[Study of urinary markers of different podocytopathies by proteomic analysis]

BACKGROUND

Focal segmental glomerulosclerosis (FSGS) is a primary podocytopathy characterized by primary podocyte detection and high proteinuria. The search for biomarkers and factors associated with the progression of this disease is an important task nowdays.

AIM

To assess the proteomic profile of urine in patients with FSGS and to isolate urinary biomarkers of podocytopathies.

MATERIALS AND METHODS

The study included 41 patients diagnosed with chronic glomerulonephritis, 27 men and 14 women. According to the morphological study, 28 patients were diagnosed with FSGS, 9 with steroid-sensitive nephrotic syndrome and 14 with steroid-resistant nephrotic syndrome. The comparison group included 13 patients with membranous nephropathy. The study of the urinary proteome was carried out by targeted liquid chromatography-mass spectrometry using multiple reaction monitoring with synthetic stable isotope labelled peptide standards.

RESULTS

The main differences in the protein profile of urine were found in the subgroups of steroid-sensitive (SS) and steroid-resistant (SR) FSGS. In the FSGS SR group, at the onset of the disease, there was a high concentration of proteins reflecting damage to the glomerular filter (apo-lipoprotein A-IV, orosomucoid, cadherin, hemopexin, vitronectin), as well as proteins associated with tubulo-interstitial inflammation and accumulation of extracellular matrix (retinol- and vitamin D-binding proteins, kininogen-1, lumican and neurophilin-2). Compared with the membranous nephropathy group, FSGS patients had significantly higher urinary concentrations of carnosinase, orosomucoid, cadherin-13, tenascin X, osteopontin, and zinc-alpha-2-glycoprotein.

CONCLUSION

Thus, in patients with SR FSGS, the proteomic profile of urine includes more proteins at elevated concentrations, which reflects severe damage to various parts of the nephron compared with patients with SS FSGS and membranous nephropathy.

Peroxide-Induced Damage to Plasminogen Molecules

Plasminogen is a zymogenic form of plasmin, an enzyme that plays a fundamental role in the dissolution of fibrin clots as well as in many other physiological processes. For the first time, by the method of gas chromatography-mass spectrometry, post-translational modifications in the primary structure of plasminogen treated with physiologically relevant amounts of hydrogen peroxide were identified. It was found that methionine and tryptophan residues located in different structural regions of plasminogen served as targets of the oxidant. Plasminogen oxidation caused a dose-dependent effect in decreasing the fibrinogenolytic activity of plasmin evidenced by the formation of fibrinogen degradation products. The possible antioxidant role of methionines in the oxidative modification of plasminogen is discussed.

The Nature of Resistance of the Coagulation Factor XIII Structure to Hypochlorite-Induced Oxidation

The damage to blood coagulation factor XIII (FXIII) at different stages of its enzymatic activation under the action of various physiological amounts of hypochlorite ion was studied. The results obtained by HPLC-MS/MS, SDS-PAGE, and colorimetry showed that, during the conversion of FXIII to FXIIIa, the vulnerability of FXIII to hypochlorite-induced oxidation increased. FXIII oxidized with 150 μM hypochlorite completely retained its enzymatic activity inherent to the intact protein, whereas FXIIIa treated with 50 μM hypochlorite showed sharply reduced enzymatic activity. It was shown that a number of methionine and cysteine residues on the catalytic subunit can perform antioxidant function; additionally, the regulatory subunits of FXIII-B contribute to the antioxidant protection of the catalytic center of the FXIII-A subunit, which, together with the tight packing of the tetrameric structure of the FXIII proenzyme, are the three factors that provide high protein resistance to the oxidizing agent.

[Structure of Neuroglobin from Cold-Water Sponge Halisarca dujardinii]

The iron-containing protein neuroglobin (Ngb) involved in the transport of oxygen is generally considered the precursor of all animal globins. In this report, we studied the structure of Ngb of the cold-water sponge Halisarca dujardinii. In sponges, the oldest multicellular organisms, the Ngb gene contains three introns. In contrast to human Ngb, its promoter contains a TATA-box, rather than CG-rich motifs. In sponges, Ngb consists of 169 amino acids showing rather low similarity with its mammalian orthologues. It lacks Glu and Arg residues in positions required for prevention of hypoxia-related apoptosis. Nevertheless, Ngb contains both proximal and distal conserved heme-biding histidines. The primary structure of H. dujardinii neuroglobin predicted by sequencing was confirmed by mass-spectrometry analysis of recombinant Ngb expressed in E. coli. The high level of Ngb expression in sponge tissues suggests its possible involvement in the gas metabolism and presumably in other key metabolic processes in H. dujardinii.

