TMTpro-18plex: The Expanded and Complete Set of TMTpro Reagents for Sample Multiplexing

The development of the TMTpro-16plex series expanded the breadth of commercial isobaric tagging reagents by nearly 50% over classic TMT-11plex. In addition to the described 16plex reagents, the proline-based TMTpro molecule can accommodate two additional combinations of heavy carbon and nitrogen isotopes. Here, we introduce the final two labeling reagents, TMTpro-134C and TMTpro-135N, which permit the simultaneous global protein profiling of 18 samples with essentially no missing values. For example, six conditions with three biological replicates can now be perfectly accommodated. We showcase the 18plex reagent set by profiling the proteome and phosphoproteome of a pair of isogenic mammary epithelial cell lines under three conditions in triplicate. We compare the depth and quantitative performance of this data set with a TMTpro-16plex experiment in which two samples were omitted. Our analysis revealed similar numbers of quantified peptides and proteins, with high quantitative correlation. We interrogated further the TMTpro-18plex data set by highlighting changes in protein abundance profiles under different conditions in the isogenic cell lines. We conclude that TMTpro-18plex further expands the sample multiplexing landscape, allowing for complex and innovative experimental designs.

Super Heavy TMTpro Labeling Reagent: An Alternative and Higher-Charge-State-Amenable Stable-Isotope-Labeled TMTpro Variant

Stable isotope labeling is a leading strategy for mass-spectrometry-based peptide quantification. Whereas TMTpro isobaric tagging can quantify up to 16 multiplexed samples in a single experiment, nonisobaric, yet chromatographically indistinguishable, variants of TMTpro reagents can be used in conjunction with the isobaric tag series for various peptide-targeting applications. Here we test the performance of two nonisobaric TMTpro variants, a stable-isotope-free TMTproZero tag and a nearly fully isotope-labeled "super-heavy" variant, shTMTpro, in a targeted assay for peptides of charge state 4+. We label each peptide with TMTproZero or Super Heavy TMTpro reagents and separately spike each peptide into a TMTpro16-labeled background (equal amount of peptide across all 16 channels). We observe that the expected 1:1 reporter ion ratio is distorted when a TMTproZero-labeled peptide is used; however, we note no such interference when shTMTpro substitutes the TMTproZero tag. Our data suggest that using the Super Heavy TMTpro reagent is an improvement over the TMTproZero reagent for the accurate quantification of high-charge-state peptides for trigger-based multiplexed assays.

Adaptation of the adult Functional Mobility Assessment (FMA) into a FMA-Family Centred (FMA-FC) paediatric version

AIM

The aims of this study were to adapt an adult wheeled mobility outcome measure, the Functional Mobility Assessment, for use with children (FMA-Family Centred) and establish the new measure's content validity, test-retest reliability, and internal consistency.

BACKGROUND

Although several tools exist to measure a child's ability to operate and move a wheeled mobility device, none focus on the ability of the wheeled mobility device to support children and their families as they perform daily activities.

METHODS

After adapting the FMA items with examples relevant to children aged 3-21, parent/caregiver and therapist stakeholder groups recommended adaptations relevant for families with children who cannot respond for themselves.

RESULTS

Six of the initial FMA items were retained with child-appropriate examples, and 4 new items were developed.

CONCLUSION

The content validity of the FMA-Family Centred was strongly supported, and internal consistency and test-retest reliability met accepted psychometric standards.

Breast tumors educate the proteome of stromal tissue in an individualized but coordinated manner

Cancer forms specialized microenvironmental niches that promote local invasion and colonization. Engrafted patient-derived xenografts (PDXs) locally invade and colonize naïve stroma in mice while enabling unambiguous molecular discrimination of human proteins in the tumor from mouse proteins in the microenvironment. To characterize how patient breast tumors form a niche and educate naïve stroma, subcutaneous breast cancer PDXs were globally profiled by species-specific quantitative proteomics. Regulation of PDX stromal proteins by breast tumors was extensive, with 35% of the stromal proteome altered by tumors consistently across different animals and passages. Differentially regulated proteins in the stroma clustered into six signatures, which included both known and previously unappreciated contributors to tumor invasion and colonization. Stromal proteomes were coordinately regulated; however, the sets of proteins altered by each tumor were highly distinct. Integrated analysis of tumor and stromal proteins, a comparison made possible in these xenograft models, indicated that the known hallmarks of cancer contribute pleiotropically to establishing and maintaining the microenvironmental niche of the tumor. Education of the stroma by the tumor is therefore an intrinsic property of breast tumors that is highly individualized, yet proceeds by consistent, nonrandom, and defined tumor-promoting molecular alterations.

Quantitative LC-MS/MS Glycomic Analysis of Biological Samples Using AminoxyTMT

Protein glycosylation plays an important role in various biological processes, such as modification of protein function, regulation of protein-protein interactions, and control of turnover rates of proteins. Moreover, glycans have been considered as potential biomarkers for many mammalian diseases and development of aberrant glycosylation profiles is an important indicator of the pathology of a disease or cancer. Hence, quantitation is an important aspect of a comprehensive glycomics study. Although numerous MS-based quantitation strategies have been developed in the past several decades, some issues affecting sensitivity and accuracy of quantitation still exist, and the development of more effective quantitation strategies is still required. Aminoxy tandem mass tag (aminoxyTMT) reagents are recently commercialized isobaric tags which enable relative quantitation of up to six different glycan samples simultaneously. In this study, liquid chromatography and mass spectrometry conditions have been optimized to achieve reliable LC-MS/MS quantitative glycomic analysis using aminoxyTMT reagents. Samples were resuspended in 0.2 M sodium chloride solution to promote the formation of sodium adduct precursor ions, which leads to higher MS/MS reporter ion yields. This method was first evaluated with glycans from model glycoproteins and pooled human blood serum samples. The observed variation of reporter ion ratios was generally less than 10% relative to the theoretical ratio. Even for the highly complex minor N-glycans, the variation was still below 15%. This strategy was further applied to the glycomic profiling of N-glycans released from blood serum samples of patients with different esophageal diseases. Our results demonstrate the benefits of utilizing aminoxyTMT reagents for reliable quantitation of biological glycomic samples.

