SARS-CoV-2 Variant Surveillance in Genomic Medicine Era

In the genomic medicine era, the emergence of SARS-CoV-2 was immediately followed by viral genome sequencing and world-wide sequences sharing. Almost in real-time, based on these sequences, resources were developed and applied around the world, such as molecular diagnostic tests, informed public health decisions, and vaccines. Molecular SARS-CoV-2 variant surveillance was a normal approach in this context yet, considering that the viral genome modification occurs commonly in viral replication process, the challenge is to identify the modifications that significantly affect virulence, transmissibility, reduced effectiveness of vaccines and therapeutics or failure of diagnostic tests. However, assessing the importance of the emergence of new mutations and linking them to epidemiological trend, is still a laborious process and faster phenotypic evaluation approaches, in conjunction with genomic data, are required in order to release timely and efficient control measures

Идентификация нового сайта метилирования в промоторном районе гена Sept9 для диагностики гепатоцеллюлярной карциномы

Background. Over 600,000 people die from hepatocellular carcinoma (HCC) each year worldwide. The disease is often detected at advanced stages and in many cases is not curable. Early diagnostic and monitoring of HCC recurrences remains a substantial problem in clinical oncology. That determines the need for a search for highly sensitive and specific biomarkers for the non-invasive of HCC diagnostics. The objective of the study. Identification of the hypermethylated locus in the promoter region of the septin 9 (Sept9) gene based on the annotated methylomes from the public databases. Experimental validation of methylation on a pilot panel of paired clinical samples of patients with HCC, as well as tissue samples from patients with benign liver tumors and lymphocytes from healthy donors. Materials and methods. To analyze the methyl data, samples of HCC from TCGA, hepatocellular adenoma from GEO (Gene Expression Omnibus) depository, peripheral blood cells and tissues of healthy donors from Methbank were used. Experimental validation of methylation levels of the identified site was carried out on a pilot panel of clinical samples by bisulphite pyrosequencing using PyroMark Q24.Results. Based on the analysis of methylome data, we selected cg20275528 site, which is characterized by high level of methylation in HCC tissues and minimal levels of methylation in non-tumor liver tissue, hepatocellular adenoma and peripheral blood of healthy donors. Experimental testing on a pilot panel of clinical specimens showed that the level of marker site methylation in HCC (42 % median) is significantly higher than in non-tumor liver tissues (3 % median) and benign neoplasms (1.5 % median) and exceeds the threshold value in HCC compared to paired samples of adjacent non-tumor liver tissue in 20 out of 30 studied cases (66.6 %). The general possibility for cg20275528 methylation detection in circulating DNA of plasma in HCC patients was shown.Conclusion. The obtained results indicate that the approach to the detection and experimental verification of diagnostically significant markers developed and tested in this study can be used to identify new differentially methylated sites and to establish new approaches for non-invasive HCC diagnosis.Введение. Ежегодно во всем мире от гепатоцеллюлярной карциномы (ГЦК) умирают более 600 тыс. человек. Заболевание часто выявляется на поздних стадиях и во многих случаях является некурабельным. Ранняя диагностика и мониторинг развития рецидивов ГЦК продолжают оставаться существенной проблемой клинической онкологии. Это определяет актуальность поиска высокочувствительных и специфичных биомаркеров для неинвазивной диагностики ГЦК. Цель исследования – идентификация гиперметилированного при ГЦК локуса в промоторном районе гена септин 9 (Sept9) на основании анализа общедоступных данных метиломных исследований; экспериментальная валидация метилирования на пилотной панели парных клинических образцов пациентов с ГЦК, а также образцов ткани пациентов с доброкачественными опухолями печени и лимфоцитов здоровых доноров.Материалы и методы. Для анализа метиломных данных были использованы выборки ГЦК TCGA, гепатоцеллюлярной аденомы из депозитария GEO (Gene Expression Omnibus), а также клеток периферической крови и тканей здоровых доноров Methbank. Экспериментальную валидацию уровней метилирования идентифицированного сайта проводили на пилотной выборке клинических образцов с использованием метода бисульфитного пиросеквенирования на приборе PyroMark Q24.Результаты. На основании анализа метиломных данных нами был выбран сайт cg20275528, который характеризуется высоким уровнем метилирования в тканях ГЦК и минимальными уровнями метилирования в клетках неопухолевой ткани печени, гепатоцеллюлярной аденомы и периферической крови здоровых доноров. Экспериментальная проверка на пилотной выборке клинических образцов показала, что уровень метилирования маркерного сайта в ГЦК (медиана 42 %) значительно выше, чем в неопухолевых тканях печени (медиана 3 %) и доброкачественных новообразованиях (медиана 1,5 %) и превышает пороговое значение в ГЦК по сравнению с парными образцами прилежащей неопухолевой ткани печени в 20 (66,6 %) из 30 исследованных случаев. Показана принципиальная возможность детекции метилирования cg20275528 в циркулирующей ДНК плазмы больных ГЦК.Заключение. Полученные результаты позволяют предположить, что разработанный и апробированный в этой работе подход к поиску и экспериментальной верификации диагностически значимых маркеров может быть использован для выявления новых дифференциально метилированных сайтов и разработки новых подходов к неинвазивной диагностике ГЦК

