[Lipidomic markers of breast cancer malignant tumor histological types]. / Lipidomnye markery gistologicheskikh tipov zlokachestvennoi opukholi molochnoi zhelezy.

The molecular profile of a tumor is associated with its histological type and can be used both to study the mechanisms of tumor progression and to diagnose it. In this work, changes in the lipid profile of a malignant breast tumor and the adjacent tissue were studied. The potential possibility of determining the histological type of the tumor by its lipid profile was evaluated. Lipid profiling was performed by reverse-phase chromato-mass-spectrometric analysis the tissue of lipid extract with identification of lipids by characteristic fragments. Potential lipid markers of the histological type of tumor were determined using the Kruskal-Wallis test. Impact of lipid markers was calculated by MetaboAnalyst. Classification models were built by support vector machines with linear kernel and 1-vs-1 architecture. Models were validated by leave-one out cross-validation. Accuracy of models based on microenvironment tissue, were 99% and 75%, accuracy of models, based on tumor tissue, were 90% and 40% for the positive ion mode and negative ion mode respectively. The lipid profile of marginal (adjacent) tissue can be used for identification histological types of breast cancer. Glycerophospholipid metabolism pathway changes were statistically significant in the adjacent tissue and tumor tissue.

[Prognostic ability of seminal plasma lipidomic analysis in predicting the success of microTESE in men with azoospermia].

INTRODUCTION: The aim of this work is to assess the possibility of metabolomic (specifically lipidomic) analysis of seminal plasma to identify patients with preserved focal spermatogenesis in the testes who may have a reasonable chance of sperm retrieval during the microTESE procedure. MATERIALS AND METHODS: lipid composition of semen plasma samples from 64 men with azoospermia and 24 fertile control men was analyzed. Lipids were isolated from semen by a modified Folch extraction method. Lipid extracts were analyzed by reverse phase liquid chromatography coupled to mass spectrometry. Lipidomic data were compared with the results of the microTESE procedure. RESULTS: Comparison of two groups revealed a statistically significant difference in concentration for 23 lipids detected in positive ion mode and 37 lipids detected in negative ion mode. Those lipids mainly belong to hexosylceramides, sphingomyelins and phosphatidylcholines, phosphatidylethanolamines and their ethers. In multivariate analysis content of SM d16: 1/18:0 lipid (beta coefficient: -7.23; 95% confidence interval [95% CI]: -11.93 to - 2.53; odds ratio: 7.23e-04; CI for odds ratio: 6.59e-06 to 7.93e-02; Walds test: -3.02; p=0.003), content of TG 14: 1_16 : 0_18: 3 lipid (beta 2.95; 95% CI 0.98 to 4.93; odds ratio: 1.92e + 01; CI for odds ratio: 2.66e + 00 to 1.39e + 02 ; Walds test: 2.93; p=0.003) and testicular volume (beta: 0.14; 95% CI: 0.04 to 2.45; odds ratio: 1.15e + 00; CI odds ratio: from 1.04e + 00 to 1.27e + 00; Walds test: 2.65; p=0.008) were significantly associated with positive MicroTESE outcome. The sensitivity of this regression model was 61%, the specificity was 83%, and the AUC was 0.75. CONCLUSIONS: seminal plasma serves as a rich source of biological markers for identifying patients with preserved focal spermatogenesis in the testes. Seminal plasma lipidomic profile of the of patients in the control group with normal spermatogenesis clearly differs from the profile of patients with azoospermia, also there was a significant difference in content of a difference in lipids between patients with positive and negative microTESE outcomes. These are preliminary results and further research is needed to confirm the validity of the resulting lipid panel.

Lipid Alterations in Early-Stage High-Grade Serous Ovarian Cancer.

Epithelial ovarian cancer (OC) ranks first in the number of deaths among diseases of the female reproductive organs. Identification of OC at early stages is highly beneficial for the treatment but is highly challenging due to the asymptomatic or low-symptom disease development. In this study, lipid extracts of venous blood samples from 41 female volunteers, including 28 therapy-naive patients with histologically verified high-grade serous ovarian cancer at different stages (5 patients with I-II stages; 23 patients with III-IV stages) and 13 apparently healthy women of reproductive age, were profiled by high-performance liquid chromatography mass spectrometry (HPLC-MS). Based on MS signals of 128 differential lipid species with statistically significant level variation between the OC patients and control group, an OPLS-DA model was developed for the recognition of OC with 100% sensitivity and specificity R 2 = 0.87 and Q2 = 0.80. The second OPLS-DA model was developed for the differentiation between I-II OC stages and control group with R 2 = 0.97 and Q2 = 0.86 based on the signal levels of 108 differential lipid species. The third OPLS-DA model was developed for the differentiation between I-II OC stages and III-IV stages based on the signal levels of 99 differential lipid species. Various lipid classes (diglycerides, triglycerides, phosphatidylchlorines, ethanolamines, sphingomyelins, ceramides, phosphatidylcholines and phosphoinositols) in blood plasma samples display distinctly characteristic profiles in I-II OC, which indicates the possibility of their use as marker oncolipids in diagnostic molecular panels of early OC stages. Our results suggest that lipid profiling by HPLC-MS can improve identification of early-stage OC and thus increase the efficiency of treatment.