Meaningful Learning Moments on a Family Medicine Clerkship: When Students Are Patient Centered

BACKGROUND AND OBJECTIVES

Reflection after patient encounters is an important aspect of clinical learning. After our medical school instituted a reflection paper assignment for all clerkships, we wanted to learn about the types of encounters that students found meaningful on a family medicine clerkship and how they impacted students' learning.

METHODS

Family and Community Medicine Clerkship students completed a reflection paper after the clerkship, based on guidelines that were used for all clerkship reflection papers at our medical school. Two reviewers independently organized student responses into themes and then jointly prioritized common themes and negotiated any initial differences into other themes.

RESULTS

A total of 272 reflection papers describing an actual learning moment in patient care were submitted during the study period of January 2011--December 2012. In describing actions performed, students most frequently wrote about aspects of patient-centered care such as listening to the patient, carefully assessing the patient's condition, or giving a detailed explanation to the patient. In describing effects of those actions, students wrote about what they learned about the patient-physician interaction, the trust that patients demonstrated in them, the approval they gained from their preceptors, and the benefits they saw from their actions.

CONCLUSIONS

An important contribution of a family medicine clerkship is the opportunity for students to further their skills in patient-centered care and realize the outcomes of providing that type of care.

Dual Labeling Biotin Switch Assay to Reduce Bias Derived From Different Cysteine Subpopulations: A Method to Maximize S-Nitrosylation Detection

RATIONALE

S-nitrosylation (SNO), an oxidative post-translational modification of cysteine residues, responds to changes in the cardiac redox-environment. Classic biotin-switch assay and its derivatives are the most common methods used for detecting SNO. In this approach, the labile SNO group is selectively replaced with a single stable tag. To date, a variety of thiol-reactive tags have been introduced. However, these methods have not produced a consistent data set, which suggests an incomplete capture by a single tag and potentially the presence of different cysteine subpopulations.

OBJECTIVE

To investigate potential labeling bias in the existing methods with a single tag to detect SNO, explore if there are distinct cysteine subpopulations, and then, develop a strategy to maximize the coverage of SNO proteome.

METHODS AND RESULTS

We obtained SNO-modified cysteine data sets for wild-type and S-nitrosoglutathione reductase knockout mouse hearts (S-nitrosoglutathione reductase is a negative regulator of S-nitrosoglutathione production) and nitric oxide-induced human embryonic kidney cell using 2 labeling reagents: the cysteine-reactive pyridyldithiol and iodoacetyl based tandem mass tags. Comparison revealed that <30% of the SNO-modified residues were detected by both tags, whereas the remaining SNO sites were only labeled by 1 reagent. Characterization of the 2 distinct subpopulations of SNO residues indicated that pyridyldithiol reagent preferentially labels cysteine residues that are more basic and hydrophobic. On the basis of this observation, we proposed a parallel dual-labeling strategy followed by an optimized proteomics workflow. This enabled the profiling of 493 SNO sites in S-nitrosoglutathione reductase knockout hearts.

CONCLUSIONS

Using a protocol comprising 2 tags for dual-labeling maximizes overall detection of SNO by reducing the previously unrecognized labeling bias derived from different cysteine subpopulations.

Capillary Electrophoresis-Electrospray Ionization-Mass Spectrometry for Quantitative Analysis of Glycans Labeled with Multiplex Carbonyl-Reactive Tandem Mass Tags

Recently developed carbonyl-reactive aminoxy tandem mass tag (aminoxyTMT) reagents enable multiplexed characterization and quantitative comparison of structurally complex glycans between different biological samples. Compared to some previously reported isotopic labeling strategies for glycans, the use of the aminoxyTMT method features a simple labeling procedure, excellent labeling efficiency, and reduced spectral complexity at the MS(1) level. Presence of the tertiary amine functionality in the reporter region of the aminoxyTMT labels leads to increased ionization efficiency of the labeled glycans thus improving electrospray ionization (ESI)-mass spectrometry (MS) detection sensitivity. The use of the labeling reagent also makes electrophoretic separation of the labeled neutral and acidic glycans feasible. In this work, we characterized the ESI and collision induced dissociation (CID) behavior of the aminoxyTMT-labeled neutral and sialylated glycans. For the high-mannose N-glycans and small sialylated oligosaccharides, CID fragmentation of [M + Na + H](2+) provides the most informative MS(2) spectra for both quantitative and qualitative analysis. For complex N-glycans, MS(3) of the protonated Y1(H) ion can be used for relative quantification without interference from the HexNAc fragments. Online capillary electrophoresis (CE)-ESI-MS/MS analyses of multiplexed aminoxyTMT-labeled human milk oligosaccharides (HMOs) and different types of N-glycans released from glycoprotein standards were demonstrated. Improved resolution and quantification accuracy of the labeled HMO isomers was achieved by coupling CE with traveling wave ion mobility (TWIM)-CID-MS/MS. N-Glycans released from human serum protein digests were labeled with six-plex aminoxyTMT and subjected to CE-ESI-MS/pseudo-MS(3) analysis, which demonstrated the potential utility of this glycan relative quantification platform for more complex biological samples.

