Highly Reproducible Automated Proteomics Sample Preparation Workflow for Quantitative Mass Spectrometry.

Sample preparation for protein quantification by mass spectrometry requires multiple processing steps including denaturation, reduction, alkylation, protease digestion, and peptide cleanup. Scaling these procedures for the analysis of numerous complex biological samples can be tedious and time-consuming, as there are many liquid transfer steps and timed reactions where technical variations can be introduced and propagated. We established an automated sample preparation workflow with a total processing time for 96 samples of 5 h, including a 2 h incubation with trypsin. Peptide cleanup is accomplished by online diversion during the LC/MS/MS analysis. In a selected reaction monitoring (SRM) assay targeting 6 plasma biomarkers and spiked ß-galactosidase, mean intraday and interday cyclic voltammograms (CVs) for 5 serum and 5 plasma samples over 5 days were <20%. In a highly multiplexed SRM assay targeting more than 70 proteins, 90% of the transitions from 6 plasma samples repeated on 3 separate days had total CVs below 20%. Similar results were obtained when the workflow was transferred to a second site: 93% of peptides had CVs below 20%. An automated trypsin digestion workflow yields uniformly processed samples in less than 5 h. Reproducible quantification of peptides was observed across replicates, days, instruments, and laboratory sites, demonstrating the broad applicability of this approach.

Acetylation of sox2 induces its nuclear export in embryonic stem cells.

Embryonic stem (ES) cells require a coordinated network of transcription factors to maintain pluripotency or trigger lineage specific differentiation. Central to these processes are the proteins Oct4, Nanog, and Sox2. Although the transcriptional targets of these factors have been extensively studied, very little is known about how the proteins themselves are regulated, especially at the post-translational level. Post-translational modifications are well documented to have broad effects on protein stability, activity, and cellular distribution. Here, we identify a key lysine residue in the nuclear export signal of Sox2 that is acetylated, and demonstrate that blocking acetylation at this site retains Sox2 in the nucleus and sustains expression of its target genes under hyperacetylation or differentiation conditions. Mimicking acetylation at this site promotes association of Sox2 with the nuclear export machinery. In addition, increased cellular acetylation leads to reduction in Sox2 levels by ubiquitination and proteasomal degradation, thus abrogating its ability to drive transcription of its target genes. Acetylation-mediated nuclear export may be a commonly used regulatory mechanism for many Sox family members, as this lysine is conserved across species and in orthologous proteins.

A Plasma Sample Preparation for Mass Spectrometry using an Automated Workstation.

Sample preparation for mass spectrometry analysis in proteomics requires enzymatic cleavage of proteins into a peptide mixture. This process involves numerous incubation and liquid transfer steps in order to achieve denaturation, reduction, alkylation, and cleavage. Adapting this workflow onto an automated workstation can increase efficiency and reduce coefficients of variance, thereby providing more reliable data for statistical comparisons between sample types. We previously described an automated proteomic sample preparation workflow1. Here, we report the development of a more efficient and better controlled workflow with the following advantages: 1) The number of liquid transfer steps is reduced from nine to six by combining reagents; 2) Pipetting time is reduced by selective tip pipetting using a 96-position pipetting head with multiple channels; 3) Potential throughput is increased by the availability of up to 45 deck positions; 4) Complete enclosure of the system provides improved temperature and environmental control and reduces the potential for contamination of samples or reagents; and 5) The addition of stable isotope labeled peptides, as well as ß-galactosidase protein, to each sample makes monitoring and quality control possible throughout the entire process. These hardware and process improvements provide good reproducibility and improve intra-assay and inter-assay precision (CV of less than 20%) for LC-MS based protein and peptide quantification. The entire workflow for digesting 96 samples in a 96-well plate can be completed in approximately 5 hours.

Application of volumetric absorptive microsampling for robust, high-throughput mass spectrometric quantification of circulating protein biomarkers.

