scholarly journals Deep proteomic profiling of vasopressin-sensitive collecting duct cells. I. Virtual Western blots and molecular weight distributions

2015 ◽  
Vol 309 (12) ◽  
pp. C785-C798 ◽  
Author(s):  
Chin-Rang Yang ◽  
Pumipat Tongyoo ◽  
Milad Emamian ◽  
Pablo C. Sandoval ◽  
Viswanathan Raghuram ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Molecular Weight ◽  
Cell Line ◽  
Collecting Duct ◽  
Mass Spectrometry Data ◽  
Epithelial Cell Line ◽  
Proteomic Profiling ◽  
Western Blots ◽  
Sds Page ◽  
Public Data

The mouse mpkCCD cell line is a continuous cultured epithelial cell line with characteristics of renal collecting duct principal cells. This line is widely used to study epithelial transport and its regulation. To provide a data resource useful for experimental design and interpretation in studies using mpkCCD cells, we have carried out “deep” proteomic profiling of these cells using three levels of fractionation (differential centrifugation, SDS-PAGE, and HPLC) followed by tandem mass spectrometry to identify and quantify proteins. The analysis of all resulting samples generated 34.6 gigabytes of spectral data. As a result, we identified 6,766 proteins in mpkCCD cells at a high level of stringency. These proteins are expressed over eight orders of magnitude of protein abundance. The data are provided to users as a public data base ( https://helixweb.nih.gov/ESBL/Database/mpkFractions/ ). The mass spectrometry data were mapped back to their gel slices to generate “virtual Western blots” for each protein. For most of the 6,766 proteins, the apparent molecular weight from SDS-PAGE agreed closely with the calculated molecular weight. However, a substantial fraction (>15%) of proteins was found to run aberrantly, with much higher or much lower mobilities than predicted. These proteins were analyzed to identify mechanisms responsible for altered mobility on SDS-PAGE, including high or low isoelectric point, high or low hydrophobicity, physiological cleavage, residence in the lysosome, posttranslational modifications, and expression of alternative isoforms due to alternative exon usage. Additionally, this analysis identified a previously unrecognized isoform of aquaporin-2 with apparent molecular mass <20 kDa.

Advancements in capturing and mining mass spectrometry data are transforming natural products research

2021 ◽  
Author(s):  
Scott A. Jarmusch ◽  
Justin J. J. van der Hooft ◽  
Pieter C. Dorrestein ◽  
Alan K. Jarmusch
Keyword(s):  
Mass Spectrometry ◽  
Data Mining ◽  
Natural Products ◽  
Data Analysis ◽  
Community Participation ◽  
Mass Spectrometry Data ◽  
Metabolomics Data ◽  
Analysis Tools ◽  
Public Data ◽  
Potential Use

This review covers the current and potential use of mass spectrometry-based metabolomics data mining in natural products. Public data, metadata, databases and data analysis tools are critical. The value and success of data mining rely on community participation.

scholarly journals Epithelial Cell Line Derived from Endometriotic Lesion Mimics Macrophage Nervous Mechanism of Pain Generation on Proteome and Metabolome Levels

Biomolecules ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1230
Author(s):  
Benjamin Neuditschko ◽  
Marlene Leibetseder ◽  
Julia Brunmair ◽  
Gerhard Hagn ◽  
Lukas Skos ◽  
...  
Keyword(s):  
Cell Line ◽  
Specific Protein ◽  
Reproductive Age ◽  
Epithelial Cell Line ◽  
Proteomic Profiling ◽  
Metabolomic Profiling ◽  
Pelvic Area ◽  
Culture Model ◽  
Neutrophil Aggregation ◽  
Cardinal Symptoms

Endometriosis is a benign disease affecting one in ten women of reproductive age worldwide. Although the pain level is not correlated to the extent of the disease, it is still one of the cardinal symptoms strongly affecting the patients’ quality of life. Yet, a molecular mechanism of this pathology, including the formation of pain, remains to be defined. Recent studies have indicated a close interaction between newly generated nerve cells and macrophages, leading to neurogenic inflammation in the pelvic area. In this context, the responsiveness of an endometriotic cell culture model was characterized upon inflammatory stimulation by employing a multi-omics approach, including proteomics, metabolomics and eicosanoid analysis. Differential proteomic profiling of the 12-Z endometriotic cell line treated with TNFα and IL1β unexpectedly showed that the inflammatory stimulation was able to induce a protein signature associated with neuroangiogenesis, specifically including neuropilins (NRP1/2). Untargeted metabolomic profiling in the same setup further revealed that the endometriotic cells were capable of the autonomous production of 7,8-dihydrobiopterin (BH2), 7,8-dihydroneopterin, normetanephrine and epinephrine. These metabolites are related to the development of neuropathic pain and the former three were found up-regulated upon inflammatory stimulation. Additionally, 12-Z cells were found to secrete the mono-oxygenated oxylipin 16-HETE, a known inhibitor of neutrophil aggregation and adhesion. Thus, inflammatory stimulation of endometriotic 12-Z cells led to specific protein and metabolite expression changes suggesting a direct involvement of these epithelial-like cells in endometriosis pain development.

