Mass spectrometry based method to increase throughput for kinome analyses using ATP probes.

Protein kinases play critical roles in many biological and pathological processes, making them important targets for therapeutic drugs. Here, we desired to increase the throughput for kinome-wide profiling. A new workflow coupling ActivX ATP probe (AAP) affinity reagents with isotopic labeling to quantify the relative levels and modification states of kinases in cell lysates is described. We compared the new workflow to a classical proteomics approach in which fractionation was used to identify low-abundance kinases. We find that AAPs enriched approximately 90 kinases in a single analysis involving six cell lines or states in a single run, an 8-fold improvement in throughput relative to the classical approach. In general, AAPs cross-linked to both the active and inactive states of kinases but performing phosphopeptide enrichment made it possible to measure the phospho sites of regulatory residues lying in the kinase activation loops, providing information on activation state. When we compared the kinome across the six cell lines, representative of different breast cancer clinical subtypes, we observed that many kinases, particularly receptor tyrosine kinases, varied widely in abundance, perhaps explaining the differential sensitivities to kinase inhibitor drugs. The improved kinome profiling methods described here represent an effective means to perform systematic analysis of kinases involved in cell signaling and oncogenic transformation and for analyzing the effect of different inhibitory drugs.

Synaptic Activity Causes Minute-scale Changes in BAF Complex Composition and Function.

Genes encoding subunits of the SWI/SNF or BAF ATP-dependent chromatin remodeling complex are among the most enriched for deleterious de novo mutations in intellectual disabilities and autism spectrum disorder, but the causative molecular pathways are not fully known 1,2 . Synaptic activity in neurons is critical for learning and memory and proper neural development 3 . Neural activity prompts calcium influx and transcription within minutes, facilitated in the nucleus by various transcription factors (TFs) and chromatin modifiers 4 . While BAF is required for activity-dependent developmental processes such as dendritic outgrowth 5-7 , the immediate molecular consequences of neural activity on BAF complexes and their functions are unknown. Here we mapped minute-scale biochemical consequences of neural activity, modeled by membrane depolarization of embryonic mouse primary cortical neurons, on BAF complexes. We used acute chemical perturbations of BAF ATPase activity and kinase signaling to define the activity-dependent effects on BAF complexes and activity-dependent BAF functions. Our studies found that BAF complexes change in subunit composition and are selectively phosphorylated within 10 minutes of depolarization. Increased levels of the core PBAF subunit Baf200/ Arid2 , uniquely containing an RFX-like DNA-binding domain, are concurrent with ATPase-dependent opening of chromatin at RFX/X-box motifs. Changes in BAF composition and phosphorylation lead to the regulation of chromatin accessibility for critical neurogenesis TFs. These biochemical effects are a convergent phenomenon downstream of multiple growth factor signaling pathways in mouse neurons and fibroblasts suggesting that BAF integrates signaling information from the membrane. In support of such a membrane-to-nucleus signaling cascade, we also identified a BAF-interacting kinase, Dclk2, whose inhibition attenuates BAF phosphorylation selectively. Our findings support a direct role of BAF complexes in responding to synaptic activity to regulate TF binding and transcription.

Correlation between protein and mRNA abundance in yeast.

We have determined the relationship between mRNA and protein expression levels for selected genes expressed in the yeast Saccharomyces cerevisiae growing at mid-log phase. The proteins contained in total yeast cell lysate were separated by high-resolution two-dimensional (2D) gel electrophoresis. Over 150 protein spots were excised and identified by capillary liquid chromatography-tandem mass spectrometry (LC-MS/MS). Protein spots were quantified by metabolic labeling and scintillation counting. Corresponding mRNA levels were calculated from serial analysis of gene expression (SAGE) frequency tables (V. E. Velculescu, L. Zhang, W. Zhou, J. Vogelstein, M. A. Basrai, D. E. Bassett, Jr., P. Hieter, B. Vogelstein, and K. W. Kinzler, Cell 88:243-251, 1997). We found that the correlation between mRNA and protein levels was insufficient to predict protein expression levels from quantitative mRNA data. Indeed, for some genes, while the mRNA levels were of the same value the protein levels varied by more than 20-fold. Conversely, invariant steady-state levels of certain proteins were observed with respective mRNA transcript levels that varied by as much as 30-fold. Another interesting observation is that codon bias is not a predictor of either protein or mRNA levels. Our results clearly delineate the technical boundaries of current approaches for quantitative analysis of protein expression and reveal that simple deduction from mRNA transcript analysis is insufficient.