Hypochlorite-Induced Damage of Plasminogen Molecules: Structural-Functional Disturbance

Plasminogen, the precursor of plasmin, is a serine protease that plays a fundamental role in the intravascular thrombolysis. For the first time, by using high-resolution mass spectrometry, data on the oxidative modifications of the plasminogen molecule under induced oxidation were obtained. The FTIR data show that, under oxidation on the protein, its secondary structure also undergoes the rearrangements. The high tolerance of plasminogen to oxidation can be due to both the closed conformation and the ability of some Met residues to serve as ROS trap.

The mechanism of the interaction of α-crystallin and UV-damaged βL-crystallin

α-Crystallin maintains the transparency of the lens by preventing the aggregation of damaged proteins. The aim of our work was to study the chaperone-like activity of native α-crystallin in near physiological conditions (temperature, ionic power, pH) using UV-damaged β_L-crystallin as the target protein. α-Crystallin in concentration depended manner inhibits the aggregation of UV-damaged β_L-crystallin. DSC investigation has shown that refolding of denatured UV-damaged β_L-crystallin was not observed under incubation with α-crystallin. α-Crystallin and UV-damaged β_L-crystallin form dynamic complexes with masses from 75 to several thousand kDa. The content of UV-damaged β_L-crystallin in such complexes increases with the mass of the complex. Complexes containing >10% of UV-damaged β_L-crystallin are prone to precipitation whereas those containing <10% of the target protein are relatively stable. Formation of a stable 75 kDa complex is indicative of α-crystallin dissociation. We suppose that α-crystallin dissociation is the result of an interaction of comparable amounts of the chaperone-like protein and the target protein. In the lens simultaneous damage of such amounts of protein, mainly β and gamma-crystallins, is impossible. The authors suggest that in the lens rare molecules of the damaged protein interact with undissociated oligomers of α-crystallin, and thus preventing aggregation.

Peroxide-Induced Oxidative Modification of Hemoglobin

The oxidative modification of human hemoglobin (Hb) treated with hydrogen peroxide was investigated. Using the mass spectrometry method, the oxidized amino acid residues of the hemoglobin molecule were detected: αTrp14, αTyr24, αArg31, αMet32, αTyr42, αHis45, αHis72, αMet76, αPro77, αLys90, αCys104, αTyr140, βHis2, βTrp15, βTrp37, βMet55, βCys93, βCys112, βTyr130, βLys144, and βHis146. The antioxidant potential of the Hb molecule in the intracellular space and in the blood plasma is discussed.

Peroxide-induced oxidative modification of hemoglobin

The oxidative modification of human hemoglobin Hb treated with ydrogen peroxide was investigated. The method of mass spectrometry were detected oxidized amino acid residues of the hemoglobin molecule: αTrp14, αTyr24, αArg31, αMet32, αTyr42, αHis45, αHis72, αMet76, αPro77, αLys90, αCys104, αTyr140, βHis2, βTrp15, βTrp37, βMet55, βCys93, βCys112, βTyr130, βLys144, βHis146. The antioxidant potential of the Hb molecule in the intracellular space and when it enters the blood plasma is discussed.

Evaluation of plasma peptides extraction methods by high-resolution mass spectrometry

Monitoring of peptides offers a promising approach for the discovery of novel biomarkers, which might be valuable for detection, treatment and prevention of large variety of diseases. Development of highly effective methods for plasma peptide extraction remains an important task. In the current study, we applied different types of plasma peptide extraction approaches to reveal efficient methods which would provide the highest peptide yield. We used different combinations of plasma treatment with acetonitrile and/or urea/guanidine, protein precipitation by acetone, gel-filtration, ultrafiltration, and two types of solid phase extraction. The extracted peptides were analyzed by LC-MS/MS. The obtained results suggest that several methods, including differential solubilization, organic precipitation, as well as some variants of ultrafiltration and solid phase extraction, provide effective plasma peptide enrichment convenient for further LC-MS/MS analysis. Alas, most of the identified peptides were extracted by only one of the applied methods. Hence, it seems reasonable to consider several methods to increase the possibility of novel biomarker discovery.

Oxidation-induced modification of the fibrinogen polypeptide chains

By using the mass-spectrometry method, the oxidative modifications of the fibrinogen Aα, Bβ, and γ polypeptide chains induced by its oxidation have been studied. The αC-region has been proven to be the most vulnerable target for the oxidizer (ozone) as compared with the other structural elements of the Aα chain. The Bβ chain mapping shows that the oxidative sites are localized within all the structural elements of the chain in which the β-nodule exhibits high susceptibility to oxidation. The γ chains are the least vulnerable to the oxidizer action. The results obtained demonstrate convincingly that the self-assembly centers dealing with interactions of knob "A": hole "a" are not involved in oxidative modification. It is concluded that the numerous oxidative sites revealed are mainly responsible for inhibiting lateral aggregation of protofibrils. The part of amino acid residues subjected to oxidation is supposed to carry out the antioxidant function.

Modification of the catalytic subunit of plasma fibrin-stabilizing factor under induced oxidation

For the first time, by using mass-spectrometry method, the oxidation-mediated modification of the catalytic FXIII-A subunit of plasma fibrin-stabilizing factor, pFXIII, has been studied. The oxidative sites were identified to belong to all structural elements of the catalytic subunit: the β-sandwich (Tyr104, Tyr117, and Cys153), the catalytic core domain (Met160, Trp165, Met266, Cys328, Asp352, Pro387, Arg409, Cys410, Tyr442, Met475, Met476, Tyr482, and Met500), the β-barrel 1 (Met596), and the β-barrel 2 (Met647, Pro676, Trp692, Cys696, and Met710), which correspond to 3.9%, 1.11%, 0.7%, and 3.2%, respectively, of oxidative modifications as compared to the detectable amounts of amino acid residues in each of the structural domains. Lack of information on some parts of the molecule may be associated with the spatial unavailability of residues, complicating analysis of the molecule. The absence of oxidative sites localized within crucial areas of the structural domains may be brought about by both the spatial inaccessibility of the oxidant to amino acid residues in the zymogen and the screening effect of the regulatory FXIII-B subunit.

[Determination of proteomic and metabolic composition of exhaled breath condensate of newborns]

Here, the possibility of proteomic and metabolomic analysis of the composition of exhaled breath condensate of neonates with respiratory support. The developed method allows non-invasive collecting sufficient amount of the material for identification of disease-specific biomarkers. Samples were collected by using a condensing device that was incorporated into the ventilation system. The collected condensate was analyzed by liquid chromatography coupled with high resolution mass spectrometry and tandem mass spectrometry. The isolated substances were identified with a use of databases for proteins and metabolites. As a result, a number of compounds that compose the exhaled breath condensate was determined and can be considered as possible biomarkers of newborn diseases or stage of development.

Exhaled breath condensate analysis from intubated newborns by nano-HPLC coupled to high resolution MS

Invasiveness of examination and therapy methods is a serious problem for intensive care and nursing of premature infants. Exhaled breath condensate (EBC) is the most attractive biofluid for non-invasive methods development in neonatology for monitoring the status of intubated infants. The aim of the study was to propose an approach for EBC sampling and analysis from mechanically ventilated neonates. EBC collection system with good reproducibility of sampling was demonstrated. Discovery-based proteomic and metabolomic studies were performed using nano-HPLC coupled to high resolution MS. Label-free semi-quantitative data were compared for intubated neonates with congenital pneumonia (12 infants) and left-sided congenital diaphragmatic hernia (12 infants) in order to define disease-specific features. Totally 119 proteins and 164 metabolites were found. A number of proteins and metabolites that can act as potential biomarkers of respiratory diseases were proposed and require further validation.

