Multiple sclerosis is chronic inflammatory disease of central nervous system. Dysregulation of immune system, migration of immune cells across blood brain barrier and their participation in development demyelinating lesions play pivotal role in the disease pathogenesis. Diagnosis and disease progression monitoring is hindered by absence of reliable, sensitive, and specific laboratory tests reflecting accurately and specifically the disease activity. Cellular microvesicles (MVs) present in blood, CSF and other body fluids represent previously unrecognized means of cell communication which takes part in many pathological conditions, including MS. As such MVs carrying tissue-specific information are new and highly promising diagnostic targets for number of diseases and evaluation of their potential in MS is of utmost interest. Detailed molecular characterization of MVs present in CSF and blood of MS patients is the aim of the proposed project.

Roztroušená skleróza (RS) je chronické zánětlivé onemocnění centrálního nervového systému. Deregulace imunitního systému, migrace imunitních buněk přes hematoencefalickou bariéru a jejich podíl na vzniku demyelinizačních lézí hrají kritickou roli v patogenezi tohoto onemocnění. Přesná a spolehlivá diagnóza a sledování progrese onemocnění jsou komplikovány absencí spolehlivých a specifických laboratorních testů. Buněčné mikrovesikuly (MVs) přítomné v krvi, mozkomíšním moku a dalších tělních tekutinách představují donedávna neznámý mechanismus mezibuněčné komunikace podílející se na patologických procesech včetně RS. MVs nesou tkáňově-specifické informace a jsou tedy i nosiči specifické informace z tkání účastnících se vzniku a rozvoje onemocnění. MVs jsou proto vysoce slibným potenciálním diagnostickým nástrojem pro mnoho různých onemocnění. Podrobná molekulární charakterizace MVs z krve a mozkomíšního moku pacientů s RS a zhodnocení potenciálu MVs pro diagnostiku a monitorování RS je cílem tohoto projektu.

• MeSH
• biochemická analýza krve MeSH
• biologické markery krev   mozkomíšní mok   MeSH
• exozómy MeSH
• imunita MeSH
• lidé MeSH
• mikropartikule MeSH
• mozkomíšní mok MeSH
• roztroušená skleróza diagnóza   MeSH
• Check Tag
• lidé MeSH

• Konspekt
• Patologie. Klinická medicína
• NLK Obory
• neurologie
• NLK Publikační typ
• závěrečné zprávy o řešení grantu AZV MZ ČR

Integral membrane proteins are under-represented in standard proteomic analyses, mostly because of their low expression and absence of trypsin-cleavage sites in their hydrophobic transmembrane segments. Novel and effective strategies for membrane proteomic analysis aim at soluble N-glycosylated segments of integral membrane proteins (CSC, SPEG, N-glyco-FASP) or selectively target the hydrophobic transmembrane alpha-helical segments employing chemical peptide cleavage by CNBr (hpTC). We combined a solid phase enrichment of glycopeptides (SPEG) with a transmembrane segment-oriented hpTC method and a standard "detergent and trypsin" approach into a three-pronged "Pitchfork" strategy to maximize the membrane proteome coverage in human lymphoma cells. This strategy enabled the identification of >1200 integral membrane proteins from all cellular compartments, including 105 CD antigens, 24 G protein-coupled receptors, and 141 solute carrier transporters. The advantage of the combination lies in the complementarity of the methods. SPEG and hpTC target different sets of membrane proteins. HpTC provided identifications of proteins and peptides with significantly higher hydrophobicity compared to SPEG and detergent-trypsin approaches. Among all identified proteins, we observed 32 so-called "missing proteins". The Pitchfork strategy presented here is universally applicable and enables deep and fast description of membrane proteomes in only 3 LC-MS/MS runs per replicate. SIGNIFICANCE: Integral membrane proteins (IMPs) are encoded by roughly a quarter of human coding genes. Their functions and their specific localization makes IMPs highly attractive drug targets. In fact, roughly half of the currently approved drugs in medicine target IMPs. Our knowledge of membrane proteomes is, however, limited. We present a new strategy for the membrane proteome analysis that combines three complementary methods targeting different features of IMPs. Using the combined strategy, we identified over 1200 IMPs in human lymphoma tissue from all sub-cellular compartments in only 3 LC-MS/MS runs per replicate. The three-pronged "Pitchfork" strategy is universally applicable, and offers a fast way toward a reasonably concise description of membrane proteomes in multiple samples.