Association of two novel proteins, TbMP52 and TbMP48, with the Trypanosoma brucei RNA editing complex.

RNA editing in kinetoplastid mitochondria inserts and deletes uridylates at multiple sites in pre-mRNAs as directed by guide RNAs. This occurs by a series of steps that are catalyzed by endoribonuclease, 3'-terminal uridylyl transferase, 3'-exouridylylase, and RNA ligase activities. A multiprotein complex that contains these activities and catalyzes deletion editing in vitro was enriched from Trypanosoma brucei mitochondria by sequential ion-exchange and gel filtration chromatography, followed by glycerol gradient sedimentation. The complex size is approximately 1,600 kDa, and the purified fraction contains 20 major polypeptides. A monoclonal antibody that was generated against the enriched complex reacts with an approximately 49-kDa protein and specifically immunoprecipitates in vitro deletion RNA editing activity. The protein recognized by the antibody was identified by mass spectrometry, and the corresponding gene, designated TbMP52, was cloned. Recombinant TbMP52 reacts with the monoclonal antibody. Another novel protein, TbMP48, which is similar to TbMP52, and its gene were also identified in the enriched complex. These results suggest that TbMP52 and TbMP48 are components of the RNA editing complex.

Four related proteins of the Trypanosoma brucei RNA editing complex.

RNA editing in kinetoplastid mitochondria occurs by a series of enzymatic steps that is catalyzed by a macromolecular complex. Four novel proteins and their corresponding genes were identified by mass spectrometric analysis of purified editing complexes from Trypanosoma brucei. These four proteins, TbMP81, TbMP63, TbMP42, and TbMP18, contain conserved sequences to various degrees. All four proteins have sequence similarity in the C terminus; TbMP18 has considerable sequence similarity to the C-terminal region of TbMP42, and TbMP81, TbMP63, and TbMP42 contain zinc finger motif(s). Monoclonal antibodies that are specific for TbMP63 and TbMP42 immunoprecipitate in vitro RNA editing activities. The proteins are present in the immunoprecipitates and sediment at 20S along with the in vitro editing, and RNA editing ligases TbMP52 and TbMP48. Recombinant TbMP63 and TbMP52 coimmunoprecipitate. These results indicate that these four proteins are components of the RNA editing complex and that TbMP63 and TbMP52 can interact.

Quantitative analysis of complex protein mixtures using isotope-coded affinity tags.

We describe an approach for the accurate quantification and concurrent sequence identification of the individual proteins within complex mixtures. The method is based on a class of new chemical reagents termed isotope-coded affinity tags (ICATs) and tandem mass spectrometry. Using this strategy, we compared protein expression in the yeast Saccharomyces cerevisiae, using either ethanol or galactose as a carbon source. The measured differences in protein expression correlated with known yeast metabolic function under glucose-repressed conditions. The method is redundant if multiple cysteinyl residues are present, and the relative quantification is highly accurate because it is based on stable isotope dilution techniques. The ICAT approach should provide a widely applicable means to compare quantitatively global protein expression in cells and tissues.

Identification of translationally controlled tumor protein in promotion of DNA homologous recombination repair in cancer cells by affinity proteomics.

Translationally controlled tumor protein(TCTP) has been implicated in the regulation of apoptosis, DNA repair and drug resistance. However, the underlying molecular mechanisms are poorly defined. To better understand the molecular mechanisms underlying TCTP involved in cellular processes, we performed an affinity purification-based proteomic profiling to identify proteins interacting with TCTP in human cervical cancer HeLa cells. We found that a group of proteins involved in DNA repair are enriched in the potential TCTP interactome. Silencing TCTP by short hairpin RNA in breast carcinoma MCF-7 cells leads to the declined repair efficiency for DNA double-strand breaks on the GFP-Pem1 reporter gene by homologous recombination, the persistent activation and the prolonged retention of γH2AX and Rad51 foci following ionizing radiation. Reciprocal immunoprecipitations indicated that TCTP forms complexes with Rad51 in vivo, and the stability maintenance of Rad51 requires TCTP in MCF-7 cells under normal cell culture conditions. Moreover, inactivation of TCTP by sertraline treatment enhances UVC irradiation-induced apoptosis in MCF-7 cells, and causes sensitization to DNA-damaging drug etoposide and DNA repair inhibitor olaparib. Thus, we have identified an important role of TCTP in promoting DNA double-stand break repair via facilitating DNA homologous recombination processes and highlighted the great potential of TCTP as a drug target to enhance conventional chemotherapy for cancer patients with high levels of TCTP expression.

Mass spectrometry and proteomics.