Automating mass spectrometry-based quantitative glycomics using aminoxy tandem mass tag reagents with SimGlycan

Protein glycosylation is a common post-translational modification, which serves critical roles in the biological processes of organisms. Monitoring of changes in the abundance and structure of glycans may be necessary to explain the correlations between protein glycosylation and various diseases. Hence, the growing importance of glycoproteomics necessitates in-depth qualitative and quantitative studies of glycans. One of the emerging trends in glycomics research is the innovation related to accurate mass spectrometry based quantitative analysis of glycans. Recently, we have introduced aminoxyTMT reagents, which enable efficient relative quantitation of carbohydrates, improved glycan ionization efficiency and increased analytical throughput. These reagents can be used for quantitative analysis of N-glycans by direct infusion or liquid chromatography (LC)-coupled to electrospray ionization mass spectrometry (ESI-MS). However, unlike in proteomics, one of the major challenges left unaddressed is the lack of informatics tools to automate the qualitative and quantitative analysis of generated data. This analysis typically includes identification/quantitation of glycans using MS/MS data and differential analysis across biological samples. We have developed software modules to streamline such protocols for quantitative analysis of aminoxyTMT labeled-glycans derived from complex mixtures. This article is part of a Special Issue entitled: Proteomics in India.

Abstract 1608: Profiling c-Met and EGFR kinase inhibitor resistance pathways in non-small lung cancer cells

Tyrosine kinase inhibitors (TKIs) against c-MET and EGFR have positive therapeutic effects in a subset of Non-Small Cell Lung Cancer (NSCLC) patients; however, their clinical efficacies are limited due to the development of TKI resistance. To determine mechanisms of TKI resistance, two NSCLC model cell lines H2170 and H358 were made resistant to the c-Met/EGFR TKIs SU11274, erlotinib or a combination of both by exposing the cells to progressively increasing concentrations of inhibitor. Initial characterization of these cell lines using phospho-specific antibodies showed that phospho-c-Met was found to be downregulated 4- and 1.5- fold in SU11274-resistant (SR) H2170 and SR H358 cells, respectively. Phospho-EGFR was found to be constitutively autophosphorylated (upregulated 19-fold) in erlotinib-resistant (ER) H2170 cells, but downregulated 6-fold in ER H358 cells. Interestingly, c-Met/EGFR downstream signaling proteins p-mTOR, p-p70S6K and p-ERK were found to be 2-4-fold upregulated, 2-fold upregulated and 2-5-fold upregulated, respectively, in ER H2170 and H358 cells. Phospho-p70S6K was also found to be upregulated 20-fold in SR H2170 cells. These results indicate that alternative signaling pathways may confer TKI resistance in these cell lines. To identify which signaling pathways may be responsible for TKI resistance, H358 parental and resistant cell lines were analyzed by mass spectrometry (MS). Differences in protein expression in cell lines treated with and without EGF and/or erlotinib were measured using higher multiplexing Thermo Scientific™ Tandem Mass Tag™ (TMT™) reagents. More than 1500 protein groups were identified and quantified using a Thermo Scientific™ Orbitrap™ Fusion™ platform with HCD-MS2 and MS3 fragmentation methods. Protein expression in ER H358 cells showed a marked increase in expression of DNA replication proteins, transcription factors, apoptosis inhibitors and some Ras-associated signal transduction pathways. To further investigate the mechanism of TKI resistance, phospho-peptide enrichment was also used in combination with TMT quantitation to profile changes in protein phosphorylation state. Overall, the combination of phospho-peptide enrichment coupled with higher multiplexing TMT and high resolution MS analysis enabled deeper global profiling of TKI resistance signaling pathways compared to previous studies without enrichment.

Citation Format: Ryan D. Bomgarden, Ryan Jacobs, Jason Fong, David Moravec, Gregory M. Botting, Michael Blank, Rosa I. Viner, John C. Rogers, Neelu Puri. Profiling c-Met and EGFR kinase inhibitor resistance pathways in non-small lung cancer cells. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1608. doi:10.1158/1538-7445.AM2014-1608

Proteomic quantification and site-mapping of S-nitrosylated proteins using isobaric iodoTMT reagents

S-Nitrosylation is a redox-based protein post-translational modification in response to nitric oxide signaling and is involved in a wide range of biological processes. Detection and quantification of protein S-nitrosylation have been challenging tasks due to instability and low abundance of the modification. Many studies have used mass spectrometry (MS)-based methods with different thiol-reactive reagents to label and identify proteins with S-nitrosylated cysteine (SNO-Cys). In this study, we developed a novel iodoTMT switch assay (ISA) using an isobaric set of thiol-reactive iodoTMTsixplex reagents to specifically detect and quantify protein S-nitrosylation. Irreversible labeling of SNO-Cys with the iodoTMTsixplex reagents enables immune-affinity detection of S-nitrosylated proteins, enrichment of iodoTMT-labeled peptides by anti-TMT resin, and importantly, unambiguous modification site-mapping and multiplex quantification by liquid chromatography–tandem MS. Additionally, we significantly improved anti-TMT peptide enrichment efficiency by competitive elution. Using ISA, we identified a set of SNO-Cys sites responding to lipopolysaccharide (LPS) stimulation in murine BV-2 microglial cells and revealed effects of S-allyl cysteine from garlic on LPS-induced protein S-nitrosylation in antioxidative signaling and mitochondrial metabolic pathways. ISA proved to be an effective proteomic approach for quantitative analysis of S-nitrosylation in complex samples and will facilitate the elucidation of molecular mechanisms of nitrosative stress in disease.

