Skirball Institute

New York City, NY, United States

Skirball Institute

New York City, NY, United States

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Huang F.-K.,New York University | Zhang G.,New York University | Lawlor K.,Sloan Kettering Cancer Center | Nazarian A.,Sloan Kettering Cancer Center | And 5 more authors.
Journal of Proteome Research | Year: 2017

Labeling peptides with isobaric tags is a popular strategy in quantitative bottom-up proteomics. In this study, we labeled six breast tumor cell lysates (1.34 mg proteins per channel) using 10-plex tandem mass tag reagents and analyzed the samples on a Q Exactive HF Quadrupole-Orbitrap mass spectrometer. We identified a total of 8,706 proteins and 28,186 phosphopeptides, including 7,394 proteins and 23,739 phosphosites common to all channels. The majority of technical replicates correlated with a R2 ≥ 0.98, indicating minimum variability was introduced after labeling. Unsupervised hierarchical clustering of phosphopeptide data sets successfully classified the breast tumor samples into Her2 (epidermal growth factor receptor 2) positive and Her2 negative groups, whereas mRNA abundance did not. The tyrosine phosphorylation levels of receptor tyrosine kinases, phosphoinositide-3-kinase, protein kinase C delta, and Src homology 2, among others, were significantly higher in the Her2 positive than the Her2 negative group. Despite ratio compression in MS2-based experiments, we demonstrated the ratios calculated using an MS2 method are highly correlated (R2 > 0.65) with ratios obtained using MS3-based quantitation (using a Thermo Orbitrap Fusion mass spectrometer) with reduced ratio suppression. Given the deep coverage of global and phosphoproteomes, our data show that MS2-based quantitation using TMT can be successfully used for large-scale multiplexed quantitative proteomics. © 2017 American Chemical Society.

Tucker A.M.,MedStar Sports Medicine | Lincoln A.E.,MedStar Research Institute | Vogel R.A.,Cardiology Section 11B | Black H.R.,Skirball Institute | And 4 more authors.
Journal of the American Society of Hypertension | Year: 2015

Previous findings suggest that professional American football players have higher blood pressures (BP) and a higher prevalence of pre-hypertension and hypertension than the general population. We sought to determine whether race is associated with differences in BP and prevalence of pre-hypertension and hypertension among a large sample of professional football players. BP was measured at 2009 team mini-camps for 1484 black (n = 1007) and white (n = 477) players from 27 National Football League (NFL) teams. Players were categorized into three position groups based on body mass index (BMI). There was no racial difference in mean systolic or diastolic BP in any of the three position groups. There were no racial differences in prevalence of hypertension (99 [9.8%] black players vs. 39 [8.2%] white players; P =.353) or pre-hypertension (557 [55.3%] black players vs. 264 [55.3%] white players; P = 1.0). Contrary to findings in the general population, BP and prevalence of pre-hypertension/hypertension did not vary with race in a large population of active NFL players. © 2015 American Society of Hypertension. All rights reserved.

Xu C.,Indiana University | Shen Y.,Howard Hughes Medical Institute | Littman D.R.,Howard Hughes Medical Institute | Littman D.R.,Skirball Institute | And 4 more authors.
Journal of Leukocyte Biology | Year: 2012

FIVM has provided many insights into the regulation of immunity. We report the validation of an approach for visualizing murine small bowel via single- and multiphoton FIVM. Tissue damage is limited to ~200 μm, immediately adjacent to the incision, as confirmed by intravital PI staining. Treatment with 10 KDa dextran-FITC and 70 KDa dextran-TR confirms that perfusion is intact. Selective filtration of 10 KDa but not 70 KDa dextran from the blood indicated that kidney function is also intact. Interestingly, lamina propria vasculature is semipermeable to 10 KDa dextran. Next, reporter mice expressing egfp from the CX3CR1 locus, egfp from the FoxP3 locus, or RFP from the IL-17F locus were used to track DC subsets, FoxP3+ Tregs, or Th17f cells, respectively. Resident cx3cr1+/egfp cells were sessile but actively probed the surrounding microenvironment. Both T cell populations patrol the lamina propria, but the Th17f cells migrate more rapidly than Tregs. Together, these data demonstrate intact vascular perfusion, while intravitally visualizing the mucosal surface of the small bowel. Lastly, the cx3cr1+ DCs and T cells display activity similar to that found in steady-state, secondary lymphoid organs.© Society for Leukocyte Biology.