Proteomics is the systematic analysis of the proteins expressed by a cell or tissue, and mass spectrometry is its essential analytical tool. In the past two years, incremental advances in standard proteome technology have increased the speed of protein identification with higher levels of automation and sensitivity. Furthermore, new approaches have provided landmark advances in determining functionally relevant properties of proteins, including their quantity and involvement within protein complexes.

Measuring gene expression by quantitative proteome analysis.

Proteome analysis is most commonly accomplished by the combination of two-dimensional gel electrophoresis for protein separation, visualization, and quantification and mass spectrometry for protein identification. Over the past year, exceptional progress has been made towards developing a new technology base for the precise quantification and identification of proteins in complex mixtures, that is, quantitative proteomics.

Mechanisms for tolerance to methamphetamine effects.

Pretreatment with incremental increases in methamphetamine causes tolerance to serotonergic effects caused by challenging with multiple high doses of methamphetamine (11.5 mg/kg/dose). The brain concentration of methamphetamine following this challenge was reduced in tolerant rats, yet the plasma concentration was elevated. The tolerance was selective for methamphetamine and did not occur when cocaine was used in the pretreatment. The possibility that tolerance affects the distribution of methamphetamine in or out of the brain through an active transport system was examined by combining the transport-blocking drug, probenecid, with a low dose of methamphetamine. The presence of probenecid enhanced methamphetamine-induced serotonergic changes in the hippocampus. The brain concentration of methamphetamine increased in the presence of probenecid; however, a similar increase in the plasma methamphetamine concentration suggests that the effects of probenecid on methamphetamine distribution are not related to the redistribution of methamphetamine that occurs in tolerant animals.

Toward a high-throughput approach to quantitative proteomic analysis: expression-dependent protein identification by mass spectrometry.

The isotope-coded affinity tag (ICAT) technology enables the concurrent identification and comparative quantitative analysis of proteins present in biological samples such as cell and tissue extracts and biological fluids by mass spectrometry. The initial implementation of this technology was based on microcapillary chromatography coupled on-line with electrospray ionization tandem mass spectrometry. This implementation lacked the ability to select proteins for identification based on their relative abundance and therefore to focus on differentially expressed proteins. In order to improve the sample throughput of this technology, we have developed a two-step approach that is focused on those proteins for which the abundance changes between samples: First, a new software program for the automated quantification of ICAT reagent labeled peptides analyzed by microcapillary electrospray ionization time-of-flight mass spectrometry determines those peptides that differ in their abundance and second, these peptides are identified by tandem mass spectrometry using an electrospray quadrupole time-of flight mass spectrometer and sequence database searching. Results from the application of this approach to the analysis of differentially expressed proteins secreted from nontumorigenic human prostate epithelial cells and metastatic cancerous human prostate epithelial cells are shown.

Quantitative proteome analysis: methods and applications.

With the completion of a rapidly increasing number of complete genomic sequences, much attention is currently focused on how the information contained in sequence databases might be interpreted in terms of the structure, function, and control of biological systems. Quantitative proteome analysis, the global analysis of protein expression, has been proposed as a method to study steady-state gene expression and perturbation-induced changes. Here, we discuss the rationale for quantitative proteome analysis, highlight the limitations in the current standard technology, and introduce a new experimental approach to quantitative proteome analysis.

Proteomics: the move to mixtures.

Proteomics can be defined as the systematic analysis of proteins for their identity, quantity and function. In contrast to a cell's static genome, the proteome is both complex and dynamic. Proteome analysis is most commonly accomplished by the combination of two-dimensional gel electrophoresis (2DE) and mass spectrometry (MS). However, this technique is under scrutiny because of a failure to detect low-abundance proteins from the analysis of whole cell lysates. Alternative approaches integrate a diversity of separation technologies and make use of the tremendous peptide separation and sequencing power provided by MS/MS. When liquid chromatography is combined with tandem mass spectrometry (LC/MS/MS) and applied to the direct analysis of mixtures, many of the limitations of 2DE for proteome analysis can be overcome. This tutorial addresses current approaches to identify and characterize large numbers of proteins and measure dynamic changes in protein expression directly from complex protein mixtures (total cell lysates).

Blockade of tachykinin NK1 receptors by CP-96345 enhances dopamine release and the striatal dopamine effects of methamphetamine in rats.