Mass spectrometry-based quantitative proteomics for dissecting multiplexed redox cysteine modifications in nitric oxide-protected cardiomyocyte under hypoxia

AIMS

Distinctive states of redox-dependent cysteine (Cys) modifications are known to regulate signaling homeostasis under various pathophysiological conditions, including myocardial injury or protection in response to ischemic stress. Recent evidence further implicates a dynamic interplay among these modified forms following changes in cellular redox environment. However, a precise delineation of multiplexed Cys modifications in a cellular context remains technically challenging. To this end, we have now developed a mass spectrometry (MS)-based quantitative approach using a set of novel iodoacetyl-based Cys-reactive isobaric tags (irreversible isobaric iodoacetyl Cys-reactive tandem mass tag [iodoTMT]) endowed with unique irreversible Cys-reactivities.

RESULTS

We have established a sequential iodoTMT-switch procedure coupled with efficient immunoenrichment and advanced shotgun liquid chromatography-MS/MS analysis. This workflow allows us to differentially quantify the multiple redox-modified forms of a Cys site in the original cellular context. In one single analysis, we have identified over 260 Cys sites showing quantitative differences in multiplexed redox modifications from the total lysates of H9c2 cardiomyocytes experiencing hypoxia in the absence and presence of S-nitrosoglutathione (GSNO), indicative of a distinct pattern of individual susceptibility to S-nitrosylation or S-glutathionylation. Among those most significantly affected are proteins functionally implicated in hypoxic damage from which we showed that GSNO would protect.

INNOVATION

We demonstrate for the first time how quantitative analysis of various Cys-redox modifications occurring in biological samples can be performed precisely and simultaneously at proteomic levels.

CONCLUSION

We have not only developed a new approach to map global Cys-redoxomic regulation in vivo, but also provided new evidences implicating Cys-redox modifications of key molecules in NO-mediated ischemic cardioprotection.

Increasing the multiplexing capacity of TMTs using reporter ion isotopologues with isobaric masses

Quantitative mass spectrometry methods offer near-comprehensive proteome coverage; however, these methods still suffer with regards to sample throughput. Multiplex quantitation via isobaric chemical tags (e.g., TMT and iTRAQ) provides an avenue for mass spectrometry-based proteome quantitation experiments to move away from simple binary comparisons and toward greater parallelization. Herein, we demonstrate a straightforward method for immediately expanding the throughput of the TMT isobaric reagents from 6-plex to 8-plex. This method is based upon our ability to resolve the isotopic shift that results from substituting a (15)N for a (13)C. In an accommodation to the preferred fragmentation pathways of ETD, the TMT-127 and -129 reagents were recently modified such that a (13)C was exchanged for a (15)N. As a result of this substitution, the new TMT reporter ions are 6.32 mDa lighter. Even though the mass difference between these reporter ion isotopologues is incredibly small, modern high-resolution and mass accuracy analyzers can resolve these ions. On the basis of our ability to resolve and accurately measure the relative intensity of these isobaric reporter ions, we demonstrate that we are able to quantify across eight samples simultaneously by combining the (13)C- and (15)N-containing reporter ions. Considering the structure of the TMT reporter ion, we believe this work serves as a blueprint for expanding the multiplexing capacity of the TMT reagents to at least 10-plex and possibly up to 18-plex.

Abstract LB-218: Profiling kinase inhibition in cancer cell extracts using active-site probes and targeted high resolution, accurate mass spectrometry

Protein kinases are enzymes that play key roles in signal transduction pathways which regulate cellular processes including growth, division, differentiation and metabolism. Kinase inhibitors are essential tools used by researchers to understand kinase function and are also therapeutic compounds used in treating cancer and other diseases. Active-site probes are one technology that can be used to determine the specificity and potency of kinase inhibitors. Desthiobiotin-ATP and -ADP are two nucleotide derivatives that have been shown to selectively label kinase active sites. Using these probes to enrich kinase active-site peptides, we identified over 150 kinases from K562 chronic myelogenous leukemia and A549 lung carcinoma cell extracts using high resolution, accurate mass (HR/AM) spectrometry. We also assessed specificity of kinase inhibitors including staurosporine and wortmannin by determining the relative quantitation of kinase active-site peptides after drug treatment. In addition, we validated kinase inhibitor targets using a parallel Western blot workflow. Overall, kinase inhibition measured using high resolution, accurate mass spectrometry had strong correlation with Western blot data and enabled global profiling of kinase inhibitor target and off-targets.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-218. doi:10.1158/1538-7445.AM2011-LB-218

Plant RMR proteins: unique vacuolar sorting receptors that couple ligand sorting with membrane internalization

In receptor-mediated sorting of soluble protein ligands in the endomembrane system of eukaryotic cells, three completely different receptor proteins for mammalian (mannose 6-phosphate receptor), yeast (Vps10p) and plant cells (vacuolar sorting receptor; VSR) have in common the features of pH-dependent ligand binding and receptor recycling. In striking contrast, the plant receptor homology-transmembrane-RING-H2 (RMR) proteins serve as sorting receptors to a separate type of vacuole, the protein storage vacuole, but do not recycle, and their trafficking pathway results in their internalization into the destination vacuole. Even though plant RMR proteins share high sequence similarity with the best-characterized mammalian PA-TM-RING family proteins, these two families of proteins appear to play distinctly different roles in plant and animal cells. Thus, this minireview focuses on this unique sorting mechanism and traffic of RMR proteins via dense vesicles in various plant cell types.

Medical student exposure to components of the patient-centered medical home during required ambulatory clerkship rotations: implications for education

PURPOSE

To determine the extent to which third-year medical students are exposed to elements of the patient-centered medical home (PCMH) during required family medicine (FM) clerkships and how this exposure varies among a sample of medical schools.

METHOD

In 2008, the authors conducted a cross-sectional survey of 104 ambulatory teaching practices that host required third-year FM clerkship students from nine U.S. medical schools. Descriptive statistics characterized learning settings and the status of PCMH features, and generalized linear mixed models examined variation among medical schools (as the 104 clinics were nested within nine medical schools).