Volumetric absorptive micro sampling (VAMS™) allows accurate sampling of 10 µL of blood from a minimally invasive finger prick and could enable remote personalized health monitoring. Moreover, VAMS overcomes effects from hematocrit and sample heterogeneity associated with dried blood spots (DBS). We describe the first application of VAMS with the Mitra® microsampling device for the quantification of protein biomarkers using an automated, high-throughput sample preparation method coupled with mass spectrometric (MS) detection. The analytical performance of the developed workflow was evaluated for 10 peptides from six clinically relevant proteins: apolipoproteins A-I, B, C-I, C-III, E, and human serum albumin (HSA). Extraction recovery from blood with three different levels of hematocrit varied between 100% and 111% for all proteins. Within-day and total assay reproducibility (i.e., 5 replicates on 5 days) ranged between 3.2-10.4% and 3.4-12.6%, respectively. In addition, after 22 weeks of storage of the Mitra microsampling devices at -80 °C, all peptide responses were within ±15% deviation from the initial response. Application to data-independent acquisition (DIA) MS further demonstrated the potential for broad applicability and the general robustness of the automated workflow by reproducible detection of 1661 peptides from 423 proteins (average 15.7%CV (n = 3) in peptide abundance), correlating to peptide abundances in corresponding plasma (R = 0.8383). In conclusion, we have developed an automated workflow for efficient extraction, digestion, and MS analysis of a variety of proteins in a fixed small volume of dried blood (i.e., 10 µL). This robust and high-throughput workflow will create manifold opportunities for the application of remote, personalized disease biomarker monitoring.

Controlling embryonic stem cell growth and differentiation by automation: enhanced and more reliable differentiation for drug discovery.

Despite significant use in basic research, embryonic stem cells have just begun to be used in the drug discovery process. Barriers to the adoption of embryonic stem cells in drug discovery include the difficulty in growing cells and inconsistent differentiation to the desired cellular phenotype. Embryonic stem cell cultures require consistent and frequent handling to maintain the cells in a pluripotent state. In addition, the preferred hanging drop method of embryoid body (EB) differentiation is not amenable to high-throughput methods, and suspension cultures of EBs show a high degree of variability. Murine embryonic stem cells passaged on an automated platform maintained ≥ 90% viability and pluripotency. We also developed a method of EB formation using 384-well microplates that form a single EB per well, with excellent uniformity across EBs. This format facilitated high-throughput differentiation and enabled screens to optimize directed differentiation into a desired cell type. Using this approach, we identified conditions that enhanced cardiomyocyte differentiation sevenfold. This optimized differentiation method showed excellent consistency for such a complex biological process. This automated approach to embryonic stem cell handling and differentiation can provide the high and consistent yields of differentiated cell types required for basic research, compound screens, and toxicity studies.

A positive regulatory role for the mSin3A-HDAC complex in pluripotency through Nanog and Sox2.

Large networks of proteins govern embryonic stem (ES) cell pluripotency. Recent analysis of the critical pluripotency factors Oct4 and Nanog has identified their interaction with multiple transcriptional repression complexes, including members of the mSin3A-HDAC complex, suggesting that these factors could be involved in the regulation of Oct4/Nanog function. mSin3A is critical for embryonic development, but the mechanism by which the mSin3A-HDAC complex is able to regulate ES cell pluripotency is undefined. Herein we show that the mSin3A-HDAC complex positively regulates Nanog expression in ES cells through Sox2, a critical ES cell transcription factor and regulator of Nanog. We have identified the mSin3A-HDAC complex to be present at the Nanog promoter only under proliferating conditions concurrent with histone acetylation. We find that Sox2 associates with mSin3A-HDAC complex members both in vitro and in vivo, similar to the interactions found between Oct4/Nanog and the mSin3A-HDAC complex. Knockdown of mSin3A-HDAC complex members or HDAC inhibitor treatment reduces Nanog expression, and overexpression of mSin3A-HDAC complex subunits stimulates Nanog expression. Our data demonstrate that the mSin3A-HDAC complex can positively regulate Nanog expression under proliferating conditions and that this activity is complementary to mSin3A-mediated p53-dependent silencing of Nanog during differentiation.

Role for Med12 in regulation of Nanog and Nanog target genes.

