СРАВНИТЕЛЬНЫЙ ПРОТЕОМНЫЙ АНАЛИЗ КОНДЕНСАТА ВЫДЫХАЕМОГО ВОЗДУХА У ПАЦИЕНТОВ С РАКОМ ЛЕГКОГО МЕТОДОМ МАСС-СПЕКТРОМЕТРИИ ВЫСОКОГО РАЗРЕШЕНИЯ

Analysis of exhaled breath condensate (EBC) is a promising non-invasive method to diagnose respiratory diseases. Most researchers emphasize the importance of proteomic analysis of EBC for early diagnosis of certain respiratory diseases including lung cancer. This study was aimed at identification of potential biomarkers of neoplastic disorders in EBC of patients with lung cancer using high-performance liquid chromatography and high resolution mass-spectrometry. The study involved 26 patients with lung carcinoma (21 males, 5 females, mean age 57 ± 12 years) and 23 healthy non-smokers (19 males, 4 females, mean age 30 ± 7 years). EBC samples were collected using a disposable portable condenser R-Tube. The most of proteins identified (65 %) belonged to keratin family including type 1 (1; 2; 5 and 6А) and type 2 (9; 10; 14; 16 and 17) cytoskeletal keratins and transport proteins (albumin, lipocalin-1). Keratin family proteins (5, 6 and 14) prevailed in lung cancer patients compared to controls (p < 0.05). Other 6 proteins were also detected predominantly in lung cancer patients including b-subunit and a-subunit of haemoglobin, nuclear ubiquitous casein (NUCKS), high-mobility group proteins (HMG-I/HMG-Y), and lactoferrin. Most of these proteins could be used as a diagnostic panel to detect lung cancer. Further investigations are needed to estimate diagnostic values of these biomarkers and their role in pathogenesis of lung cancer.Анализ конденсата выдыхаемого воздуха (КВВ) является перспективным неинвазивным методом оценки состояния дыхательной системы. Многие исследователи указывают на важность анализа протеома КВВ для раннего выявления заболеваний респираторного тракта, в т. ч. диагностики рака легкого (РЛ). В исследовании, в которое были включены 2 группы доноров: основная – больные РЛ (n = 26; 21 мужчина, 5 женщин; средний возраст – 56,5 ± 11,5 года) и контрольная (n = 23; 19 мужчин, 4 женщины; средний возраст – 30,0 ± 7,0 года) – здоровые некурящие добровольцы, у больных РЛ методом высокоэффективной жидкостной хроматографии и тандемной масс-спектрометрии была проведена идентификация потенциальных белков-онкомаркеров в КВВ. Образцы КВВ были собраны с помощью одноразового портативного конденсора R-Tube. Основную часть (65 %)  идентифицированных белков составили белки кератиновой группы, в т. ч. кератины цитоскелетные 1-го (1, 2, 5 и 6А) и 2-го (9, 10, 14, 16 и 17) типов, а также группа транспортных белков (альбумин, липокалин-1). Было показано, что группа кератинов (5, 6 и 14) более значительно выражена (р < 0,05) у онкологических больных по сравнению со здоровым контролем. Также 6 белков были преимущественно определены в КВВ доноров основной группы, в т. ч. b- и a-субъединицы гемоглобина, ядерный убиквитиновый казеин (NUCKS), белки группы высокой мобильности (HMG-I/HMG-Y), лактоферрин. Большинство выявленных белков может быть предложено в качестве панели для диагностики РЛ. Однако необходимы дальнейшие исследования для определения диагностической значимости предложенных биомаркеров и их роли в патогенезе РЛ

Tandemly repeated DNA families in the mouse genome

<p>Abstract</p> <p>Background</p> <p>Functional and morphological studies of tandem DNA repeats, that combine high portion of most genomes, are mostly limited due to the incomplete characterization of these genome elements. We report here a genome wide analysis of the large tandem repeats (TR) found in the mouse genome assemblies.</p> <p>Results</p> <p>Using a bioinformatics approach, we identified large TR with array size more than 3 kb in two mouse whole genome shotgun (WGS) assemblies. Large TR were classified based on sequence similarity, chromosome position, monomer length, array variability, and GC content; we identified four superfamilies, eight families, and 62 subfamilies - including 60 not previously described. 1) The superfamily of centromeric minor satellite is only found in the unassembled part of the reference genome. 2) The pericentromeric major satellite is the most abundant superfamily and reveals high order repeat structure. 3) Transposable elements related superfamily contains two families. 4) The superfamily of heterogeneous tandem repeats includes four families. One family is found only in the WGS, while two families represent tandem repeats with either single or multi locus location. Despite multi locus location, TRPC-21A-MM is placed into a separated family due to its abundance, strictly pericentromeric location, and resemblance to big human satellites.</p> <p>To confirm our data, we next performed <it>in situ </it>hybridization with three repeats from distinct families. TRPC-21A-MM probe hybridized to chromosomes 3 and 17, multi locus TR-22A-MM probe hybridized to ten chromosomes, and single locus TR-54B-MM probe hybridized with the long loops that emerge from chromosome ends. In addition to <it>in silico </it>predicted several extra-chromosomes were positive for TR by <it>in situ </it>analysis, potentially indicating inaccurate genome assembly of the heterochromatic genome regions.</p> <p>Conclusions</p> <p>Chromosome-specific TR had been predicted for mouse but no reliable cytogenetic probes were available before. We report new analysis that identified <it>in silico </it>and confirmed <it>in situ </it>3/17 chromosome-specific probe TRPC-21-MM. Thus, the new classification had proven to be useful tool for continuation of genome study, while annotated TR can be the valuable source of cytogenetic probes for chromosome recognition.</p