RESULTS

Participating schools captured data on 104 eligible clerkship sites (44%). These practices were primarily community-based, single-specialty clinics (n = 48; 46%), and more than half (n = 55; 53%) were part of integrated health systems. Electronic health records (EHRs) were in place in 60 (58%), and no significant difference existed in EHR use according to medical school, despite up to a 10-fold variation from school to school in other PCMH features. Among sites with EHRs, 8 (14%) did not allow access to medical students. Preceptor attitudes about how practice transformation and new information technology are affecting the quality of medical education differ widely from site to site.

CONCLUSIONS

Primary care transformation toward the PCMH is already well under way in a national sample of FM teaching sites, and this transformation is having important effects on medical student education.

Ideals, activities, dissonance, and processing: a conceptual model to guide educators' efforts to stimulate student reflection

PURPOSE

Medical schools are increasingly incorporating opportunities for reflection into their curricula. However, little is known about the cognitive and/or emotional processes that occur when learners participate in activities designed to promote reflection. The purpose of this study was to identify and elucidate those processes.

METHOD

In 2008, the authors analyzed qualitative data from focus groups that were originally conducted to evaluate an educational activity designed to promote reflection. These data afforded the opportunity to explore the processes of reflection in detail. Transcripts (94 pages, single-spaced) from four focus groups were analyzed using a narrative framework. The authors spent approximately 40 hours in group and 240 hours in individual coding activities.

RESULTS

The authors developed a conceptual model of five major elements in students' reflective processes: the educational activity, the presence or absence of cognitive or emotional dissonance, and two methods of processing dissonance (preservation or reconciliation). The model also incorporates the relationship between the student's internal ideal of what a doctor is or does and the student's perception of the teacher's ideal of what a doctor is or does. The model further identifies points at which educators may be able to influence the processes of reflection and the development of professional ideals.

CONCLUSIONS

Students' cognitive and emotional processes have important effects on the success of educational activities intended to stimulate reflection. Although additional research is needed, this model-which incorporates ideals, activities, dissonance, and processing-can guide educators as they plan and implement such activities.

Quantitative phosphoproteomic analysis of the STAT3/IL-6/HIF1alpha signaling network: an initial study in GSC11 glioblastoma stem cells

Initiation and maintenance of several cancers including glioblastoma (GBM) may be driven by a small subset of cells called cancer stem cells (CSCs). CSCs may provide a repository of cells in tumor cell populations that are refractory to chemotherapeutic agents developed for the treatment of tumors. STAT3 is a key transcription factor associated with regulation of multiple stem cell types. Recently, a novel autocrine loop (IL-6/STAT3/HIF1alpha) has been observed in multiple tumor types (pancreatic, prostate, lung, and colon). The objective of this study was to probe perturbations of this loop in a glioblastoma cancer stem cell line (GSC11) derived from a human tumor by use of a JAK2/STAT3 phosphorylation inhibitor (WP1193), IL-6 stimulation, and hypoxia. A quantitative phosphoproteomic approach that employed phosphoprotein enrichment, chemical tagging with isobaric tags, phosphopeptide enrichment, and tandem mass spectrometry in a high-resolution instrument was applied. A total of 3414 proteins were identified in this study. A rapid Western blotting technique (<1 h) was used to confirm alterations in key protein expression and phosphorylation levels observed in the mass spectrometric experiments. About 10% of the phosphoproteins were linked to the IL-6 pathway, and the majority of remaining proteins could be assigned to other interlinked networks. By multiple comparisons between the sample conditions, we observed expected changes and gained novel insights into the contribution of each factor to the IL6/STAT3/HIF1alpha autocrine loop and the CSC response to perturbations by hypoxia, inhibition of STAT3 phosphorylation, and IL-6 stimulation.

Reducing agent-mediated precipitation of high-abundance plasma proteins

Depletion of high-abundance proteins is regarded as a critical sample preparation step for most plasma proteomic analyses and profiling strategies. This report describes a process that rapidly and reproducibly precipitates high-abundance disulfide-rich proteins, including albumin and transferrin, from serum and plasma. A low volume of concentrated reducing agent, viz. dithiothreitol (DTT) or tris(2-carboxyethyl)phosphine (TCEP), was added directly to plasma followed by a brief incubation at ambient temperature. Removal of the precipitate via centrifugation and identification of the protein content revealed an albumin-enriched pellet. Direct analysis of the supernatant by MALDI-TOF-MS afforded peptidome and small protein profiles with enhanced features and minimal ionization of full-length albumin. The reproducible and quantitative nature of the method has been demonstrated by monitoring the plasma levels of an antiangiogenic protein biologic, rKringle5 (rK5). The 10.5-kDa analyte was only reliably detected in plasma after treatment with reducing agent, ionizing linearly from 150 to 1200 fmol (on-target) with a mean CV of 7%. This method distinguishes itself from immunoaffinity resin-based approaches since it can be scaled to large milliliter quantities and it is compatible with plasma from all species tested.

Discovery, identification, and characterization of candidate pharmacodynamic markers of methionine aminopeptidase-2 inhibition

The catalytic activity of methionine aminopeptidase-2 (MetAP2) has been pharmacologically linked to cell growth, angiogenesis, and tumor progression, making this an attractive target for cancer therapy. An assay for monitoring specific protein changes in response to MetAP2 inhibition, allowing pharmacokinetic (PK)/pharmacodynamic (PD) models to be established, could dramatically improve clinical decision-making. Candidate MetAP2-specific protein substrates were discovered from undigested cell culture-derived proteomes by MALDI-/SELDI-MS profiling and a biochemical method using (35)S-Met labeled protein lysates. Substrates were identified either as intact proteins by FT-ICR-MS or applying in-gel protease digestions followed by LC-MS/MS. The combination of these approaches led to the discovery of novel MetAP2-specific substrates including thioredoxin-1 (Trx-1), SH3 binding glutamic acid rich-like protein (SH3BGRL), and eukaryotic elongation factor-2 (eEF2). These studies also confirmed glyceraldehye 3-phosphate dehydrogenase (GAPDH) and cyclophillin A (CypA) as MetAP2 substrates. Additional data in support of these proteins as MetAP2-specific substrates were provided by in vitro MetAP1/MetAP2 enzyme assays with the corresponding N-terminal derived peptides and 1D/2D Western analyses of cellular and tissue lysates. FT-ICR-MS characterization of all intact species of the 18 kDa substrate, CypA, enabled a SELDI-MS cell-based assay to be developed for correlating N-terminal processing and inhibition of proliferation. The MetAP2-specific protein substrates discovered in this study have diverse properties that should facilitate the development of reagents for testing in preclinical and clinical environments.