[Lipidomic markers of tumor progress in breast cancer patients]. / Lipidomnye markery opukholevoi progressii u bol'nykh rakom molochnoi zhelezy.

Research of cancer progression mechanisms and their impact on metabolism of tumor cells and tumor microenvironment cells is an important element in drug development for cancer target therapy. In this study, changes in tumor tissue and margin tissue lipid profiles, were associated with the following clinical and morphological characteristics: tumor size, cancer stage, multifocalite, tumor grade, number of lymph node metastasis, Nottingham prognostic index, total malignancy score, level of Ki67 protein. Lipid profiling was performed by reverse-phase chromato-mass spectrometry analysis of lipid tissue extract with lipid identification by characteristic fragments. In the lipid profile of tumor tissue 13 characteristic lipids were selected. Their levels significantly correlated with at least 5 clinical and morphological features. Eight of 13 belonged to phosphatidylcholines. In lipid profile of tumor microenviroment tissue 13 lipid features were selected. Their levels significantly correlated with at least 5 clinical and morphological features. Four of 13 belonged to oxidized lipids, 4 lipid features belonged to sphingomyelins, four of 13 belonged to phosphatidylethanolamines. The tumor microenvironment tissue lipid profile correlated with tumor size, cancer stage, tumor grade, number of axillary metastases, Nottingham prognostic index. The tumor tissue lipid profile correlated with tumor size, tumor grade, total malignant score, and number of axillary metastases.

[Analysis of metabolic pathways in intrauterine growth restriction]. / Analiz metabolicheskikh putei pri zaderzhke rosta ploda.

Objective was to analyze metabolic pathways based on a study of the metabolomic profile of pregnant women with intrauterine growth restriction. The metabolic profile of pregnant women with fetal growth restriction has been analyzed using liquid chromatography-mass spectrometry. At the second stage pathways were identified using SMPDB and MetaboAnalyst databases to clarify the relationship between metabolites. Biological networks allow to determine the effect of proteins on the metabolic pathways involved in pathogenesis of IUGR and determine the epigenetic mechanisms of its formation.

[Comparative Analysis of the Performance of Mascot and IdentiPy Algorithms on a Benchmark Dataset Obtained by Tandem Mass Spectrometry Analysis of Testicular Biopsies].

Proteome profiling of human testicular biopsies was performed using tandem mass spectrometry with electrospray ionization. Protein identification results were compared for the Mascot commercial search engine, the SearchGUI noncommercial package, and their analog IdentiProt based on the open-source IdentiPy algorithm (http://hg.theorchromo.ru/identipy). A feature of IdentiPy is an automatic optimization of MS/MS search parameters. A set of protein identifications obtained with IdentiPy was consequently greater by one third than the sets with the other search engines. For the first time, an IdentiPy/IdentiProt search was conducted within the Progenesis LC-MS framework, which allows spectrum alignment, and the proteome profile obtained with alignment was compared with that obtained using the ProteoWizard converter. A total of 16 human chromosome 18 proteins were identified, including the myelin basic protein, which is not characteristic of testicular tissue.

[Features of the urine peptidome under the condition of hypertensive pathologies of pregnancy]. / Osobennosti peptidoma mochi pri gipertenzivnykh patologiiakh beremennykh.

In order to find a peptide panel to differentiate close hypertensive conditions a case-control study was designed for 64 women from 4 groups: preeclampsia (PE), chronic hypertension superimposed with PE, chronic hypertension, and healthy individuals. Chromatography coupled with mass-spectrometry and subsequent bioinformatic analysis showed several patterns in the changes of the urine peptidome. There were 36 peptides common for four groups. Twenty two of them 22 belonged to alpha-1-chain of collagen I, nine peptides were from alpha-1-chain of collagen III, two from alpha-2-chain of collagen I, one from alpha-1/2-chain of collagen I, one from alpha-1-chain of collagen I/XVIII and one from uromodulin. Patients with hypertensive disorders had 34 common peptides: 12 from alpha-1-chain of collagen I, 10 from fibrinogen alpha-chain, eight from alpha-1-chain of collagen III, and 4 per other types of collagen. Comparative analysis revealed 12 peptides, which could be used as a diagnostic panel for confident discrimination of pregnant women with various hypertensive disorders.

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.

[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.

Studying the Proteomic Composition of Expired Air Condensate in Newborns on Breathing Support.

This study was designed to collect and perform a proteomic analysis of expired air condensate in newborns receiving respiratory support at the Department of Resuscitation and Intensive Care. The proteomic composition of expired air condensate was evaluated in newborns at various stages of development and with different abnormalities.

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.

An untargeted approach for the analysis of the urine peptidome of women with preeclampsia.