• MeSH
• chromatografie kapalinová MeSH
• heterografty MeSH
• lidé MeSH
• lymfom z plášťových buněk metabolismus   MeSH
• membránové proteiny metabolismus   MeSH
• myši MeSH
• nádorové proteiny metabolismus   MeSH
• proteom metabolismus   MeSH
• tandemová hmotnostní spektrometrie MeSH
• transplantace nádorů MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Cerebrospinal fluid (CSF) is in direct contact with the central nervous system. This makes human CSF an attractive source of potential biomarkers for neurologic diseases. Similarly to blood plasma, proteomic analysis of CSF is complicated by a high dynamic range of individual protein concentrations and by the presence of several highly abundant proteins. To deal with the abundant human CSF proteins, methods developed for blood plasma/serum are routinely used. Multiple affinity removal systems and protein enrichment of less abundant proteins using a combinatorial peptide ligand library are among the most frequent approaches. However, their relative impact on CSF proteome coverage has never been evaluated side-by-side in a single study. Therefore, we explored the effect of CSF depletion using MARS 14 cartridge and ProteoMiner ligand library on the number of CSF proteins identified in subsequent LC-MS/MS analysis. LC-MS/MS analysis of crude (non-treated) CSF provided roughly 500 identified proteins. Depletion of CSF by MARS 14 cartridge increased the number of identifications to nearly 800, while treatment of CSF using ProteoMiner enabled identification of 600 proteins. To explore the potential losses of CSF proteins during the depletion process, we also analyzed the "waste" fractions generated by both methods, i.e., proteins retained by the MARS 14 cartridge, and the molecules present in the flow-through fraction from ProteoMiner. More than 250 proteins were bound to MARS 14 cartridge, 100 of those were not identified in the corresponding depleted CSF. Similarly, analysis of the waste fraction in ProteoMiner workflow provided almost 70 unique proteins not found in the CSF depleted by the ligand library. Both depletion strategies significantly increased the number of identified CSF proteins compared to crude CSF. However, MARS 14 depletion provided a markedly higher number of identified proteins (773) compared to ProteoMiner (611). Further, we showed that CSF proteins are lost due to co-depletion (MARS 14) or exclusion (ProteoMiner) during the depletion process. This suggests that the routinely discarded "waste" fractions contain proteins of potential interest and should be included in CSF biomarker studies.

• Publikační typ
• časopisecké články MeSH

Evaluating nanoparticle (NP) toxicity in human cell systems is a fundamental requirement for future NP biomedical applications. In this study, we have designed a screening assay for assessing different types of cell death induced by NPs in human umbilical vein endothelial cell (HUVEC) culture. This assay consists of WST-8, LDH and Hoechst 33342 staining, all performed in one well, which enables an evaluation of cell viability, necrosis and apoptosis, respectively, in the same cell sample. The 96-well format and automated processing of fluorescent images enhances the assay rapidity and reproducibility. After testing the assay functionality with agents that induced different types of cell death, we investigated the endothelial toxicity of superparamagnetic iron oxide nanoparticles (SPIONs, 8 nm), silica nanoparticles (SiNPs, 7-14 nm) and carboxylated multiwall carbon nanotubes (CNTCOOHs, 60 nm). Our results indicated that all the tested NP types induced decreases in cell viability after 24 hours at a concentration of 100 μg/ml. SPIONs caused the lowest toxicity in HUVECs. By contrast, SiNPs induced pronounced necrosis and apoptosis. A time course experiment showed the gradual toxic effect of all the tested NPs. CNTCOOHs inhibited tetrazolium derivatives at 100 μg/ml, causing false negative results from the WST-8 and LDH assay. In summary, our data demonstrate that the presented "three-in-one" screening assay is capable of evaluating NP toxicity effectively and reliably. Due to its simultaneous utilization of two different methods to assess cell viability, this assay is also capable of revealing, if NPs interfere with tetrazolium salts.