Anastasia A.,New York Medical College | Deinhardt K.,Skirball Institute | Deinhardt K.,University of Southampton | Wang S.,New York Medical College | And 8 more authors.
PLoS ONE | Year: 2014

Pericyte and vascular smooth muscle cell (SMC) recruitment to the developing vasculature is an important step in blood vessel maturation. Brain-derived neurotrophic factor (BDNF), expressed by endothelial cells, activates the receptor tyrosine kinase TrkB to stabilize the cardiac microvasculature in the perinatal period. However, the effects of the BDNF/TrkB signaling on pericytes/SMCs and the mechanisms downstream of TrkB that promote vessel maturation are unknown. To confirm the involvement of TrkB in vessel maturation, we evaluated TrkB deficient (trkb-/-) embryos and observed severe cardiac vascular abnormalities leading to lethality in late gestation to early prenatal life. Ultrastructural analysis demonstrates that trkb-/- embryos exhibit defects in endothelial cell integrity and perivascular edema. As TrkB is selectively expressed by pericytes and SMCs in the developing cardiac vasculature, we generated mice deficient in TrkB in these cells. Mice with TrkB deficiency in perivascular cells exhibit reduced pericyte/SMC coverage of the cardiac microvasculature, abnormal endothelial cell ultrastructure, and increased vascular permeability. To dissect biological actions and the signaling pathways downstream of TrkB in pericytes/SMCs, human umbilical SMCs were treated with BDNF. This induced membranous protrusions and cell migration, events dependent on myosin light chain phosphorylation. Moreover, inhibition of Rho GTPase and the Rho-associated protein kinase (ROCK) prevented membrane protrusion and myosin light chain phosphorylation in response to BDNF. These results suggest an important role for BDNF in regulating migration of TrkB-expressing pericytes/SMCs to promote cardiac blood vessel ensheathment and functional integrity during development. © 2014 Anastasia et al.

Oyallon J.,UK National Institute for Medical Research | Oyallon J.,Skirball Institute | Apitz H.,UK National Institute for Medical Research | Miguel-Aliaga I.,University of Cambridge | And 4 more authors.
Developmental Biology | Year: 2012

During the development of locomotion circuits it is essential that motoneurons with distinct subtype identities select the correct trajectories and target muscles. In vertebrates, the generation of motoneurons and myelinating glia depends on Olig2, one of the five Olig family bHLH transcription factors. We investigated the so far unknown function of the single Drosophila homolog Oli. Combining behavioral and genetic approaches, we demonstrate that oli is not required for gliogenesis, but plays pivotal roles in regulating larval and adult locomotion, and axon pathfinding and targeting of embryonic motoneurons. In the embryonic nervous system, Oli is primarily expressed in postmitotic progeny, and in particular, in distinct ventral motoneuron subtypes. oli mediates axonal trajectory selection of these motoneurons within the ventral nerve cord and targeting to specific muscles. Genetic interaction assays suggest that oli acts as part of a conserved transcription factor ensemble including Lim3, Islet and Hb9. Moreover, oli is expressed in postembryonic leg-innervating motoneuron lineages and required in glutamatergic neurons for walking. Finally, over-expression of vertebrate Olig2 partially rescues the walking defects of oli-deficient flies. Thus, our findings reveal a remarkably conserved role of Drosophila Oli and vertebrate family members in regulating motoneuron development, while the steps that require their function differ in detail. © 2012.