Exploring the learning curve in medical education: using self-assessment as a measure of learning

BACKGROUND

Learning is a complex process that follows predictable patterns. The authors explored whether students' self-assessment of competencies could be used as a measure of learning within medical school.

METHOD

Medical students (all grade levels) rated their achievement of competencies at the beginning and end of an academic year. Repeated-measures ANOVA and [eta]2 were used to determine differences.

RESULTS

Five hundred thirty-three students participated (response rate = 79.3%). Self-assessment ratings between four grade levels were significant (P < .001, [eta]2 = 0.33), with the steepest difference between MS2 and MS3; professionalism ratings remained relatively stable. The largest percent increase within an academic year occurred between MS1 and MS2, with little increase within MS3 and MS4.

CONCLUSIONS

Medical students' self-assessment ratings of competencies indicated differences between grade levels and during an academic year, following a sigmoidal curve. These results have implications for medical education and indicate the need to develop longitudinal measures to track changes in learning.

Localization of vacuolar transport receptors and cargo proteins in the Golgi apparatus of developing Arabidopsis embryos

Using immunogold electron microscopy, we have investigated the relative distribution of two types of vacuolar sorting receptors (VSR) and two different types of lumenal cargo proteins, which are potential ligands for these receptors in the secretory pathway of developing Arabidopsis embryos. Interestingly, both cargo proteins are deposited in the protein storage vacuole, which is the only vacuole present during the bent-cotyledon stage of embryo development. Cruciferin and aleurain do not share the same pattern of distribution in the Golgi apparatus. Cruciferin is mainly detected in the cis and medial cisternae, especially at the rims where storage proteins aggregate into dense vesicles (DVs). Aleurain is found throughout the Golgi stack, particularly in the trans cisternae and trans Golgi network where clathrin-coated vesicles (CCVs) are formed. Nevertheless, aleurain was detected in both DV and CCV. VSR-At1, a VSR that recognizes N-terminal vacuolar sorting determinants (VSDs) of the NPIR type, localizes mainly to the trans Golgi and is hardly detectable in DV. Receptor homology-transmembrane-RING H2 domain (RMR), a VSR that recognizes C-terminal VSDs, has a distribution that is very similar to that of cruciferin and is found in DV. Our results do not support a role for VSR-At1 in storage protein sorting, instead RMR proteins because of their distribution similar to that of cruciferin in the Golgi apparatus and their presence in DV are more likely candidates. Aleurain, which has an NPIR motif and seems to be primarily sorted via VSR-At1 into CCV, also possesses putative hydrophobic sorting determinants at its C-terminus that could allow the additional incorporation of this protein into DV.

Cross-sectional comparison of electronic and paper medical records on medication counseling in primary care clinics: a Southern Primary-Care Urban Research Network (SPUR-Net) study

INTRODUCTION

This study compared the frequency of oral counseling and written information by primary care physicians at paper medical record (PMR) clinics and electronic medical record (EMR) clinics, and assessed relationships between medication counseling and medication outcomes (knowledge, questions, reported adherence and side effects, and medication fill).

METHODS

A cross-sectional study with two convenience samples of English-speaking adult patients receiving > or =1 prescription at the primary care index visit was conducted in two PMR clinics, with 184 (48% response) patients seen by one of 22 physicians, and in two EMR clinics, with 249 (37% response) patients seen by one of 25 physicians. Data were from medical record reviews of the index visit and 2-week post-visit telephone interviews.

RESULTS

Three mutually exclusive counseling categories were evaluated. Patients received 1,095 prescriptions, 61% with oral counseling for indications, 21% with oral counseling for indications and side effects, and 12% with written information plus oral ("multi-mode") counseling. General linear mixed models found 1) less multi-mode counseling in PMR clinics (2%) than EMR clinics (20%); 2) PMR and EMR clinics were similar in oral counseling for indications and side effects; and 3) PMR clinics provided more oral counseling only for indications (69%) than EMR (53%) clinics. The impact of receiving oral or written counseling on patients' reports of having questions about their medications was inconclusive. Not receiving oral counseling for indications was associated with more questions, but not receiving written information was associated with fewer questions. Filling a prescription was lower when no oral counseling for indications and side effects was reported, but the absence of written information was associated with more prescriptions fills.

CONCLUSIONS

Physicians' use of EMR to print medication information did not seem to compromise their oral counseling for medication indications and side effects. This feature of the EMR was underutilized by physicians; however, future studies addressing patient recall and evaluating the quality and content of medication counseling are needed.