Preeclampsia (PE) is a pregnancy complication characterized by high blood pressure and proteinuria. The disorder usually occurs after the 20th week of pregnancy and gets worse over time. PE increases the risk of poor outcomes for both the mother and the baby. In the study we applied LC-MS/MS method for the analysis of the urine peptidome of women with PE. Samples were prepared using size-exclusion chromatography method which gives more than twice peptides identities if compared with solid phase extraction. Thirty urine samples from women with mild and severe preeclampsia and the control group were analyzed. In total 1786 peptides were identified using complementary search engines (Mascot, MaxQuant and PEAKS). A high level of agreement in peptide identification was observed with previously published data. Label-free data comparison resulted in 35 peptides which reliably distinguished a particular PE group (severe or mild) from controls. Our results revealed unique identifications (correlate to alpha-1-antitrypsin, collagen alpha-1(I) chain, collagen alpha-1 (III) chain, and uromodulin, for instance) that can potentially serve as early indicators of PE.

Probing the mechanisms of ambient ionization by laser-induced fluorescence spectroscopy.

The ionization mechanisms of several atmospheric pressure ion sources based on desorption and ionization of samples deposited on a surface were studied. Home-built desorption electrospray ionization (DESI), laserspray ionization (LSI), and atmospheric pressure matrix-assisted laser desorption/ionization (AP-MALDI) sources were characterized using low-molecular-weight compounds, in particular fluorescent dyes. Detection of the desorbed and ionized species was performed by laser-induced fluorescence and ion cyclotron resonance mass spectrometry. The dependences of the signal intensities on various experimental parameters were studied. The data obtained reveals common features, such as formation of solvated species and clusters in the ionization processes, in all of the techniques considered.

[Proteomic analysis of heart mitochondria from Bos taurus. I. Application of proteomics methods to identification of transmembrane domains of proteins of the internal mitochondrial membrane].

This study is part of a large-scale investigation of the proteome of mitochondria from the heart muscle of Bos taurus. We developed a special approach to simplification of the protein mixture by separation of mitochondrial fractions with stable protein compositions. At the first stage of this approach, we isolated and purified internal mitochondrial membranes. The protein composition of this fraction was analyzed by the following proteomic methods: enzymatic or/and chemical cleavage of the proteins, chromatographic fractionation of the complex mixture of the resulting peptides, mass-spectrometric identification of these peptides, and a search for proteins in databases of amino acid sequences. We reliably identified 147 unique proteins with the use of the SwissProt database. The subcellular location and functions of these proteins were analyzed. Approaches to studies of transmembrane domains of integral membrane proteins of the internal mitochondrial membrane were proposed on the basis of proteomic methods of analysis. Considerable coincidence of the experimental data with the results of determination of the 3D structures of the proteins by X-ray analysis was shown.

Identification of polymers as major components of atmospheric organic aerosols.

Results from photooxidation of aromatic compounds in a reaction chamber show that a substantial fraction of the organic aerosol mass is composed of polymers. This polymerization results from reactions of carbonyls and their hydrates. After aging for more than 20 hours, about 50% of the particle mass consists of polymers with a molecular mass up to 1000 daltons. This results in a lower volatility of this secondary organic aerosol and a higher aerosol yield than a model using vapor pressures of individual organic species would predict.

Deceleration of high-energy matrix-assisted laser desorption/ionization ions in an open cell for Fourier transform ion cyclotron resonance mass spectrometry.

A new method of ion deceleration in a Fourier transform ion cyclotron resonance (FTICR) open cell is described that improves the performance of FTICR-MS instruments equipped with an internal source for laser desorption/ionization. Ion deceleration occurs in the front trapping cylinder of an open cylindrical cell. Decelerating voltages up to 100 V can be applied for 10-500 micros to the front cylinder during ion introduction. The deceleration field is uniformly distributed along the cylinder length giving a "smooth" deceleration, which means that the deceleration is effective over a large time interval and a large m/z range. This results in improved trapping efficiency of high-energy ions. We demonstrate efficient trapping of high (m/z 66 kDa) mass ions and the possibility to reduce the width of the kinetic energy distribution of MALDI ions with this arrangement.

Broad-band fourier transform quadrupole ion trap mass spectrometry.

Broad-band nondestructive ion detection is achieved in a quadrupole ion trap mass spectrometer by impulsive excitation of a collection of trapped ions of different masses and recording of ion image currents induced on a small detector electrode embedded in but isolated from the adjacent end cap electrode. The image currents are directly measured using a simple differential preamplifier, filter, and amplifier combination and then Fourier analyzed to obtain broad-band frequency domain spectra characteristic of the sample ions. The use of the detector electrode provides a significant reduction in capacitive coupling with the ring electrode. This minimizes coupling of the rf drive signal, which can saturate the front-end stage of the detection circuit and prevent measurement of the relatively weaker ion image currents. Although impulsive excitation is preferred due to its broad-band characteristics and simplicity of use, results are also given for narrow-band ac and broad-band SWIFT (stored wave-form inverse Fourier transform) excitation. Data using argon, acetophenone, and n-butylbenzene show that a resolution of better than 1000 is obtained with a detection bandwidth of 400 kHz. An advantage of nondestructive ion detection is the ability to measure a single-ion population multiple times. This is demonstrated using argon as the sample gas with an average remeasurement efficiency of >90%. Tandem mass spectrometry experiments using a population of acetophenone ions are also shown.