Nanog, Oct4, and Sox2 form the core of a transcription factor network that maintains embryonic stem cells in the pluripotent state in both humans and mice. These critical factors have been implicated as both positive and negative regulators of transcription, varying by promoter and differentiation state of the cell. The Mediator complex, a ubiquitous conserved complex of approximately 30 subunits, facilitates transcription by coordinating RNA polymerase II binding to target promoters via gene-specific activators and can be divided into several functional subcomplexes. Med12 is part of a subcomplex of four proteins associated with the core Mediator complex and has been found to function both in repressing and activating transcription when recruited to target promoters. We identified an interaction between Med12 and Nanog and present evidence of involvement of Med12 in regulation of Nanog function. Gene expression analysis of embryonic stem cells knocked down for Med12 showed a similarity to Nanog knockdown, with increased expression of Nanog-repressed targets and decreased expression of Nanog-activated targets. Using chromatin immunoprecipitation, we found that Med12 and Nanog co-occupied Nanog target promoters in embryonic stem cells and that Med12 dissociated from target promoters upon differentiation with kinetics similar to Nanog. Our results indicate that Nanog and Med12 function in concert to regulate Nanog target genes and identify a novel role for Med12 in embryonic stem cell regulation.

Host resistance to lung infection mediated by major vault protein in epithelial cells.

The airway epithelium plays an essential role in innate immunity to lung pathogens. Ribonucleoprotein particles primarily composed of major vault protein (MVP) are highly expressed in cells that encounter xenobiotics. However, a clear biologic function for MVP is not established. We report here that MVP is rapidly recruited to lipid rafts when human lung epithelial cells are infected with Pseudomonas aeruginosa, and maximal recruitment is dependent on bacterial binding to the cystic fibrosis transmembrane conductance regulator. MVP was also essential for optimal epithelial cell internalization and clearance of P. aeruginosa. These results suggest that MVP makes a substantial contribution to epithelial cell-mediated resistance to infection.

Replication of a holographic ion-etched spherical blazed grating for use at extreme-ultraviolet wavelengths: topography.

We have measured the topography of a holographic ion-etched spherical blazed grating and three of its replicas using an atomic force microscope. The master grating had a roughness of less than 5 angstroms rms, a blaze angle of 2.5 degrees, and an antiblaze angle of 3.3 degrees. Thus the groove profile was more triangular than sawtooth. We find that the replication process did not significantly change the master grating. Moreover, we find no significant difference in roughness, blaze angle, or antiblaze angle between the master and its replicas before or after multilayer coating. However, bumps were observed on the gratings after coating, the cause of which is not understood. Although widespread, they occupy a relatively small fraction of the total area.

Replication of a holographic ion-etched spherical blazed grating for use at extreme-ultraviolet wavelengths: efficiency.

Using synchrotron radiation, we have measured the efficiency at an angle of incidence of 10 degrees of a holographic ion-etched spherical blazed grating and three of its fourth-generation replicas. The measured efficiency profile of replicas 1 and 3 prior to multilayer coating oscillated from thin-film interference produced by the replicas' Al/Al2O3/SiO2 structure. A Mo2C/Si multilayer coating was applied to the master grating and replicas 1 and 2. After coating, the maximum grating efficiency occurred in the -2nd order and the maximum values were 12.4% at 143.8 angstroms for the master and 11.6% at 145.2 angstroms for replicas 1 and 2. On the basis of measurements obtained after coating, the derived groove efficiency was 22.2% for the master, 19.4% for replica 1, and 19.3% for replica 2. The groove efficiency of the uncoated replica 3 was 24.3% at 142.5 angstroms. We find that the replicas are reasonably faithful copies of the ion-etched master, and models based on measured atomic force microscope groove profiles are in general agreement with measured results. However, subtle issues remain regarding the widths of the peak order profile and the location of its maximum wavelength.

Near-normal-incidence extreme-ultraviolet efficiency of a flat crystalline anisotropically etched blazed grating.

We have measured the extreme-ultraviolet (EUV) efficiency at an angle of incidence of 10 degrees of a flat crystalline anisotropically etched blazed grating. The measured efficiencies are high for uncoated gratings and agree well with a calculated model derived from a reasonable estimate of the groove profile. The highest groove efficiencies derived from the measurements are 48.8% at 19.07 nm and 64.1% at 16.53 nm for the -2 and -3 orders, respectively, which are comparable to the best values obtained yet from a holographic ion-etched blazed grating. This presents opportunities to instrument designs for high-resolution EUV spectroscopy in astrophysics where high efficiency in high orders is desirable.