Fatty acid amide hydrolase inhibitors display broad selectivity and inhibit multiple carboxylesterases as off-targets

Fatty acid amide hydrolase (FAAH) is the primary regulator of several bioactive lipid amides including anandamide. Inhibitors of FAAH are potentially useful for the treatment of pain, anxiety, depression, and other nervous system disorders. However, FAAH inhibitors must display selectivity for this enzyme relative to the numerous other serine hydrolases present in the human proteome in order to be therapeutically acceptable. Here we employed activity-based protein profiling (ABPP) to assess the selectivity of FAAH inhibitors in multiple rat and human tissues. We discovered that some inhibitors, including carbamate compounds SA-47 and SA-72, and AM404 are exceptionally selective while others, like URB597, BMS-1, OL-135, and LY2077855 are less selective, displaying multiple off-targets. Since proteins around 60kDa constitute the major off-targets for URB597 and several other FAAH inhibitors with different chemical structures, we employed the multi-dimensional protein identification technology (MudPIT) approach to analyze their identities. We identified multiple carboxylesterase isozymes as bona fide off-targets of FAAH inhibitors. Consistently, enzymatic assay confirmed inhibition of carboxylesterase activities in rat liver by FAAH inhibitors. Since carboxylesterases hydrolyze a variety of ester-containing drugs and prodrugs, we speculate that certain FAAH inhibitors, by inhibiting carboxylesterases, might have drug-drug interactions with other medicines if developed as therapeutic agents.

A role for caleosin in degradation of oil-body storage lipid during seed germination

Caleosin is a Ca(2+)-binding oil-body surface protein. To assess its role in the degradation of oil-bodies, two independent insertion mutants lacking caleosin were studied. Both mutants demonstrated significant delay of breakdown of the 20:1 storage lipid at 48 and 60 h of germination. Additionally, although germination rates for seeds were not affected by the mutations, mutant seedlings grew more slowly than wild type when measured at 48 h of germination, a defect that was corrected with continued growth for 72 and 96 h in the light. After 48 h of germination, wild-type central vacuoles had smooth contours and demonstrated internalization of oil bodies and of membrane containing alpha- and delta-tonoplast intrinsic proteins (TIPs), markers for protein storage vacuoles. In contrast, mutant central vacuoles had distorted limiting membranes displaying domains with clumps of the two TIPs, and they contained fewer oil bodies. Thus, during germination caleosin plays a role in the degradation of storage lipid in oil bodies. Its role involves both the normal modification of storage vacuole membrane and the interaction of oil bodies with vacuoles. The results indicate that interaction of oil bodies with vacuoles is one mechanism that contributes to the degradation of storage lipid.

Association of Catsper1 or -2 with Cav3.3 Leads to Suppression of T-type Calcium Channel Activity

Sperm-specific CatSper1 and CatSper2 proteins are critical to sperm-hyperactivated motility and male fertility. Although architecturally resembling voltage-gated ion channels, neither CatSper1 nor CatSper2 alone forms functional ion channels in heterologous expression systems, which may be related to the absence of yet unidentified accessory subunits. Here we isolated CatSper1- and CatSper2-associated protein(s) from human sperm and analyzed their identities by a multidimensional protein identification technology approach. We identified the T-type voltage-gated calcium channel Ca(v)3.3 as binding to both CatSper1 and CatSper2. The specificity of their interactions was verified by co-immunoprecipitation in transfected mammalian cells. Electrophysiological studies revealed that the co-expression of CatSper1 or CatSper2 specifically inhibited the amplitude of Ca(v)3.3-evoked T-type calcium current without altering other biophysical properties of Ca(v)3.3. Immunostaining studies revealed co-localization of CatSper1 and Ca(v)3.3 on the principal piece of human sperm tail. Furthermore, fluorescence resonance energy transfer analysis revealed close proximity and physical association of these two proteins on the sperm tail. These studies demonstrate that CatSper1 and CatSper2 can associate with and modulate the function of the Ca(v)3.3 channel, which might be important in the regulation of sperm function.

Selective membrane protein internalization accompanies movement from the endoplasmic reticulum to the protein storage vacuole pathway in Arabidopsis

In plant cells, certain membrane proteins move by unknown mechanisms directly from the endoplasmic reticulum (ER) to prevacuolar or vacuole-like organelles where membrane is internalized to form a dense, lattice-like structure. Here, we identify a sequence motif, PIEPPPHH, in the cytoplasmic tail of a membrane protein that directs the protein from the ER to vacuoles where it is internalized. A type II membrane protein in Arabidopsis thaliana, (At)SRC2 (for Soybean Gene Regulated by Cold-2), binds specifically to PIEPPPHH and moves from the ER to the same vacuoles where it is internalized. Not all proteins that move in this pathway are internalized because another Arabidopsis type II membrane protein, (At)VAP (for Vesicle-Associated Protein), localizes to the same organelles but remains exposed on the limiting membrane. The identification of (At)SRC2 and its preference for interaction with a targeting motif specific for the ER-to-vacuole pathway may provide tools for future dissection of mechanisms involved in this unique trafficking system.

A unique family of proteins associated with internalized membranes in protein storage vacuoles of the Brassicaceae

The protein storage vacuole (PSV) is a specialized organelle in plant seeds that accumulates storage proteins and phytate during seed development. In many plant species, such as tomato and tobacco, the PSV contains two types of microscopically visible intra-organellar inclusions: a large crystalline lattice of membranes and proteins, the crystalloid, and one or a few large phytate crystals, the globoids. In seeds of the family Brassicaceae, the PSVs lack visible crystalloids and have many small globoids dispersed throughout. We biochemically fractionated PSVs from Brassica napus and defined a crystalloid-like fraction that contained integral membrane protein markers found in crystalloids of other plants. Protein analyses identified a previously undescribed family of proteins, the Brassicaceae PSV-embedded proteins (BPEPs), associated with 'crystalloid' and globoid fractions. The defining characteristics of the BPEPs are an N-terminal signal peptide and tandem MATH domains, which may mediate protein-protein interactions. Database analyses indicated that the BPEPs are unique to Brassicaceae. Immunofluorescence studies using anti-BPEP antibodies and antibodies to other biochemical markers to label B. napus and Arabidopsis thaliana seed sections localized the BPEPs to structures within the PSVs, whose appearance was consistent with a diffuse network of internalized membranes and globoids. These results demonstrate that Brassicaceae PSVs contain internalized membranes, and raise the possibility that BPEPs modify these internal membrane structures to yield a PSV morphology different from that of tomato or tobacco.