News Article | December 8, 2016

Researchers at the Institute of Molecular Biology (IMB) and Johannes Gutenberg University Mainz (JGU) have shown that a new way of regulating genes is vital for the activity of the nervous system. They found that this form of regulation, a chemical modification on RNA called m6A, is also important in influencing whether flies become male or female. This study clearly shows that RNA modifications play an important role. In their study, published in Nature, the scientists show that the m6A RNA modification occurs at high levels in the developing fly's nervous system and that it is important for this system to function. When they disrupted the molecular pathway that modifies the RNA, the flies behaved abnormally: they had problems folding their wings correctly, could not orientate themselves anymore, and moved more slowly than flies whose RNA modifications were normal. The effect on locomotion results from an impaired function of the brain. The researchers also show that m6A is important to fine-tune sex determination, i.e., whether a fly develops as male or female. Dr. Jean-Yves Roignant, a group leader at IMB and corresponding author on the study, says, "The discovery that RNA modifications are so abundant on messenger RNAs was not anticipated until a few years ago and to my view this is one of the most exciting discoveries in the field in the last 15 years. Our study now sheds light on what they do in living organisms. We show that the m6A modification plays an important role in the function of the nervous system and in sex determination in the fruit fly, Drosophila. As this modification is also enriched in the vertebrate nervous system, it is conceivable that it has similar roles in humans." In order for our bodies to function normally, it is important for genes to be turned on or off in the right cells at the right times. It is already well established that DNA modifications are important to regulate the activity of genes. These molecular marks on the DNA act as signals to the cell machinery that converts the information contained within a gene into a protein, and help determine how a particular gene is regulated. These signals can be added and removed, which changes whether genes are active or inactive. Many different modifications have also been identified on RNA, but what they do in vivo was not well understood. m6A is the most prevalent of these RNA modifications, and scientists have shown that it can be added and removed in an analogous way to DNA modifications. The present publication is the first comprehensive study investigating the role of all components involved in the biogenesis of the m6A RNA modification in a multicellular organism. Besides finding an important role for m6A in embryonic development, Dr. Jean-Yves Roignant and his team also identified a new component of the molecular machinery that regulates this RNA modification - Spenito. They next intend to investigate how this machinery works in more detail. Tina Lence, a PhD student in the Roignant lab at IMB and first author of the paper, says, "Now we have found that m6A is there and that it is important for neuronal functions, we want to understand more about its precise role. For example, is m6A important in all circumstances, or is it more involved in the fine-tuning of gene expression or in response to changes in the environment?" This emerging field of RNA modifications, also called epitranscriptomics, is likely to yield many more exciting findings in the future. Researchers involved in the study are based at IMB, Mainz University's Institute of Pharmacy and Biochemistry and the Institute of Zoology, and at the Kimmel Center for Biology and Medicine of the Skirball Institute in New York, USA.

Acehan D.,Structural Biology Program | Acehan D.,Skirball Institute | Malhotra A.,New York University | Xu Y.,New York University | And 6 more authors.
Biophysical Journal | Year: 2011

F1F0 ATP synthase forms dimers that tend to assemble into large supramolecular structures. We show that the presence of cardiolipin is critical for the degree of oligomerization and the degree of order in these ATP synthase assemblies. This conclusion was drawn from the statistical analysis of cryoelectron tomograms of cristae vesicles isolated from Drosophila flight-muscle mitochondria, which are very rich in ATP synthase. Our study included a wild-type control, a cardiolipin synthase mutant with nearly complete loss of cardiolipin, and a tafazzin mutant with reduced cardiolipin levels. In the wild-type, the highcurvature edge of crista vesicles was densely populated with ATP synthase molecules that were typically organized in one or two rows of dimers. In both mutants, the density of ATP synthase was reduced at the high-curvature zone despite unchanged expression levels. Compared to the wild-type, dimer rows were less extended in the mutants and there was more scatter in the orientation of dimers. These data suggest that cardiolipin promotes the ribbonlike assembly of ATP synthase dimers and thus affects lateral organization and morphology of the crista membrane. © 2011 by the Biophysical Society.