• MeSH
• apoptóza účinky léků   MeSH
• biotest MeSH
• endoteliální buňky pupečníkové žíly (lidské) MeSH
• endoteliální buňky účinky léků   MeSH
• lidé MeSH
• nanočástice aplikace a dávkování   MeSH
• preklinické hodnocení léčiv metody   MeSH
• velikost částic MeSH
• viabilita buněk účinky léků   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Iron is an essential biogenic element for both prokaryotic and eukaryotic cells. In humans iron is present in hundreds of different metalloproteins. The peptide hormone hepcidin serves as a master regulator of iron homeostasis on the level of single cells and whole organism - by altering cell surface expression of cellular iron exporter - protein ferroportin. Altered levels of extracellular hepcidin lead to pathological conditions such as hemochromatosis and iron loading or, on the other side, iron restrictive anemias. Therapeutic modulation of hepcidin is a new and promising approach to treatment of these conditions. In this review, a summary of the current knowledge of hepcidin function, regulation and pathological involvements are provided, followed by a section covering the therapeutic potential of hepcidin and the current strategies how to modulate its levels and biological functions for therapeutic purposes.

• MeSH
• hepcidiny farmakologie   terapeutické užití   MeSH
• homeostáza účinky léků   MeSH
• lidé MeSH
• proteiny přenášející kationty metabolismus   MeSH
• železo metabolismus   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

Integral membrane proteins (IMPs) are coded by 20-30% of human genes and execute important functions - transmembrane transport, signal transduction, cell-cell communication, cell adhesion to the extracellular matrix, and many other processes. Due to their hydrophobicity, low expression and lack of trypsin cleavage sites in their transmembrane segments, IMPs have been generally under-represented in routine proteomic analyses. However, the field of membrane proteomics has changed markedly in the past decade, namely due to the introduction of filter assisted sample preparation (FASP), the establishment of cell surface capture (CSC) protocols, and the development of methods that enable analysis of the hydrophobic transmembrane segments. This review will summarize the recent developments in the field and outline the most successful strategies for the analysis of integral membrane proteins. SIGNIFICANCE: Integral membrane proteins (IMPs) are attractive therapeutic targets mostly due to their many important functions. However, our knowledge of the membrane proteome is severely limited to effectively exploit their potential. This is mostly due to the lack of appropriate techniques or methods compatible with the typical features of IMPs, namely hydrophobicity, low expression and lack of trypsin cleavage sites. This review summarizes the most recent development in membrane proteomics and outlines the most successful strategies for their large-scale analysis.

• MeSH
• lidé MeSH
• membránové proteiny analýza   MeSH
• proteomika metody   trendy   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH

Chronic myeloid leukemia (CML) therapy has markedly improved patient prognosis after introduction of imatinib mesylate for clinical use. However, a subset of patients develops resistance to imatinib and other tyrosine kinase inhibitors (TKIs), mainly due to point mutations in the region encoding the kinase domain of the fused BCR-ABL oncogene. To identify potential therapeutic targets in imatinib‑resistant CML cells, we derived imatinib-resistant CML-T1 human cell line clone (CML-T1/IR) by prolonged exposure to imatinib in growth media. Mutational analysis revealed that the Y235H mutation in BCR-ABL is probably the main cause of CML-T1/IR resistance to imatinib. To identify alternative therapeutic targets for selective elimination of imatinib-resistant cells, we compared the proteome profiles of CML-T1 and CML-T1/IR cells using 2-DE-MS. We identified eight differentially expressed proteins, with strongly upregulated Na+/H+ exchanger regulatory factor 1 (NHERF1) in the resistant cells, suggesting that this protein may influence cytosolic pH, Ca2+ concentration or signaling pathways such as Wnt in CML-T1/IR cells. We tested several compounds including drugs in clinical use that interfere with the aforementioned processes and tested their relative toxicity to CML-T1 and CML-T1/IR cells. Calcium channel blockers, calcium signaling antagonists and modulators of calcium homeostasis, namely thapsigargin, ionomycin, verapamil, carboxyamidotriazole and immunosuppressive drugs cyclosporine A and tacrolimus (FK-506) were selectively toxic to CML-T1/IR cells. The putative cellular targets of these compounds in CML-T1/IR cells are postulated in this study. We propose that Ca2+ homeostasis can be a potential therapeutic target in CML cells resistant to TKIs. We demonstrate that a proteomic approach may be used to characterize a TKI-resistant population of CML cells enabling future individualized treatment options for patients.