Purification, crystallization and preliminary crystallographic studies of the ligand-binding domain of a plant vacuolar sorting receptor

Vacuolar sorting receptor (VSR) proteins bind soluble protein ligands in a sequence-specific manner and target them to the lytic vacuole in plant cells. A VSR from Arabidopsis thaliana, AtBP80b, has been successfully purified after heterologous expression in Drosophila S2 cells. The AtBP80b protein (560 amino acids) was crystallized by the hanging-drop method with a PEG 400-based precipitant. Preliminary X-ray diffraction studies of an AtBP80b crystal showed that it belongs to the cubic space group P2(1)3 (or P4(2)32) and has unit-cell parameters a = b = c = 145.9 A. Crystals of the VSR diffract beyond 2.5 A resolution.

Observations on the teaching and learning occurring in offices of community-based family and community medicine clerkship preceptors

BACKGROUND AND OBJECTIVES

Previous reports have defined the time that community preceptors spend teaching students, but much remains to be learned about the process and content of office-based teaching. Our objective was to understand better the teaching process and content by documenting how often preceptors used the microskills described in the Five-step "Microskills" Model of Clinical Teaching and how often they discussed tasks described in the Task-oriented Processes in Care (TOPIC) teaching model when working with their students.

METHODS

Using a checklist combining these two models, two independent observers documented the teaching and learning that occurred between 12 preceptors and their students.

RESULTS

Inter-rater concordance was 96.2%. Preceptors frequently used two of the teaching microskills, "probe for supporting evidence" and "teach general rules." Preceptors and students frequently discussed many information-processing and management tasks in the TOPIC model.

CONCLUSIONS

Despite the lack of training in using either model, preceptors frequently used some teaching microskills and discussed many TOPIC model tasks. This finding supports both models as relevant teaching models but further observational study of preceptors trained in using both models is needed. For the TOPIC model, preceptor development may help preceptors to more explicitly refer to TOPIC tasks when teaching clinical content to students.

Alpha tonoplast intrinsic protein is specifically associated with vacuole membrane involved in an autophagic process

Autophagy in plant cells is induced by nutrient starvation. Initially, double membrane-bound organelles, termed autophagosomes, enclose a portion of cytoplasm, and then fuse with a vacuole or lysosome to give an autolysosome. Autolysosomes can be visualized by incubating cells in the presence of a membrane-permeable cysteine protease inhibitor. The inhibitor presumably decreases proteolytic degradation of the autolysosome contents that are composed of portions of cytoplasm enclosed by the membrane originating from the inner membrane of autophagosomes, and allows them to accumulate. The origin of membranes that give rise to autophagosomes and autolysosomes is unknown. Here we use an acidotropic fluorescent dye, LysoTracker Red, to label autolysosomes specifically. We demonstrate that autolysosome membranes are marked by the presence of alpha-tonoplast intrinsic protein (alpha-TIP) but not by gamma-TIP or delta-TIP. The identification of a TIP specifically associated with membranes derived from an autophagic process may help our understanding of how plant cells generate and maintain functionally distinct types of vacuoles.

Medical student attitudes toward the doctor-patient relationship

CONTEXT

Medical educators have emphasized the importance of teaching patient-centred care.

OBJECTIVES

To describe and quantify the attitudes of medical students towards patient-centred care and to examine: (a) the differences in these attitudes between students in early and later years of medical school; and (b) factors associated with patient-centred attitudes.

METHODS

We surveyed 673 students in the first, third, and fourth years of medical school. Our survey utilized the Patient-Practitioner Orientation Scale (PPOS), a validated instrument designed to measure individual preferences towards various aspects of the doctor-patient relationship. Total PPOS scores can range from patient-centred (egalitarian, whole person oriented) to disease- or doctor-centred (paternalistic, less attuned to psychosocial issues). Additional demographic data including gender, age, ethnicity, undergraduate coursework, family medical background and specialty choice were collected from the fourth year class.

RESULTS

A total of 510 students (76%) completed data collection. Female gender (P < 0.001) and earlier year of medical school (P = 0.03) were significantly associated with patient-centred attitudes. Among fourth year students (n = 89), characteristics associated with more patient-centred attitudes included female gender, European-American ethnicity, and primary-care career choice (P < 0.05 for each comparison).

CONCLUSION

Despite emphasis on the need for curricula that foster patient-centred attitudes among medical students, our data suggest that students in later years of medical school have attitudes that are more doctor-centred or paternalistic compared to students in earlier years. Given the emphasis placed on patient satisfaction and patient-centred care in the current medical environment, our results warrant further research and dialogue to explore the dynamics in medical education that may foster or inhibit student attitudes toward patient-centred care.

The protein storage vacuole: a unique compound organelle

Storage proteins are deposited into protein storage vacuoles (PSVs) during plant seed development and maturation and stably accumulate to high levels; subsequently, during germination the storage proteins are rapidly degraded to provide nutrients for use by the embryo. Here, we show that a PSV has within it a membrane-bound compartment containing crystals of phytic acid and proteins that are characteristic of a lytic vacuole. This compound organization, a vacuole within a vacuole whereby storage functions are separated from lytic functions, has not been described previously for organelles within the secretory pathway of eukaryotic cells. The partitioning of storage and lytic functions within the same vacuole may reflect the need to keep the functions separate during seed development and maturation and yet provide a ready source of digestive enzymes to initiate degradative processes early in germination.