Darie C.C.,Skirball Institute | Darie C.C.,Clarkson University | Deinhardt K.,Skirball Institute | Deinhardt K.,New York University | And 6 more authors.
Proteomics | Year: 2011

Receptor tyrosine kinases (RTKs) are proteins that upon ligand stimulation undergo dimerization and autophosphorylation. Eph receptors (EphRs) are RTKs that are found in different cell types, from both tissues that are developing and from mature tissues, and play important roles in the development of the central nervous system and peripheral nervous system. EphRs also play roles in synapse formation, neural crest formation, angiogenesis and in remodeling the vascular system. Interaction of EphRs with their ephrin ligands lead to activation of signal transduction pathways and formation of many transient protein-protein interactions that ultimately leads to cytoskeletal remodeling. However, the sequence of events at the molecular level is not well understood. We used blue native PAGE and MS to analyze the transient protein-protein interactions that resulted from the stimulation of EphB2 receptors by their ephrinB1-Fc ligands. We analyzed the phosphotyrosine-containing protein complexes immunoprecipitated from the cell lysates of both unstimulated (-) and ephrinB1-Fc-stimulated (+) NG108 cells. Our experiments allowed us to identify many signaling proteins, either known to be part of EphB2 signaling or new for this pathway, which are involved in transient protein-protein interactions upon ephrinB1-Fc stimulation. These data led us to investigate the roles of proteins such as FAK, WAVEs and Nischarin in EphB2 signaling. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Hed A.E.,New York University | Khaitan A.,New York University | Kozhaya L.,New York University | Manel N.,New York University | And 7 more authors.
Journal of Infectious Diseases | Year: 2010

Background. Identification of the Th17 T cell subset as important mediators of host defense and pathology prompted us to determine their susceptibility to human immunodeficiency virus (HIV) infection. Methods and results. We found that a sizeable portion of Th17 cells express HIV coreceptor CCR5 and produce very low levels of CCR5 ligands macrophage inflammatory protein (MIP)-1α and MIP-1β. Accordingly, CCR5+ Th17 cells were efficiently infected with CCR5-tropic HIV and were depleted during viral replication in vitro. Remarkably, HIV-infected individuals receiving treatment had significantly reduced Th17 cell counts, compared with HIV-uninfected subjects, regardless of viral load or CD4 cell count, whereas treatment-naive subjects had normal levels. However, there was a preferential reduction in CCR5+ T cells that were also CCR6 positive, which is expressed on all Th17 cells, compared with CCR6-CCR5+ cells, in both treated and untreated HIV-infected subjects. This observation suggests preferential targeting of CCR6+CCR5+ Th17 cells by CCR5-tropic viruses in vivo. Th17 cell levels also inversely correlated with activated CD4+ T cells in HIV-infected individuals who are receiving treatment. Conclusions. Our findings suggest a complex perturbation of Th17 subsets during the course of HIV disease potentially through both direct viral infection and virus indirect mechanisms, such as immune activation. © 2010 by the Infectious Diseases Society of America. All rights reserved.

Zhang G.,Skirball Institute | Zhang G.,New York University | Neubert T.A.,Skirball Institute | Neubert T.A.,New York University
Journal of Proteome Research | Year: 2011

There are three quantitative phosphoproteomic strategies most commonly used to study receptor tyrosine kinase (RTK) signaling. These strategies quantify changes in: (1) all three forms of phosphosites (phosphoserine, phosphothreonine and phosphotyrosine) following enrichment of phosphopeptides by titanium dioxide or immobilized metal affinity chromatography; (2) phosphotyrosine sites following anti- phosphotyrosine antibody enrichment of phosphotyrosine peptides; or (3) phosphotyrosine proteins and their binding partners following anti-phosphotyrosine protein immunoprecipitation. However, it is not clear from literature which strategy is more effective. In this study, we assessed the utility of these three phosphoproteomic strategies in RTK signaling studies by using EphB receptor signaling as an example. We used all three strategies with stable isotope labeling with amino acids in cell culture (SILAC) to compare changes in phosphoproteomes upon EphB receptor activation. We used bioinformatic analysis to compare results from the three analyses. Our results show that the three strategies provide complementary information about RTK pathways. © 2011 American Chemical Society.

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