Liquid biopsies come of age: towards implementation of circulating tumour DNA

Improvements in genomic and molecular methods are expanding the range of potential applications for circulating tumour DNA (ctDNA), both in a research setting and as a ‘liquid biopsy’ for cancer management. Proof-of-principle studies have demonstrated the translational potential of ctDNA for prognostication, molecular profiling and monitoring. The field is now in an exciting transitional period in which ctDNA analysis is beginning to be applied clinically, although there is still much to learn about the biology of cell-free DNA. This is an opportune time to appraise potential approaches to ctDNA analysis, and to consider their applications in personalized oncology and in cancer research.We would like to acknowledge the support of The University of Cambridge, Cancer Research UK (grant numbers A11906, A20240, A15601) (to N.R., J.D.B.), the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement n. 337905 (to N.R.), the Cambridge Experimental Cancer Medicine Centre, and Hutchison Whampoa Limited (to N.R.), AstraZeneca (to R.B., S.P.), the Cambridge Experimental Cancer Medicine Centre (ECMC) (to R.B., S.P.), and NIHR Biomedical Research Centre (BRC) (to R.B., S.P.). J.G.C. acknowledges clinical fellowship support from SEOM

Whole-cells of Yarrowia lipolytica applied in “one pot” indolizine biosynthesis

International audienceA series of yeast strains was tested in order to evaluate their catalytic potential in biocatalysis of one-pot indolizine’s synthesis. Yeast cultivation was performed in a submerged system at 28◦ C for 72 h at 180 rpm. An assessment of the reagents’ toxicity on yeast viability and metabolic functionality concluded that the growth potential of three Yarrowia lipolytica strains were least affected by the reactants compared to the other yeast strains. Further, crude fermentation products (biomass and cell-free supernatant)—obtained by submerged cultivation of these yeasts—were used in multistep cascade reactions for the production of fluorescent indolizine compounds with important biologic activities. A whole–cell catalyzed multicomponent reaction of activated alkynes, α-bromo-carbonyl reagents and 4,4′-bipyridine, at room temperature in buffer solution led to the efficient synthesis of bis-indolizines 4a, 4b and 4c, in good-to-excellent yields (47%–77%). The metabolites of the selected Y. lipolytica strains can be considered effective biocatalysts in cycloaddition reactions and the high purity and bioconversion yields of the synthesized indolizines indicates a great potential of this type of “green” catalysts. Seeds of Triticum estivum L. were used to investigate the impact of the final products on the germination and seedling growth. The most sensitive physiological parameters suggest that indolizines, at the concentrations tested, have non-toxic effect on germination and seedling growth of wheat, fact also confirmed by confocal laser scanning microscopy images