Localization of cystic fibrosis transmembrane conductance regulator to lipid rafts of epithelial cells is required for Pseudomonas aeruginosa-induced cellular activation.

The cystic fibrosis (CF) transmembrane conductance regulator (CFTR) protein is an epithelial cell receptor for the outer core oligosaccharide of the Pseudomonas aeruginosa LPS. Bacterial binding leads to CFTR-dependent bacterial internalization, initiation of NF-kappaB nuclear translocation, cellular desquamation, and eventual apoptosis of the infected cells, all of which are critical for innate immune resistance to infection with this pathogen. Lack of this reaction in CF patients underlies their hypersusceptibility to chronic P. aeruginosa infection. In this study we tested whether these epithelial cell responses are dependent upon the localization of CFTR to lipid rafts. Confocal microscopy showed that green fluorescent protein-tagged CFTR (GFP-CFTR) and the lipid raft marker ganglioside GM1 colocalized at sites of P. aeruginosa contact and internalization. GFP-CFTR localized to low density Triton X-100-insoluble fractions in lysates of Madin-Darby canine kidney GFP-CFTR cells, and P. aeruginosa infection increased the levels of GFP-CFTR in these fractions as determined by Western blot. Cells expressing GFP-DeltaF508-CFTR did not have rafts with detectable CFTR protein. Extraction of cell surface cholesterol via cyclodextrin treatment of the cells inhibited CFTR entry into rafts. In addition, cyclodextrin treatment of both human and canine epithelial cells inhibited cellular ingestion of P. aeruginosa, NF-kappaB nuclear translocation, and apoptosis. These results indicate that lipid raft localization of CFTR is required for signaling in response to P. aeruginosa infection. Such signaling is needed for the coordination of innate immunity to P. aeruginosa lung infection, a process that is defective in CF.

Wadsworth mount redux: paraboloidal versus spherical gratings.

Spherical and paraboloidal diffraction gratings are considered for use on an experiment involving a collection of satelliteborne spectrographs that will investigate astrophysical plasmas in the spectral region from approximately 100 to 300 A. We shall use eight spectrographs: Wadsworth mounts in near-normal incidence with effective focal lengths of 3 m, each centered on a chosen wavelength in this spectral range. Ray tracings show that paraboloidal gratings used in the Wadsworth mount have a significant increase in resolution over spherical gratings of the same effective focal length, used in the same mounting, as long as the spectral ranges are small (approximately 10% of the central wavelength). This increase in resolution is due to the spatial extent of coma for a paraboloidal grating that is less than the circle of least confusion of spherical gratings.

Pseudomonas aeruginosa-induced apoptosis is defective in respiratory epithelial cells expressing mutant cystic fibrosis transmembrane conductance regulator.

Chronic lung infection with Pseudomonas aeruginosa constitutes the most severe manifestation of cystic fibrosis, a scenario that results from defects in early clearance of the microbe. Early clearance involves epithelial cell ingestion of bacteria, rapid activation of nuclear factor-kappa B and cellular desquamation within minutes of P. aeruginosa infection, processes that are deficient in cells with mutant alleles of Cftr. Analyzing the effect of Cftr genotype on the apoptotic response of airway epithelial cells to P. aeruginosa, we found that human bronchial epithelial cells expressing Delta F508 cystic fibrosis transmembrane conductance regulator (CFTR) underwent significantly delayed apoptosis compared with cells expressing wild-type (WT) CFTR. Mice with a WT Cftr allele had apoptotic cells in their lungs after P. aeruginosa infections, whereas mice homozygous for the Delta F508 or G551D Cftr alleles showed little apoptosis in response to acute infection. Pseudomonal infection induced expression of CD95 and CD95 ligand, a response that was also delayed in cells homozygous for mutant Cftr alleles. Thus, WT CFTR expression promotes a rapid expression of CD95/CD95 ligand and apoptotic response to P. aeruginosa infection. Prompt apoptosis of infected epithelial cells may be critical for clearance of P. aeruginosa, and CFTR-associated defects in apoptosis may contribute to the pathogenesis of the lung disease in cystic fibrosis.