• MeSH
• bcr-abl fúzové proteiny metabolismus   MeSH
• chemorezistence účinky léků   MeSH
• chronická myeloidní leukemie farmakoterapie   metabolismus   MeSH
• homeostáza účinky léků   MeSH
• imatinib mesylát farmakologie   MeSH
• inhibitory proteinkinas farmakologie   MeSH
• lidé MeSH
• mutace účinky léků   MeSH
• nádorové buněčné linie MeSH
• proteom metabolismus   MeSH
• proteomika metody   MeSH
• signální transdukce účinky léků   MeSH
• vápník metabolismus   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

Integral membrane proteins are generally under-represented in routine proteomic analyses, mostly because of their relatively low abundance, hydrophobicity and lack of trypsin-cleavage sites. To increase the coverage of membrane proteomes, various strategies have been developed, targeting mostly the extra-membrane segments of membrane proteins. We focused our attention to the rather overlooked hydrophobic transmembrane segments. Such peptides can be isolated after carbonate stripping and protease "shaving" of membranes isolated by simple centrifugation procedure. The treated membranes with embedded hydrophobic peptides can then be solubilized in organic solvents, re-digested with CNBr, delipidated and subjected to LC-MS/MS analysis. We modified the original "hppK" method, and applied it for the analysis of human lymphoma cells. We identified 1224 proteins of which two-thirds were IMPs with 1-16 transmembrane segments. This method allowed us to identify 13 "missing proteins" - proteins with no previous evidence on protein level. BIOLOGICAL SIGNIFICANCE: Integral membrane proteins execute numerous essential functions and represent substantial part of eukaryotic proteomes. Our knowledge of their function and expression is, however, limited. Novel approaches extending our knowledge of membrane proteome are therefore highly desired. As we demonstrate here, a non-conventional method which targets rather overlooked hydrophobic transmembrane segments of integral membrane proteins has wide potential to provide the missing information on the membrane proteome. We show that it can deliver identification and potentially also quantification of hundreds of integral membrane proteins including the so called "missing proteins".

• MeSH
• chromatografie kapalinová metody   MeSH
• hydrofobní a hydrofilní interakce MeSH
• lidé MeSH
• lymfom z plášťových buněk chemie   MeSH
• membránové proteiny analýza   MeSH
• nádorové proteiny analýza   MeSH
• peptidy analýza   MeSH
• proteom chemie   MeSH
• proteomika metody   MeSH
• tandemová hmotnostní spektrometrie metody   MeSH
• trypsin chemie   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Mantle cell lymphoma (MCL) is a chronically relapsing aggressive type of B-cell non-Hodgkin lymphoma considered incurable by currently used treatment approaches. Fludarabine is a purine analog clinically still widely used in the therapy of relapsed MCL. Molecular mechanisms of fludarabine resistance have not, however, been studied in the setting of MCL so far. We therefore derived fludarabine-resistant MCL cells (Mino/FR) and performed their detailed functional and proteomic characterization compared to the original fludarabine sensitive cells (Mino). We demonstrated that Mino/FR were highly cross-resistant to other antinucleosides (cytarabine, cladribine, gemcitabine) and to an inhibitor of Bruton tyrosine kinase (BTK) ibrutinib. Sensitivity to other types of anti-lymphoma agents was altered only mildly (methotrexate, doxorubicin, bortezomib) or remained unaffacted (cisplatin, bendamustine). The detailed proteomic analysis of Mino/FR compared to Mino cells unveiled over 300 differentially expressed proteins. Mino/FR were characterized by the marked downregulation of deoxycytidine kinase (dCK) and BTK (thus explaining the observed crossresistance to antinucleosides and ibrutinib), but also by the upregulation of several enzymes of de novo nucleotide synthesis, as well as the up-regulation of the numerous proteins of DNA repair and replication. The significant upregulation of the key antiapoptotic protein Bcl-2 in Mino/FR cells was associated with the markedly increased sensitivity of the fludarabine-resistant MCL cells to Bcl-2-specific inhibitor ABT199 compared to fludarabine-sensitive cells. Our data thus demonstrate that a detailed molecular analysis of drug-resistant tumor cells can indeed open a way to personalized therapy of resistant malignancies.

• MeSH
• antitumorózní látky farmakologie   MeSH
• chemorezistence * MeSH
• chromatografie kapalinová metody   MeSH
• izotopové značení metody   MeSH
• lidé MeSH
• lymfom z plášťových buněk farmakoterapie   metabolismus   MeSH
• nádorové biomarkery metabolismus   MeSH
• nádorové buňky kultivované MeSH
• proteomika metody   MeSH
• tandemová hmotnostní spektrometrie metody   MeSH
• vidarabin analogy a deriváty   farmakologie   MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH