scholarly journals Combining Mass Spectrometry and Peptide Arrays to Profile the Specificities of Histone Deacetylases

ChemBioChem ◽  
2009 ◽  
Vol 10 (13) ◽  
pp. 2159-2161 ◽  
Author(s):  
Zachary A. Gurard-Levin ◽  
Joohoon Kim ◽  
Milan Mrksich
Keyword(s):  
Mass Spectrometry ◽  
Histone Deacetylases ◽  
Peptide Arrays

scholarly journals Combining SAMDI Mass Spectrometry and Peptide Arrays to Profile Phosphatase Activities

2018 ◽  
pp. 389-403 ◽  
Author(s):  
Lindsey C. Szymczak ◽  
Che-Fan Huang ◽  
Eric J. Berns ◽  
Milan Mrksich
Keyword(s):  
Mass Spectrometry ◽  
Peptide Arrays ◽  
Phosphatase Activities

scholarly journals Multiple Histone Deacetylases and the CREB-binding Protein Regulate Pre-mRNA 3′-End Processing

2006 ◽  
Vol 282 (7) ◽  
pp. 4470-4478 ◽  
Author(s):  
Tadahiro Shimazu ◽  
Sueharu Horinouchi ◽  
Minoru Yoshida
Keyword(s):  
Mass Spectrometry ◽  
Complex Formation ◽  
Nuclear Localization ◽  
Histone Deacetylases ◽  
Trichostatin A ◽  
Specific Inhibitor ◽  
Creb Binding Protein ◽  
Processing Machinery ◽  
Importin Α

Trichostatin A (TSA), a specific inhibitor of histone deacetylases (HDACs), induces acetylation of various non-histone proteins such as p53 and α-tubulin. We purified several acetylated proteins by the affinity to an anti-acetylated lysine (AcLys) antibody from cells treated with TSA and identified them by mass spectrometry. Here we report on acetylation of CFIm25, a component of mammalian cleavage factor Im (CF Im), and poly(A) polymerase (PAP), a polyadenylating enzyme for the pre-mRNA 3′-end. The residues acetylated in these proteins were mapped onto the regions required for interaction with each other. Whereas CBP acetylated these proteins, HDAC1, HDAC3, HDAC10, SIRT1, and SIRT2 were involved in in vivo deacetylation. Acetylation of the CFIm25 occurred depending on the cleavage factor complex formation. Importantly, the interaction between PAP and CF Im complex was decreased by acetylation. We also demonstrated that acetylation of PAP inhibited the nuclear localization of PAP by inhibiting the binding to the importin α/β complex. These results suggest that CBP and HDACs regulate the 3′-end processing machinery and modulate the localization of PAP through the acetylation and deacetylation cycle.

scholarly journals Profiling Deacetylase Activities in Cell Lysates with Peptide Arrays and SAMDI Mass Spectrometry

2013 ◽  
Vol 85 (22) ◽  
pp. 10635-10642 ◽  
Author(s):  
Hsin-Yu Kuo ◽  
Teresa A. DeLuca ◽  
William M. Miller ◽  
Milan Mrksich
Keyword(s):  
Mass Spectrometry ◽  
Peptide Arrays ◽  
Cell Lysates

SELDI Bone Marrow Profiling of B-Lineage Childhood Lymphoblastic Leukemia: Identity of Several Differential Markers.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 1090-1090
Author(s):  
Sioyong Lim ◽  
Liqun Huang ◽  
Shirley Kow Yin Kham ◽  
Fook Tim Chew ◽  
Allen Eng Juh Yeoh
Keyword(s):  
Mass Spectrometry ◽  
Bone Marrow ◽  
Chromosomal Aberrations ◽  
Histone Deacetylases ◽  
Lymphoblastic Leukemia ◽  
Regulation Of Gene Expression ◽  
Chromosomal Translocations ◽  
Histone H4 ◽  
Histone Hyperacetylation ◽  
B Lineage

Abstract Background: Childhood Acute Lymphoblastic Leukemia (cALL) is the most common form of pediatric cancer, accounting for 30% of newly diagnosed cases every year. cALL is a heterogeneous disease and the underlying pathways of leukemogenesis have yet to be unraveled. It is known that 30% of cALL is caused by genetic lesions due to chromosomal translocations or abnormalities. SELDI (Surface Enhanced Laser Desorption/Ionization-Time of Flight-Mass Spectrometry) is a promising proteomic platform for the discovery of useful markers to study diagnosis and prognosis of cancers. The protein signatures generated have clinical significance in many cancers. We analyzed 49 B-lineage cALL samples and compared to 4 non-leukemia controls (Immune Thrombocytopenia Purpura, ITP) using this technology. Materials and Methods: Total cell lysates from 49 cALL bone marrow aspirates were obtained from patients with chromosomal aberrations [hyperdiploidy (n=12), TEL-AML1 (n=13), BCR-ABL (n=5), E2A-PBX1 (n=3) and others (n=1)] and patients without any known/detected chromosomal aberrations (n=15). The MS (mass spectrometry) data were collected, filtered through stringent parameters and was analyzed using Ciphergen® Biomarker Wizard and further confirmed via gel electrophoresis. The significantly differential proteins were then excised, trypsin-digested and further analyzed by TOF-TOF MS to obtain the identities of these markers. Results: A total of 10 significantly differential protein markers were observed ranging from 6 kDa to 80 kDa. Identities of 6 of the 10 markers have been obtained. Peptide mass fingerprinting of these markers showed significant presence of histone H4 but absence of myeloperoxidase (MPO), lactoferrin (LF), S100A8 calcium binding protein (MRP-8), defensin alpha 1 and neutrophil granule peptide (HP1) in cALL patients. Discussion: Unsurprisingly, MPO, LF and HP1 are of myeloid origin and therefore not found in cALL. However, histone modification and regulation has been shown to be involved in the development of leukemia since they regulate transcription by chromatin modulation. Histone hyperacetylation and deacetylation are associated with many cancers and hyperacetylated histone H4 was reported in the early stages of squamous cell carcinoma. Histone hyperacetylation might then suggest a disregulation of apoptosis that might be one of the channels of leukemogenesis. It is also postulated that chromatin regulation and control might assist in understanding chromosomal translocations so commonly observed in cALL, since regulation of gene expression through histone acetylation and deacetylation appears to be disrupted by a number of such fusion proteins. The TEL-AML1 fusion protein has been shown to recruit histone deacetylases thereby inhibiting transcription and altering self-renewal capacity and differentiation capacity of hematopoetic stem cells. Similar activity has also been shown in myeloid leukemia and inhibitors of histone deacetylases (anti-tumoral effect) are now being used as drugs in clinical trials. The preliminary results from SELDI are very encouraging and might offer us some insights into leukemogenesis.

Abstract 443: Class I Histone Deacetylases Mediate Cardiac I/R Injury and Modify the Mitochondrial Acetylome

2016 ◽  
Vol 119 (suppl_1) ◽  
Author(s):  
Daniel J Herr ◽  
Sverre E Aune ◽  
Jennifer R Bethard ◽  
Lauren E Ball ◽  
Donald R Menick
Keyword(s):  
Mass Spectrometry ◽  
Reperfusion Injury ◽  
Histone Deacetylases ◽  
Cardiac Tissue ◽  
Ischemia Reperfusion ◽  
Left Ventricular ◽  
Class I ◽  
Mass Spectrometry Analysis ◽  
Hdac Inhibition ◽  
Class I Hdacs

