Integrated teaching and software computer laboratory for the disciplines of svch@kr department

Описывается учебно-методическое и программное обеспечение компьютерных лабораторных практикумов, разработанных на базе следующих систем: в системе моделирования <pLabs на базе комплекса EduCAD; в Borland C++; на базе системы Sydney; в среде объектного программирования Delphi 5.Describes a teaching software and computer laboratory exercises, developed on the basis of the following systems: system modeling (pLabs based on complex EduCAD; in Borland C++; on the basis of Sydney; object programming environment in Delphi 5

Прогностическая роль экспрессии маркера PBRM1 при светлоклеточном раке почки

Background. Clear-cell renal-cell carcinoma (CCRCC) is the most common histological type of cancer of this localization. Changes in 16 genes were identified as significant in carcinogenesis of CCRCC. After VHL suppressor gene, PBRM1 gene is the second by frequency of genetic abnormalities in CCRCC and it is mutated in 40—50 % cases of CCRCC.The study objectiveis to analyze the effect of abnormalities in PBRM1 protein expression on survival of patients with CCRCC.Materials and methods. The study included 137patients with newly diagnosed and histologically confirmed CCRCC. For all study participant, detailed medical history and questionnaire data were acquired. Prior to treatment, blood samples and tumor tissue removed during surgery were obtainedfrom all patients. All patients are annually followed up for current information on their life status, disease dynamics, treatment. Minimalfollow-up time is 22 months, maximal is 128 months, mean is 61.8 months, median is 48 months. Immunohistochemical (IHC) testing of PBRM1 expression was performed using standard technique with polyclonal rabbit antibodies PB1[N1N2] N-term (GeneTex 100781) with 1:50 dilution, DAB staining. Normally, protein product of the wild type PBRM1 gene is functioning and can be detected in the nucleus. Absence of nuclear expression of PBRM1 points to genetic or epigenetic abnormalities.Results.Renal cancer-specific survival is significantly lower in patients without expression of the PRBM1 protein in tumor cells. The longest 5- (84 %) and 10-year (84 %) survival was observed in patients with diffuse nuclear expression of the PBRM1 protein. Difference in survival of these patients compared to patients without PRBM1 protein expression is statistically significant (p = 0.004). We have performed an analysis of the association between survival of patients with CCRCC andfocal nuclear PBRM1 expression. In these patients, survival is lower than in patients with diffuse expression but higher than in patients without nuclear expression of PBRM1 (p = 0.02). Cytoplasmic expression of PBRM1 doesn’t affect survival.Conclusion.The obtained results point to prognostic value of PBRM1 gene activity which is abnormal in almost half of all CCRCC cases. IHC testing is an appropriate, reliable and affordable method for determination of PBRM1 protein expression and therefore can be used in practice. Favorable course and prognosis in patients with stage I—II CCRCC and preserved nuclear expression of the PBRM1 protein should be noted: 5-year survival for these patients is 100 %. This observation is crucial for making decisions on treatment of these patients.Введение. Светлоклеточный почечно-клеточный рак (скПКР) является наиболее частым гистологическим типом рака этой локализации. Выделяют 16 генов, нарушения которых играют значительную роль в канцерогенезе скПКР. Вторым по частоте генетических нарушений в скПКР после гена-супрессора VHL является ген PBRM1, который мутирует в 40—50 % случаев скПКР.Цель исследования — анализ влияния нарушений экспрессии белка PBRM1 на выживаемость пациентов со скПКР.Материалы и методы. В исследование были включены 137пациентов с впервые выявленным и гистологически верифицированным диагнозом скПКР. Для каждого участника исследования были собраны детальная медицинская информация и данные анкетирования. От всех больных до начала лечения были получены образцы крови и удаленной во время хирургической операции опухолевой ткани. Все пациенты ежегодно прослеживаются в целях получения актуальной информации об их жизненном статусе, динамике заболевания, лечении. Минимальное время прослеживания — 22мес, максимальное — 128мес, среднее — 61,8мес, медиана — 48мес. Иммуногистохимическое (ИГХ) исследование экспрессии PBRM1 было выполнено по стандартной методике c поликлональными кроличьими антителами PB1[N1N2] N-term (GeneTex 100781) в разведении 1:50, проявление проводилось с использованием DAB. Белковый продукт гена PBRM1 дикого типа в норме функционирует и выявляется в ядре. Отсутствие ядерной экспрессии PBRM1 указывает на генетические или эпигенетические нарушения.Результаты. Специфическая для рака почки выживаемость статистически достоверно ниже у больных, в опухолевых клетках которых нет экспрессии белка PRBM1. Наилучшая 5- (84 %) и 10-летняя (84 %) выживаемость отмечена у больных с диф­фузной ядерной экспрессией белка PBRM1. Различия в выживаемости этих больных и тех, у которых нет экспрессии белка PBRM1, статистически высоко достоверны (р = 0,004). Нами впервые проведен анализ выживаемости больных скПКР с фо­кальной ядерной экспрессией PBRM1. У этих пациентов выживаемость ниже, чем у больных с диффузной экспрессией, но выше, чем у больных с отсутствием ядерной экспрессии PBRM1 (р = 0,02). Цитоплазматическая экспрессия PBRM1 на выживаемость не влияет.Заключение. Таким образом, полученные нами результаты указывают на прогностическую значимость активности гена PBRM1, нарушение функции которого встречается почти в половине случаев скПКР. ИГХ-исследование является адекватным, надежным и доступным методом для определения экспрессии белка PBRM1 и, соответственно, может применяться на практике. Особен­но следует отметить благоприятное течение и прогноз болезни у пациентов с I—II стадиями скПКР, у которых сохранена ядер­ная экспрессия белка PBRM1: 5-летняя выживаемость у них составляет 100 %. Это наблюдение крайне важно для принятия решения по тактике лечения таких больных