Proteomic Analysis of the Urine for Diagnostics in Newborns

Proteomic analysis of the urine was used for noninvasive diagnostics of abnormalities in newborns treated in the neonatal intensive care unit. This approach can be used to differentiate between infectious and noninfectious respiratory disorders.

[Endogenous content of the nitric oxide in the cell layers of the eye retina]

Nitric oxide is a universal molecule that regulates many different functions in an organism. In the eye retina nitric oxide plays both a regulatory role by modulation of the synaptic transmission between photoreceptors and bipolar cells and a toxic role in apoptosis induction in the outer nuclear layer and in the layer of ganglion cells. In this paper there has been made the first attempt to estimate the endogenous NO concentration in retina layers in vivo. The concentration of the nitric oxide was determined by two indepen- dent techniques: ESR spectrometry using spin trap for in vivo determination and NO-sensitive microelectrode for in situ determination in the survival isolated frog retina. The distinct NO con- centration was detected only in the ganglion cells layer (~0.25 μM) and in the inner segments layer of the photoreceptors (~0.6 μM). The activity and the kinetic characteristic of the NO-synthase localized in the same layers were also determined. Key words: retina cells layers, nitric oxide, ESR, NO-sensitive microelectrodes.

[Tear fluid proteome variability in healthy donors]

The variability of control samples is the main problem in clinical proteomics and reliable sources for estimation of variability of normal content of different proteins are not numerous. Most of the investigations of normal human tear proteome include pool of samples as reference materials. But it is impossible to use such experimental approach to establish the range of variability of different tear proteome components. This study is the first attempt to estimate the variability of proteins content in healthy donors tear using high-performance liquid chromatography and tandem mass spectrometry. The protein profiles from 11 individual healthy donors were analyzed. Essential variability of the minor proteins was revealed while the presence of 6 major proteins in all 11 samples was invariable. We found the Lacritin glycosylation in all samples of tear fluid received from healthy donors. It seems that this modification is typical for healthy donors tear. The analysis of the pool samples was also carried out to estimate the availability for this approach for the search of ophthalmologic diseases biomarkers.

Role of NO-synthase in regulation of protein metabolism of stretched rat m. soleus muscle during functional unloading

Gravitational unloading causes atrophy of muscle fibers and can lead to destruction of cytoskeletal and contractile proteins. Along with the atrophic changes, unloaded muscle frequently demonstrates significant shifts in the ratio of muscle fibers expressing fast and slow myosin heavy chain isoforms. Stretching of the m. soleus during hindlimb suspension prevents its atrophy. We supposed that neuronal NO-synthase (NOS) (which is attached to membrane dystrophin-sarcoglycan complex) can contribute to maintenance of protein metabolism in the muscle and prevent its atrophy when m. soleus is stretched. To test this hypothesis, we used Wistar rats (56 animals) in experiments with hindlimb suspension during 14 days. The group of hindlimb suspended rats with stretched m. soleus was injected with L-NAME to block NOS activity. We found that m. soleus mass and its protein content in hindlimb-suspended rats with stretched m. soleus were preserved due to prevention of protein degradation. NOS is involved in maintenance of expression of some muscle proteins. Proliferation of satellite cells in stretched m. soleus may be due to nNOS activity, but maintenance of muscle mass upon stretching is regulated not by NOS alone.

[Modification of the nitric oxide concentration regulates the development of the apoptosis in the eye retina]

Using model elaborated it was shown that the retinal ischemia initiated the development of the apoptosis in the inner layers of the retina. Administration of NOS inhibitor prevented the development of the apoptosis in the retina. To ascertain if nitric oxide could induce the retinal apoptosis by itself the nontoxic donor of nitric oxide (dinitrosyl iron complex) was injected intravitreally. Administration of DNIC in low concentrations induced the development of the apoptosis in the same retinal layers as in ischemia. The injection of dinitrosyl iron complex at the higher concentration resulted in the decrease of the apoptosis level. Administration of dinitrosyl iron complex with excess of glutathione didn't lead to the development of the retinal apoptosis. The obtained data demonstrates the neurotoxic properties of the excess of nitric oxide in the retina.