scholarly journals 2155. Accelerated Confirmation of Porin Loss in Carbapenem-Resistant Enterobacterales: A MALDI-TOF Mass Spectrometry-Based Approach

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S731-S731
Author(s):  
Carlos Correa-Martinez ◽  
Evgeny A Idelevich ◽  
Karsten Becker
Keyword(s):  
Mass Spectrometry ◽  
Molecular Weight ◽  
Gold Standard ◽  
Sodium Dodecylsulfate ◽  
Resistant Bacteria ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Carbapenem Resistant ◽  
Sds Page ◽  
Tof Ms

Abstract Background The accurate identification of carbapenem resistance mechanisms is decisive for the appropriate selection of antibiotic regimens. Numerous methods can detect carbapenemase-producing carbapenem-resistant bacteria (CPCR). However, non-CPCR (NCPCR) are routinely assumed to display porin loss as a diagnosis of exclusion. No further confirmatory tests are performed since the gold standard (sodium dodecylsulfate polyacrylamide gel electrophoresis, SDS–PAGE) is laborious and time consuming. We propose a test for rapid and easy detection of porin loss by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Methods Clinical meropenem-resistant Enterobacterales strains (10 CPCR, 10 NCPCR) and control strains recommended by EUCAST (5 carbapenemase-producing, one with porin loss, one-negative control) were analyzed. Membrane proteins were extracted by successive centrifugation of bacterial suspensions (McFarland 0.5) and addition of ethanol, formic acid and acetonitrile. MALDI-TOF MS of the protein extracts was performed on a 96-spot target (Bruker Daltonics, Germany). Peaks between 35 and 40 kDa were analyzed for the presence of porins and compared with the bands observed in the SDS–PAGE of the protein extracts. Results Within the molecular weight range of 35–40 kDa, the MALDI-TOF MS-based method revealed peaks in all CPCR isolates corresponding to those observed in the carbapenemase-producing control strains. In contrast, the control strain with porin loss as well as all CNCR isolates showed a lower quantity of peaks in this range. All peaks observed correlated with the bands observed in the SDS–PAGE of the protein extracts at the corresponding molecular weight (Figure 1). Conclusion Yielding results that reliably correspond to the current gold standard, we propose a method for accelerated detection of porin loss as an alternative to the diagnosis of exclusion usually made in routine settings. With a processing time of approximately 20 minutes, the method can be easily implemented in the clinical setting. Applying this MALDI-TOF MS-based approach, valuable information will be provided about a resistance mechanism that otherwise remains unexplained. Disclosures All authors: No reported disclosures.

Estrogen-dependent expression of the cystic fibrosis transmembrane regulator gene in a novel uterine epithelial cell line

1994 ◽  
Vol 107 (9) ◽  
pp. 2439-2448
Author(s):  
L. Rochwerger ◽  
S. Dho ◽  
L. Parker ◽  
J.K. Foskett ◽  
M. Buchwald
Keyword(s):  
Epithelial Cells ◽  
Cell Line ◽  
Steroid Hormones ◽  
Primary Cultures ◽  
T Antigen ◽  
Epithelial Cell Line ◽  
Normal Female ◽  
Western Blots ◽  
Uterine Epithelial Cell

We have demonstrated previously the modulation of CFTR expression by estrogen in vivo in the rat uterine epithelium. The purpose of this study was to establish a suitable in vitro system to investigate the regulation of CFTR by steroid hormones. Primary cultures of rat uterine epithelial cells, which showed high levels of CFTR expression in vitro, were infected with an adeno/SV40 virus. One clone, UIT 1.16, which retained the morphology of the primary epithelial cells yet proliferated beyond the life span of the primary culture, was isolated and characterized. Successful immortalization of UIT 1.16 cells was verified by the presence of a band corresponding to the SV40 large T-antigen in western blots, as well as by their ability to proliferate continuously. Transmission electron microscopy studies revealed that these cells maintained the characteristics of a polarized epithelium with well-established membrane domains and specialized intercellular junctions. A high transepithelial electrical resistance was also observed when cells were assayed in modified Ussing chambers. When the basolateral cellular membrane of cells grown in vitrogen-coated filters was permeabilized with nystatin, a forskolin-stimulated Cl- permeability was observed in the apical membrane, similar to that present in other CFTR-expressing epithelial cells. UIT 1.16 cells showed high levels of CFTR expression on northern blots. The expression of CFTR was dependent on the presence of estrogen in the culture medium, since almost undetectable levels of CFTR mRNA were observed when the cells were cultured in medium containing serum depleted of steroid hormones. However, addition of estrogen to this medium prevented the disappearance of CFTR mRNA, confirming estrogen-regulated expression of CFTR in the UIT 1.16 cell line. The newly developed UIT 1.16 cell line provides a valuable model to analyze the regulation of CFTR expression by steroid hormones. Moreover, the cell line could also be used to investigate the role of CFTR in the uterus during the normal female cycle as well as for the study of other uterine epithelial functions and the agents that regulate them.