The nonpeptide, tachykinin NK1 receptor antagonist, CP-96345, permits the study of the physiological role of extrapyramidal substance P systems. Using microdialysis, we observed that locally applied CP-96345 (200 nM) caused a significant increase in dopamine release in the striatum as well as substantially enhancing striatal dopamine release caused by a low dose of methamphetamine (0.5 mg/kg s.c.). In addition, multiple systemic administrations of CP-96345 almost doubled the dopamine-mediated responses of the striatal neurotensin and dynorphin systems to high doses of methamphetamine (10 mg/kg/dose s.c.). Our findings suggest that the physiological role of substance P released in the striatum is to decrease the activity of the nigrostriatal dopamine pathway.

A comparison of phenobarbital and codeine incorporation into pigmented and nonpigmented rat hair.

Drugs and endogenous compounds circulating in the blood may ultimately become incorporated into a growing hair shaft. Hair analysis for drugs of abuse is a growing field in the area of forensic and clinical toxicology. However, the underlying principles that govern drug incorporation into hair are not known. In this study, we examined the incorporation of a weak acid, phenobarbital, and a weak base, codeine, into Sprague-Dawley (SD) rat hair. Codeine or phenobarbital was administered to male SD rats at 40 mg/kg/day for 5 days by intraperitoneal (ip) injection. Hair was collected from the back 14 days after beginning the 5-day dosing protocol and analyzed by gas chromatography/mass spectrometry (GC/MS) for codeine and phenobarbital. The time-courses of phenobarbital and codeine in plasma were also obtained after a single ip injection (40 mg/kg). Concentrations of codeine and phenobarbital in SD hair samples were 0.98 +/- 0.10 and 17.01 +/- 1.40 ng/mg hair. respectively. The areas under the curve (AUC) of plasma concentration versus time for codeine and phenobarbital were 1.58 and 414.50 micrograms h/microL, respectively. Notwithstanding the greater phenobarbital concentrations in hair, when plasma concentrations were considered, codeine was apparently incorporated to a 15-fold greater extent than phenobarbital. Because hair pigmentation may be important in drug incorporation, the incorporation of these two drugs was also studied in Long-Evans (LE; produces both black and white hair on the same animal) rats after 40 mg/kg/day of ip drug administration for 5 days. Hair was collected at the same time as the previous experiment. Concentrations of codeine in hair were 44-times greater in pigmented than nonpigmented hair from the same animals. In contrast, hair concentrations of phenobarbital were identical in both pigmented and nonpigmented hair. These data suggest that hair pigmentation greatly affects weak base incorporation but not weak acid incorporation into hair. Because hair concentrations of phenobarbital are not affected by pigmentation, phenobarbital may be an ideal drug to separate out factors other than pigmentation involved in incorporation of drugs into hair.

Incorporation of drugs for the treatment of substance abuse into pigmented and nonpigmented hair.

Hair analysis for drugs may be useful for the long-term monitoring of recidivism and treatment compliance. L-alpha-Acetylmethadol, buprenorphine, and methadone are drugs that are used for the treatment of substance abuse. The purpose of this study was to study the relationship between dose, plasma concentration, hair concentration, and hair pigmentation for these compounds and their major metabolites in an animal model. Male Long-Evans rats received either L-alpha-acetylmethadol (1 and 3 mg/kg; n = 6), buprenorphine (1 and 3 mg/kg; n = 5), or methadone (4 and 8 mg/kg; n = 5) by intraperitoneal injection daily for 5 days. Fourteen days after beginning drug administration, newly grown hair was collected and analyzed for either L-alpha-acetylmethadol and two metabolites (L-alpha-acetyl-N-normethadol and L-alpha-acetyl-N,N-dinormethadol), methadone and two metabolites (D,L-2-ethyl-1,5-dimethyl-3,3-diphenylpyrrolinium and D,L-2-ethyl-5-methyl-3,3-diphenyl-1-pyrroline), or buprenorphine and one metabolite (norbuprenorphine). The plasma time course (AUC) for each compound was also determined after a single administration of each drug at the specified doses. There was an approximate dose-dependent increase in measured hair concentration of each parent drug in pigmented hair. The concentrations of L-alpha-acetylmethadol, methadone, and buprenorphine in nonpigmented hair were significantly less than that measured in pigmented hair at either the high or low dose. The metabolites L-alpha-acetyl-N-normethadol and D,L-2-ethyl-1,5dimethyl-3,3-diphenylpyrrolinium were detected at lower concentrations than their respective parent compounds (L-alpha-acetylmethadol or methadone) in pigmented hair. However, the L-alpha-acetyl-N,N-dinormethadol metabolite concentrations in pigmented hair were significantly greater than those of the parent drug after either the low or the high L-alpha-acetylmethadol dose. These data demonstrate that L-alpha-acetylmethadol, methadone, buprenorphine, and metabolites are distributed into hair in a dose-related manner with a preference for pigmented hair.