[Nitrites can be reduced in retinal vessels during hypoxia and protect the retina against ischemia and apoptosis]

The possibility and the mechanism of the reduction of nitrites in retinal vessels under the acute hypoxia in vivo have been investigated. An experimental model of the rat retina ischemia was elaborated using the laser coagulation of retinal vessels. It was demonstrated that the vessel thrombosis does not occur if the nitrite concentration in the vessels is increased. It was proposed that, under acute hypoxia, nitrites are reduced to NO, which results in a drastic vasodilatation. Considering that the effect takes less than a minute, this reduction cannot be due to hypoxic acidosis but is more likely associated with NO reduction by heme proteins. It was found that the increased concentration of nitrites protects the retina from the development of ischemia progress and that the preliminary administration of nitrites prevents apoptosis in the retina and a decrease in its photoelectric activity.

[Protective effect of nitric oxide on cytoskeletal proteins in skeletal muscles under eccentric exercise]

The protective effect of nitric oxide (NO) on the cytoskeletal muscle proteins desmin and dystrophin has been studied under eccentric exercise. Experiments were performed on 28 male Wistar rats, which were divided into four groups: cage control (C, n = 7); group of eccentric exercise (running down a motor-driven treadmill, inclination 16 degrees) (20 m/min, 40 min running) (R, n = 7); eccentric exercise + L-arginine group (RA, n = 7) (with a daily supplementation of 500 mg/kg wt L-arginine for 3 days before the running); and eccentric exercise + L-NAME group (RN, n = 7) (with a daily supplementation of 90 mg/kg wt L-NAME (Nomega-nitro-L-arginine methyl ester, nNOS blocker) for 3 days before the running). It was found that increasing the NO concentration (in RA group) prevents the disruption of the dystrophin layer and decreases the loss of desmin in m. soleus under eccentric contraction, whereas in the R and RN groups the level of damage to dystrophin and desmin was significantly higher compared to the control rats. The inhibition of nNOS (by L-NAME) increases the nNOS mRNA level in the m. soleus, whereas increasing the NO concentration in m. soleus (L-arginine administration) does not affect the level of nNOS mRNA during the eccentric running. It was concluded that NO has a protective action on the cytoskeletal proteins desmin and dystrophin in skeletal muscle under eccentric contraction-induced damage.

The relation between sphingomyelinase activity, lipid peroxide oxidation and NO-releasing in mice liver and brain

We used animal models to study connection between oxidating system and sphingomyelin signaling cascade, because this models are more close related to people disease. Activation of n-sphingomyelinase (n-SMase) in mice liver and brain is coincided in time with increased level of peroxide products (conjugated dienes) after injection of tumor necrosis factor alpha (TNF-alpha). We found that ceramide can induce peroxide oxidation and lead to accumulation of TNF-alpha in animal organs. Nitric oxide (NO) donors (S-nitrosoglutathione and dinitrosyl iron complex) reversibly inhibited activity of n-SMase and decreased level of lipid peroxidation products. This data proposed that both SMase and messengers of oxidative systems could be targets for NO-derived oxidants.

Connection of lipid peroxide oxidation with the sphingomyelin pathway in the development of Alzheimer's disease

Alzheimer's disease (AD) is characterized by progressive decline in cognition, memory and intellect. It has been hypothesized that amyloid-beta peptide (A-beta) may have a prominent role in neurodegeneration. Oxidative mechanisms have been implicated in this pathway. There is substantial evidence that inflammatory mechanisms, induced by tumour necrosis factor alpha (TNF-alpha), are also involved in AD. TNF-alpha activates receptors linked to multiple effector systems, including a sphingomyelin pathway and peroxide oxidation. We have determined the changes of neutral sphingomyelinase activity, sphingomyelin and ceramide contents, and the level of lipid peroxide products (conjugated dienes), in the cerebral cortex, hippocampus and cerebellum of rats within 3 h and 7 days of intracerebral injection of A-beta and TNF-alpha. A single injection of A-beta and TNF-alpha has been shown to increase the level of peroxide products in the hippocampus and cerebral cortex within 3 h and 7 days. Sphingomyelinase activity and ceramide levels have been found to increase 7 days after A-beta administration. We found that activation of the sphingomyelin pathway lies downstream from the oxidative stress.