spatially regulated phosphorylation...
Abstract Almost 400 genes affect yeast telomere length, including Est1 , which is critical for recruitment and activation of telomerase. Here we use mass spectrometry to identify novel telomerase regulators by their co-purification with the holoenzyme. In addition all known subunits, over 100 proteins are associated, three subunits essential Cdc48-Npl4-Ufd1 complex as well E3 ubiquitin ligases. The Cdc48 evolutionarily conserved targets ubiquitinated degradation. levels ∼40-fold higher in...
Replicative DNA helicases expose the two strands of double helix to replication apparatus, but accessory are often needed help forks move past naturally occurring hard-to-replicate sites, such as tightly bound proteins, RNA/DNA hybrids, and secondary structures. Although Schizosaccharomyces pombe 5'-to-3' helicase Pfh1 is known promote fork progression, its genomic targets, dynamics, mechanisms action largely unknown. Here we address these questions by integrating genome-wide identification...
The cuprizone (CPZ) model is widely used for modeling demyelination in multiple sclerosis (MS) and testing potential remyelination therapies. We integrated single-cell spatial transcriptomics (ST) to fine map the cellular molecular responses during de remyelination. ST revealed global neuroinflammation brain beyond corpus callosum, with region-specific differences. identified oligodendroglia microglia as two major cell types significant transcriptomic changes model. Ligand‒receptor pairing...
Summary Unbiased proteomics has been employed to interrogate central nervous system (CNS) tissues (brain, spinal cord) and fluid matrices (CSF, plasma) from amyotrophic lateral sclerosis (ALS) patients; yet, a limitation of conventional bulk tissue studies is that motor neuron (MN) proteome signals may be confounded by admixed non-MN proteins. Recent advances in trace sample have enabled quantitative protein abundance datasets single human MNs (Cong et al., 2020b). In this study, we...
Deleted in breast cancer 1 (DBC1) has emerged as an important regulator of multiple cellular processes, ranging from gene expression to cell cycle progression. DBC1 been linked tumorigenesis both inhibitor histone deacetylases, HDAC3 and sirtuin 1, a transcriptional cofactor for nuclear hormone receptors. However, despite mounting interest DBC1, relatively little is known about the range its interacting partners scope functions. Here, we carried out functional proteomics-based investigation...
Class IIa histone deacetylases (HDACs) are critical transcriptional regulators, shuttling between nuclear and cytoplasmic cellular compartments. Within the nucleus, these HDACs repress transcription as components of multiprotein complexes, such corepressor beclin-6 (BCoR) complexes. Cytoplasmic relocalization relieves this repressive function. HDAC is controlled, in part, by phosphorylations flanking localization signal (NLS). Furthermore, we have reported that phosphorylation within NLS...
Characterizing perturbation of molecular pathways in congenital Zika virus (ZIKV) infection is critical for improved therapeutic approaches. Leveraging integrative systems biology, proteomics, and RNA-seq, we analyzed embryonic brain tissues from an immunocompetent, wild-type ZIKV mouse model. induced a robust immune response accompanied by the downregulation neurodevelopmental gene programs. We identified negative correlation between polyprotein abundance host cell cycle-inducing proteins....
Abstract We report on the combination of nanodroplet sample preparation, ultra-low-flow nanoLC, high-field asymmetric ion mobility spectrometry (FAIMS), and latest-generation Orbitrap Eclipse Tribrid mass spectrometer for greatly improved single-cell proteome profiling. FAIMS effectively filtered out singly charged ions more effective MS analysis multiply peptides, resulting in an average 1056 protein groups identified from single HeLa cells without MS1-level feature matching. This is 2.3...
•Detecting temporal change in proteins depends on fold and variability.•Replicate time courses improve reliability of detecting dynamics.•Temporal experiments require a dense sampling cells to track gradual transitions.•Time-course trajectory more samples than two-state comparisons. Single-cell measurements are uniquely capable characterizing cell-to-cell heterogeneity have been used explore the large diversity cell types physiological functions present tissues other complex assemblies. An...
Abstract Single cell proteomics is an emerging sub-field within with the potential to revolutionize our understanding of cellular heterogeneity and interactions. Recent efforts have largely focused on technological advancements in sample preparation, chromatography instrumentation enable measuring proteins present these ultra-limited samples. Although data acquisition rapidly improved ability analyze single cells, software pipelines used analysis were originally written for traditional bulk...
Abstract Translation canonically begins at a single AUG and terminates the stop codon, generating one protein species per transcript. However, some transcripts may use alternative initiation sites or sustain translation past their multiple isoforms. Through other mechanisms such as splicing, both neurons glia exhibit remarkable transcriptional diversity, these forms of post-transcriptional regulation are impacted by neural activity disease. Here, using ribosome footprinting, we demonstrate...
Abstract Single cell measurements are uniquely capable of characterizing cell-to-cell heterogeneity, and have been used to explore the large diversity types physiological functions present in tissues other complex assemblies. An intriguing application single proteomics is characterization proteome dynamics during biological transitions, like cellular differentiation or disease progression. Time course experiments, which regularly take state rely on ability detect dynamic trajectories a data...
Abstract The goal of proteomics is to identify and quantify the complete set proteins in a biological sample. Single cell specializes identification quantitation for individual cells, often used elucidate cellular heterogeneity. significant reduction ions introduced into mass spectrometer single samples could impact features MS2 fragmentation spectra. As all peptide software tools have been developed on spectra from bulk associated ion rich spectra, potential spectral change great interest....