Distribution of codeine and morphine into rat hair after long-term daily dosing with codeine.

Hair analysis for drugs of abuse provides a possible long-term measure of drug use not possible with urinalysis. Many drugs and their metabolites have been detected in hair; however, the factors influencing the incorporation of chemicals into hair are poorly understood. An animal model for chemical uptake into hair utilizing controlled drug administration was developed to ascertain if increasing doses of codeine are reflected in the concentrations of codeine and its metabolites found in hair. Male Sprague-Dawley rats were administered codeine at 5, 10, or 20 mg/kg (intraperitoneally; n = 6) daily for 21 days. At various times during and after the dosing protocol, approximately 50 mg of hair was shaved from a different area of the animals' backs and analyzed for codeine and morphine concentrations by ion-trap gas chromatography-mass spectrometry. Peak hair codeine concentrations for the 5-, 10-, and 20-mg/kg groups occurred 20 days after beginning the dosing protocol and were 0.57 +/- 0.13, 0.80 +/- 0.10, and 1.95 +/- 0.35 ng/mg hair, respectively. Morphine peak concentrations occurred at the same time and were 1.08 +/- 0.28, 1.21 +/- 0.09, and 2.10 +/- 0.26 ng/mg hair for the 5-, 10-, and 20-mg/kg groups, respectively. Long-term dosing in the rat resulted in similar or greater hair concentrations of morphine (metabolite) than codeine. The plasma pharmacokinetics of codeine and morphine were also obtained after a single, intraperitoneal codeine administration of 20 mg/kg. An experiment involving washing the rat hair with methanol or phosphate buffer (pH 9.0) did not reduce the concentration of codeine or morphine measured in hair as compared with nonwashed control hair. Data obtained in this study indicate that after controlled administration the incorporation of codeine and its metabolite, morphine, into rat hair occurs in a distinct dose-proportional manner.

Quantitative analysis of methadone and two major metabolites in hair by positive chemical ionization ion trap mass spectrometry.

A sensitive and specific method for the quantitative determination of D,L-methadone (MD) and its metabolites, D,L-2-ethyl-1,5-dimethyl-3, 3-diphenylpyrrolinium (EDDP) and D,L-2-ethyl-5-methyl-3, 3-diphenyl-1-pyrroline (EMDP), in hair has been developed. Deuterated internal standards of MD, EMDP, and EDDP were added to 20-mg hair samples and digested overnight at room temperature with 1N sodium hydroxide. Calibration standards containing known concentrations of MD, EMDP, and EDDP dried onto human hair were also digested. Digest solutions were extracted by a liquid-liquid extraction procedure and analyzed with splitless injection on a Finnigan MagnumTM ion trap mass spectrometer. Chromatographic separation was achieved with helium carrier gas on a DB-5MS-30M-0.25-micron capillary column. Positive chemicaionization was used with acetone as the reagent gas. The assay was linear from 0.5 ng/mg (MD and EDDP) or 1.0 ng/mg (EMDP) to 50.0 ng/mg of human hair with correlation coefficients greater than 0.99. Intra-assay and interassay coefficients of variation were determined to be less than 20% for all three analytes at 2.0 and 10.0 ng/mg of hair. Recovery was estimated to be greater than 70% (MD and EDDP) and 53% (EMDP) at 2.0 and 10.0 ng/mg of hair. The method has been applied to the analysis of both human and rat hair. Male long-Evans rats were shaved prior to dosing to obtain their drug-free hair. Animals were then administered 15 mg/kg MD by intraperitoneal injection daily for five days. Fourteen days after the first dose, hair was collected and analyzed for MD, EMDP, and EDDP. The mean plus standard error of the mean (SEM; n = 3) concentrations of MD and EDDP in pigmented hair were 31.1 ng/mg +/- 9.6 ng/mg and 8.6 +/- 2.4 ng/mg, respectively. EMDP was detected in the hair of one of three rats. In another experiment, hair was collected from two human subjects who had received long-term methadone therapy for the treatment of heroin addiction. Subject A received 60 mg of methadone daily for at least six months; subject B received 80 mg of methadone daily for at least six months. The hair concentrations of MD were 10.1 ng/mg and 21.0 ng/mg for Subjects A and B, respectively. The hair concentrations of EDDP were 0.5 ng/mg and 2.6 ng/mg for Subjects A and B, respectively. EMDP was not detected in the hair of these two subjects. This method is being used to evaluate the incorporation of MD, EMDP, and EDDP in human and rat hair in dose-response studies.