Recombinant Plasmin from Lemna: Purification, Characterization and In Vitro Comparison with Human Plasma-Derived Plasmin.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 4001-4001
Author(s):  
Gary L. Brookhart ◽  
Michael D. Tomalski ◽  
Karim C. Lounes ◽  
Piet Meijer ◽  
Cornelis Kluft ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Human Plasma ◽  
Lemna Minor ◽  
Tissue Type ◽  
Stable Complex ◽  
Dependent Manner ◽  
Dna Encoding ◽  
Concentration Dependent Manner ◽  
Western Blots ◽  
Sds Page

Abstract Background: The fibrinolytic enzyme plasmin has gained renewed interest as a direct thrombolytic agent. Local delivery of plasmin via catheter into thrombi, combined with the efficient neutralization of plasmin that may escape from the clot by its inhibitors α2-antiplasmin (α2-AP) and α2-macroglobulin may provide safe and effective removal of pathologic blood clots. Objective: To overcome the potential for pathogen contamination associated with plasmin prepared from pooled human plasma, we have generated recombinant plasmin (r-PLM) from transgenic Lemna plants and compared its biological properties with those of plasma-derived plasmin (pd-PLM). Results: Lemna minor, an aquatic plant, was transfected with the c-DNA encoding human plasminogen, and grown in media under controlled conditions. Lemna-derived plasminogen (r-PLG) was extracted from plant-tissue, separated on lysine-Sepharose and subsequently converted into plasmin (r-PLM), using urokinase-type plasminogen activator (u-PA). r-PLM was further purified to homogeneity using affinity chromatography on benzamidine-Sepharose. r-PLG and r-PLM co-migrate with pd-PLG and pd-PLM on non-reducing SDS-PAGE with the respective molecular weights of about 90,000 kDa and 82,000 kDa. When analyzed on reducing SDS-PAGE, r-PLM, just like pd-PLM, separates into a 56,000 kDa heavy chain and a 26,000 light chain. On Western blots r-PLG and r-PLM cross-react with polyclonal antibodies that were raised against pd-PLG, indicating immunologic identity of r-PLG/PLM and pd-PLG/PLM. All three plasminogen activators (PA), tissue-type PA, u-PA and streptokinase, activate r-PLG. Activity assays using the PLM-specific chromogenic substrate S-2403 show that catalytic rates of r-PLM are indistinguishable from pd-PLM, indicating that in this assay r-PLM and pd-PLM have comparable activity. Purified r-PLM and pd-PLM have similar specific activities. Like pd-PLM, r-PLM activity is inhibited by its physiological inhibitor α2-AP and Kunitz-type inhibitors SBTI and aprotinin. Inhibition of r-PLM by α2-AP results in the formation of a high-molecular weight SDS-stable complex, which migrates on SDS-PAGE with a molecular weight of 150,000 kDa, the cumulative molecular weight of r-PLM (82,000 kDa) and α2-AP (65,000 kDa). In microtiter-based fibrinolysis assays, both pd- and r-plasmin dissolve fibrin clots at the same rate and in a concentration-dependent manner. Conclusion: This work demonstrates that proteins of the fibrinolytic system can be expressed in Lemna. Lemna-derived r-PLM and pd-PLM have comparable biochemical properties, activity, and are equally sensitive to known plasmin inhibitors. Plant-derived r-PLM may be a valuable alternative to PLM preparations from pooled human plasma.

scholarly journals Induction of cell migration by pro-urokinase binding to its receptor: possible mechanism for signal transduction in human epithelial cells.