Спектр мутаций гена VHL при спорадическом светлоклеточном почечно-клеточном раке

The VHL gene alterations are the early and characteristic feature of clear cell renal cell carcinoma (ccRCC). We have examined VHL mutations in sporadic 98 ccRCC cases to evaluate their localization in relation to functionally important motifs of the VHL protein. The DNA samples were obtained from snap-frozen carcinoma biopsies and used for Sanger sequencing, while 62 ccRCC DNA cases were studied by next generation sequencing (NGS) analysis in parallel. In 73 (74.4 %) оf 98 ccRCC cases the somatic non-silent VHL mutations were identified. Loss of function VHL mutations (nonsilent, frameshifts or in splicing sites) were detected in 40 (40.8 %) ccRCC, while missense mutations – in 35 (35.7 %) ccRCC. In total 76 mutations important for VHL functioning were detected in 72 (73 %) ccRCC samples, of them 15 mutations (deletion / insertion in-frame or frameshifts) were identified for the first time. Four ccRCC cases contained two mutations each. Most of missense mutations disturb the sites of VHL interactions with HIF, РКС or kinesin. The pathogenicity of p.P154P silent mutation and intronic mutations near mRNA VHL splicing sites was discussed. The obtained results are important for understanding the role of VHL mutations in ccRCC progression and prognosis.Нарушения гена VHL являются ранней и характерной особенностью светлоклеточного почечно-клеточного рака (скПКР). Проведен анализ мутаций VHL в 98 образцах скПКР для определения их локализации относительно функционально значимых мотивов белка VHL. Анализ мутаций VHL проводили в ДНК из свежезамороженных тканей опухоли секвенированием по Сэнгеру, параллельно 62 образца скПКР подвергли cеквенированию нового поколения (next generation sequencing, NGS). В 73 (74,4 %) из 98 образцов скПКР обнаружены нон-сайлент-мутации в кодирующей части гена VHL. Мутации, нарушающие функции белка VHL (нонсенс-мутации, мутации в сайтах сплайсинга и делеции / инсерции со сдвигом рамки считывания), выявлены в 40 (40,8 %) образцах скПКР, миссенс-мутации – в 35 (35,7 %). Всего обнаружено 76 мутаций, влияющих на функции белка VHL в 72 (73 %) образцах скПКР, причем 15 мутаций не были описаны ранее (делеции / инсерции VHL со сдвигом или без сдвига рамки считывания). В 4 случаях скПКР выявлено по 2 мутации VHL. Большинство миссенс-мутаций нарушают сайты взаимодействия белка VHL с HIF, РKС или кинезином. Рассмотрен вопрос о патогенности сайлент-мутации p.P154P и мутаций в интронах вблизи сайтов сплайсинга. Полученные результаты важны для изучения роли мутаций VHL в прогрессировании и прогнозе скПКР

Joint effects of intensity and duration of cigarette smoking on the risk of head and neck cancer: A bivariate spline model approach

Objectives: This study aimed at re-evaluating the strength and shape of the dose-response relationship between the combined (or joint) effect of intensity and duration of cigarette smoking and the risk of head and neck cancer (HNC). We explored this issue considering bivariate spline models, where smoking intensity and duration were treated as interacting continuous exposures. Materials and Methods: We pooled individual-level data from 33 case-control studies (18,260 HNC cases and 29,844 controls) participating in the International Head and Neck Cancer Epidemiology (INHANCE) consortium. In bivariate regression spline models, exposures to cigarette smoking intensity and duration (compared with never smokers) were modeled as a linear piecewise function within a logistic regression also including potential confounders. We jointly estimated the optimal knot locations and regression parameters within the Bayesian framework. Results: For oral-cavity/pharyngeal (OCP) cancers, an odds ratio (OR) &gt;5 was reached after 30 years in current smokers of ∼20 or more cigarettes/day. Patterns of OCP cancer risk in current smokers differed across strata of alcohol intensity. For laryngeal cancer, ORs &gt;20 were found for current smokers of ≥20 cigarettes/day for ≥30 years. In former smokers who quit ≥10 years ago, the ORs were approximately halved for OCP cancers, and ∼1/3 for laryngeal cancer, as compared to the same levels of intensity and duration in current smokers. Conclusion: Referring to bivariate spline models, this study better quantified the joint effect of intensity and duration of cigarette smoking on HNC risk, further stressing the need of smoking cessation policies