Although rapid reperfusion of ischemic tissue is the treatment of choice for myocardial infarction, a significant amount of damage occurs as a result of reperfusion itself. The role of epigenetic enzymes in modulating this damage has become an area of interest in basic cardiac research. Previously, we have shown that pharmacological inhibition of the class I histone deacetylases (HDACs) with MS-275 (entinostat) preserves left-ventricular (LV) function and substantially reduces the area of infarcted tissue in isolated rat hearts subjected to ischemia-reperfusion (IR) injury. Interestingly, we have also observed that class I HDAC inhibition during 60 minutes of reperfusion alone is sufficient to protect cardiac tissue viability following I/R injury. Therefore, we hypothesized that class I HDACs mediate reperfusion injury by modulating acetylation of non-canonical pathways. To examine this, hearts from male Sprague-Dawley rats were subjected to I/R injury +/- class I HDAC inhibition during reperfusion. We then performed mass spectrometry to analyze the changes in the acetylome between sham and I/R groups with and without class I HDAC inhibition. Unexpectedly, mass spectrometry analysis revealed significant changes in the acetylation state of multiple mitochondrial enzymes. Further biochemical studies show that class I HDACs localize to the mitochondrial fraction of cardiac tissue homogenates and may modulate mitochondrial acetylation by direct or indirect mechanisms. This study emphasizes the importance of exploring class I HDAC inhibitors for protection against ischemia-reperfusion injury.

How SIMS microscopy can be used in medicine

1992 ◽  
Vol 50 (2) ◽  
pp. 1602-1603
Author(s):  
Philippe Fragu
Keyword(s):  
Mass Spectrometry ◽  
Biomedical Applications ◽  
Secondary Ion Mass Spectrometry ◽  
Chemical Elements ◽  
Biological Applications ◽  
The Past ◽  
Potential Source ◽  
Secondary Ion ◽  
Chemical Integrity ◽  
Scientific Endeavour

The identification, localization and quantification of intracellular chemical elements is an area of scientific endeavour which has not ceased to develop over the past 30 years. Secondary Ion Mass Spectrometry (SIMS) microscopy is widely used for elemental localization problems in geochemistry, metallurgy and electronics. Although the first commercial instruments were available in 1968, biological applications have been gradual as investigators have systematically examined the potential source of artefacts inherent in the method and sought to develop strategies for the analysis of soft biological material with a lateral resolution equivalent to that of the light microscope. In 1992, the prospects offered by this technique are even more encouraging as prototypes of new ion probes appear capable of achieving the ultimate goal, namely the quantitative analysis of micron and submicron regions. The purpose of this review is to underline the requirements for biomedical applications of SIMS microscopy.Sample preparation methodology should preserve both the structural and the chemical integrity of the tissue.

Imaging of Al-Li-Cu alloys with a Scanning Ion Microprobe

1990 ◽  
Vol 48 (2) ◽  
pp. 314-315
Author(s):  
K.K. Soni ◽  
D.B. Williams ◽  
J.M. Chabala ◽  
R. Levi-Setti ◽  
D.E. Newbury
Keyword(s):  
Mass Spectrometry ◽  
Secondary Ion Mass Spectrometry ◽  
Equilibrium Phase ◽  
Icosahedral Symmetry ◽  
Ion Microprobe ◽  
X Ray ◽  
Cu Alloys ◽  
Two Phases ◽  
The University ◽  
Secondary Ion

In contrast to the inability of x-ray microanalysis to detect Li, secondary ion mass spectrometry (SIMS) generates a very strong Li+ signal. The latter’s potential was recently exploited by Williams et al. in the study of binary Al-Li alloys. The present study of Al-Li-Cu was done using the high resolution scanning ion microprobe (SIM) at the University of Chicago (UC). The UC SIM employs a 40 keV, ∼70 nm diameter Ga+ probe extracted from a liquid Ga source, which is scanned over areas smaller than 160×160 μm2 using a 512×512 raster. During this experiment, the sample was held at 2 × 10-8 torr.In the Al-Li-Cu system, two phases of major importance are T1 and T2, with nominal compositions of Al2LiCu and Al6Li3Cu respectively. In commercial alloys, T1 develops a plate-like structure with a thickness <∼2 nm and is therefore inaccessible to conventional microanalytical techniques. T2 is the equilibrium phase with apparent icosahedral symmetry and its presence is undesirable in industrial alloys.

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