1994 ◽  
Vol 126 (1) ◽  
pp. 259-270 ◽  
Author(s):  
N Busso ◽  
S K Masur ◽  
D Lazega ◽  
S Waxman ◽  
L Ossowski
Keyword(s):  
Signal Transduction ◽  
Cell Line ◽  
Solid Phase ◽  
Shape Change ◽  
Epithelial Cell Line ◽  
Cell Fractionation ◽  
Western Blots ◽  
Glycosyl Phosphatidylinositol ◽  
Cell Lysates ◽  
Pkc Epsilon

A human epithelial cell line, WISH, and a mouse cell line, LB6-uPAR, transfected with the human urokinase receptor (uPAR), both expressed high affinity uPAR but undetectable levels of urokinase (uPA). In two independent assays, binding of exogenous pro-uPA produced an up to threefold enhancement of migration. The migration was time and concentration dependent and did not involve extracellular proteolysis. This biologic response suggested that uPAR can trigger an intracellular signal. Since this receptor is a glycosyl-phosphatidylinositol-linked protein, we postulated that it must do so by interacting with other proteins, among which, by analogy to other systems, would be a kinase. To test this hypothesis, we carried out a solid phase capture of uPAR from WISH cell lysates using either antibodies against uPAR or pro-uPA adsorbed to plastic wells, followed by in vitro phosphorylation of the immobilized proteins. SDS-PAGE and autoradiography revealed two phosphorylated protein bands of 47 and 55 kD. Both proteins were phosphorylated on serine residues. Partial sequence of the two proteins showed a 100% homology to cytokeratin 18 (CK18) and 8 (CK8), respectively. A similar pattern of phosphorylation was obtained with lysates from A459 cells, a lung carcinoma, but not HL60, LB6-uPAR or HEp3 cell lysates, suggesting that the identified multiprotein uPAR-complex may be specific for simple epithelia. Moreover, immunocapture with antibody to another glycosyl-phosphatidylinositol-linked protein, CD55, which is highly expressed in WISH cells, was ineffective. The kinase was tentatively identified as protein kinase C, because it was inhibited by an analogue of staurosporine more specific for PKC and not by a PKA or tyrosine kinase inhibitors. The kinase was tentatively identified as PKC epsilon because of its resistance to PMA down-modulation, independence of Ca2+ for activity, and reaction with a specific anti-PKC epsilon antibody in Western blots. Cell fractionation into cytosolic and particulate fractions revealed that all four proteins, the kinase, uPAR, CK18, and CK8, were present in the particulate fraction. In vivo, CK8, and to a lesser degree CK18, were found to be phosphorylated on serine residues. Occupation of uPAR elicited a time-dependent increase in the phosphorylation intensity of CK8, a cell shape change and a redistribution of the cytokeratin filaments. These results strongly suggest that uPAR serves not only as an anchor for uPA but participates in a signal transduction pathway resulting in a pronounced biological response.

scholarly journals Deep proteomic profiling of vasopressin-sensitive collecting duct cells. II. Bioinformatic analysis of vasopressin signaling

2015 ◽  
Vol 309 (12) ◽  
pp. C799-C812 ◽  
Author(s):  
Chin-Rang Yang ◽  
Viswanathan Raghuram ◽  
Milad Emamian ◽  
Pablo C. Sandoval ◽  
Mark A. Knepper
Keyword(s):  
Protein Kinases ◽  
Isotope Labeling ◽  
Collecting Duct ◽  
Bioinformatic Analysis ◽  
Small Gtpase ◽  
Mass Spectrometry Data ◽  
Proteomic Profiling ◽  
Eukaryotic Translation ◽  
Aquaporin 2 ◽  
Proteomic Data

Vasopressin controls osmotic water transport in the renal collecting duct through regulation of aquaporin-2 (AQP2). We carried out bioinformatic analysis of quantitative proteomic data from the accompanying article to investigate the mechanisms involved. The experiments used stable isotope labeling by amino acids in cell culture in cultured mpkCCD cells to quantify each protein species in each of five differential-centrifugation (DC) fractions with or without the vasopressin analog 1-desamino-8-d-arginine-vasopressin (dDAVP). The mass spectrometry data and parallel Western blot experiments confirmed that dDAVP addition is associated with an increase in AQP2 abundance in the 17,000- g pellet and a corresponding decrease in the 200,000- g pellet. Remarkably, all subunits of the cytoplasmic ribosome also increased in the 17,000- g pellet in response to dDAVP ( P < 10−34), with a concomitant decrease in the 200,000- g pellet. Eukaryotic translation initiation complex 3 (eIF3) subunits underwent parallel changes ( P < 10−6). These findings are consistent with translocation of assembled ribosomes and eIF3 complexes into the rough endoplasmic reticulum in response to dDAVP. Conversely, there was a systematic decrease in small GTPase abundances in the 17,000- g fraction. In contrast, most proteins, including protein kinases, showed no systematic redistribution among DC fractions. Of the 521 protein kinases coded by the mouse genome, 246 were identified, but many fewer were found to colocalize with AQP2 among DC fractions. Bayes' rule was used to integrate the new colocalization data with prior data to identify protein kinases most likely to phosphorylate aquaporin-2 at Ser256 ( Camk2b > Camk2d > Prkaca) and Ser261 ( Mapk1 = Mapk3 > Mapk14).

Sign in / Sign up

Export Citation Format

Share Document