Transoral laser microsurgery for laryngeal cancer: A primer and review of laser dosimetry

Transoral laser microsurgery (TLM) is an emerging technique for the management of laryngeal and other head and neck malignancies. It is increasingly being used in place of traditional open surgery because of lower morbidity and improved organ preservation. Since the surgery is performed from the inside working outward as opposed to working from the outside in, there is less damage to the supporting structures that lie external to the tumor. Coupling the laser to a micromanipulator and a microscope allows precise tissue cutting and hemostasis; thereby improving visualization and precise ablation. The basic approach and principles of performing TLM, the devices currently in use, and the associated dosimetry parameters will be discussed. The benefits of using TLM over conventional surgery, common complications and the different settings used depending on the location of the tumor will also be discussed. Although the CO2 laser is the most versatile and the best-suited laser for TLM applications, a variety of lasers and different parameters are used in the treatment of laryngeal cancer. Improved instrumentation has lead to an increased utilization of TLM by head and neck cancer surgeons and has resulted in improved outcomes. Laser energy levels and spot size are adjusted to vary the precision of cutting and amount of hemostasis obtained

Risk factors for head and neck cancer in more and less developed countries: Analysis from the INHANCE consortium

Objective: We analyzed the pooled case-control data from the International Head and Neck Cancer Epidemiology (INHANCE) consortium to compare cigarette smoking and alcohol consumption risk factors for head and neck cancer between less developed and more developed countries. Subjects and Methods: The location of each study was categorized as either a less developed or more developed country. We compared the risk of overall head and neck cancer and cancer of specific anatomic subsites associated with cigarette smoking and alcohol consumption. Additionally, age and sex distribution between categories was compared. Results: The odds ratios for head and neck cancer sites associated with smoking duration differed between less developed and more developed countries. Smoking greater than 20&nbsp;years conferred a higher risk for oral cavity and laryngeal cancer in more developed countries, whereas the risk was greater for oropharynx and hypopharynx cancer in less developed countries. Alcohol consumed for more than 20&nbsp;years conferred a higher risk for oropharynx, hypopharynx, and larynx cancer in less developed countries. The proportion of cases that were young (&lt;45&nbsp;years) or female differed by country type for some HNC subsites. Conclusion: These findings suggest the degree of industrialization and economic development affects the relationship between smoking and alcohol with head and neck cancer

Geographic variation of mutagenic exposures in kidney cancer genomes

International differences in the incidence of many cancer types indicate the existence of carcinogen exposures that have not yet been identified by conventional epidemiology make a substantial contribution to cancer burden1. In clear cell renal cell carcinoma, obesity, hypertension and tobacco smoking are risk factors, but they do not explain the geographical variation in its incidence2. Underlying causes can be inferred by sequencing the genomes of cancers from populations with different incidence rates and detecting differences in patterns of somatic mutations. Here we sequenced 962 clear cell renal cell carcinomas from 11 countries with varying incidence. The somatic mutation profiles differed between countries. In Romania, Serbia and Thailand, mutational signatures characteristic of aristolochic acid compounds were present in most cases, but these were rare elsewhere. In Japan, a mutational signature of unknown cause was found in more than 70% of cases but in less than 2% elsewhere. A further mutational signature of unknown cause was ubiquitous but exhibited higher mutation loads in countries with higher incidence rates of kidney cancer. Known signatures of tobacco smoking correlated with tobacco consumption, but no signature was associated with obesity or hypertension, suggesting that non-mutagenic mechanisms of action underlie these risk factors. The results of this study indicate the existence of multiple, geographically variable, mutagenic exposures that potentially affect tens of millions of people and illustrate the opportunities for new insights into cancer causation through large-scale global cancer genomics

Genome-wide association analyses identify new susceptibility loci for oral cavity and pharyngeal cancer.

We conducted a genome-wide association study of oral cavity and pharyngeal cancer in 6,034 cases and 6,585 controls from Europe, North America and South America. We detected eight significantly associated loci (P &lt; 5 × 10−8), seven of which are new for these cancer sites. Oral and pharyngeal cancers combined were associated with loci at 6p21.32 (rs3828805, HLA-DQB1), 10q26.13 (rs201982221, LHPP) and 11p15.4 (rs1453414, OR52N2–TRIM5). Oral cancer was associated with two new regions, 2p23.3 (rs6547741, GPN1) and 9q34.12 (rs928674, LAMC3), and with known cancer-related loci—9p21.3 (rs8181047, CDKN2B-AS1) and 5p15.33 (rs10462706, CLPTM1L). Oropharyngeal cancer associations were limited to the human leukocyte antigen (HLA) region, and classical HLA allele imputation showed a protective association with the class II haplotype HLA-DRB1*1301–HLA-DQA1*0103–HLA-DQB1*0603 (odds ratio (OR) = 0.59, P = 2.7 × 10−9). Stratified analyses on a subgroup of oropharyngeal cases with information available on human papillomavirus (HPV) status indicated that this association was considerably stronger in HPV-positive (OR = 0.23, P = 1.6 × 10−6) than in HPV-negative (OR = 0.75, P = 0.16) cancers