Data on somatic mutations obtained by whole exome sequencing of FFPE tissue samples from Russian patients with prostate cancer.

Prostate cancer (PCa) is the most frequently diagnosed among men malignant disease that remains poorly characterized at the molecular level. Advanced PCa is not curable, and the current treatment methods can only increase the life expectancy by several months. Identification of the genetic aberrations in tumor cells provides clues to understanding the mechanisms of PCa pathogenesis and the basis for developing new therapeutic approaches. Here we present data on somatic mutations, namely single nucleotide variations (SNVs), small insertions and deletions, detected in prostate tumor tissue obtained from Russian patients with PCa. Moreover, we provide a raw dataset on the whole exome and targeted DNA sequencing of tumor and non-tumor prostate tissue obtained from Russian patients with PCa and benign prostatic hyperplasia (BPH). This data is available at NCBI Sequence Read Archive under Accession No. PRJNA506922.

[Targeted gene sequencing panels: applicability for neoantigen profiling of colon and rectal adenocarcinoma]. / Vozmozhnosti primeneniia targetnykh panelei dlia opredeleniia neoantigennogo profilia obraztsov adenokartsinomy tolstoi i priamoi kishki.

Cancer immunotherapy represents a promising and rapidly developing approach for the treatment of oncological diseases. Among the methods of personalized adjuvant immunotherapy, neoantigenic peptide-based drugs have demonstrated substantial efficiency. These drugs are designed to target mutant proteins arising from somatic alterations in the genome of tumor cells and thus stimulate immune response against tumor tissues. The methods of individual screening for potentially immunogenic mutations are mostly based on next-generation exome sequencing of tumor samples, which is a complex and costly procedure for clinical application. Targeted gene sequencing panels limited to a certain set of genes represent a reasonable alternative to WES. Targeted sequencing is also more efficient when there is a low amount of the sample DNA available. We have estimated the potential efficiency of targeted oncological panels in terms of somatic neoantigen profiling in colorectal cancer (colon and rectal adenocarcinoma). The clinical practice of identification of frequent somatic variants does not provide enough data for designing an efficient personalized drug when applied to low and medium mutated cancers such as colorectal cancer. Our analysis of 11 commercially available panels containing different number of genes has shown that neither the larger size of a panel nor its initial customization for colorectal cancer provides a significantly better estimation of an individual somatic mutation profile. The optimal approach is to use the general-purpose medium-sized cancer panels (2300-11200 amplicons and/or 150-600 genes). These panels allow to detect a sufficient number of immunogenic epitopes (>3) per patient for over 30-50% of patients.

Genome analysis of Acidiplasma sp. MBA-1, a polyextremophilic archaeon predominant in the microbial community of a bioleaching reactor.

Results of genome analysis of a member of the family Ferroplasmaceae, Acidiplasma sp. strain MBA-1, an extremely acidophilic, moderately thermophilic archaeon oxidizing ferrous iron under oxic conditions and utilizing organic compounds. This strain was previously shown to predominate in the community carrying out biooxidation of pyrite-arsenopyrite gold-bearing concentrate. The genome was sequenced using the Illumina HiSeq 2000 platform. A total of 2306800 pairwise reads were obtained, corresponding to 300-fold coverage. Assembly was carried out by three programs in parallel. The optimal assembly contained nine contigs, the genome size was 1747364 bp, and N50 was 446845 bp. Annotation of the genome revealed 1749 protein-encoding sequences, as well as 46 tRNA genes and one rRNA gene copy. The results of genome analysis confirmed the previous data on the physiology of this organism. The gene of sulfocyanin (TZ01_06185), a blue copper-containing protein playing the key role in the iron-oxidizing electron transport chain, was identified in the genome. The genes encoding sulfur oxidoreductase (TZ01_04750) and sulfateadenilyl transferase (TZ01_04545), the enzymes of sulfur oxidation, were also identified. The genes involved in the transport and catabolism of organic compounds and the genes of the 3-hydroxypropionate/4-hydroxybutyrate cycle were revealed. The genome of Acidiplasma sp. MBA-1 is the first genome of this genus deposited to a public database DDBJ/EMBL/GenBank (accession no. JYHS00000000) and is of interest for further investigation of Acidiplasma archaea.

The mystery of the fourth clone: comparative genomic analysis of four non-typeable Streptococcus pneumoniae strains with different susceptibilities to optochin.

Optochin-resistant pneumococci can be rarely caught in clinical microbiology laboratories because of the routine identification of all such strains as viridans group non-pneumococci. We were lucky to find four non-typeable Streptococcus pneumoniae clones demonstrating the different susceptibilities to optochin: one of them (Spn_13856) was resistant to optochin, while the other three (Spn_1719, Spn_27, and Spn_2298) were susceptible. Whole genome nucleotide sequences of these strains were compared to reveal the differences between the optochin-resistant and optochin-susceptible strains. Two adjacent genes coding maltose O-acetyltransferase and uridine phosphorylase which were presented in the genomes of all optochin-susceptible strains and missed in the optochin-resistant strain were revealed. Non-synonymous substitutions in 14 protein-coding genes were discovered, including the Ala49Ser mutation in the C-subunit of the F0 part of the ATP synthase rotor usually associated with pneumococcal optochin resistance. Modeling of a process of optochin interaction with the F0 part of the ATP synthase rotor indicates that the complex of optochin with "domain C" composed by wild-type C-subunits is more stable than the same complex composed of Ala49Ser mutant C-subunits.