No abstract

Missing (MP) and functionally uncharacterized proteins (uPE1) comprise less than 5% of the total number of proteins encoded by human Chr18 genes. Within half a year, since the January 2020 version of NextProt, the number of entries in the MP+uPE1 datasets changed, mainly due to the achievements of antibody-based proteomics. Assuming that the proteome is closely related to the transcriptome scaffold, quantitative PCR, Illumina HiSeq, and Oxford Nanopore Technology were applied to characterize the liver samples of three male donors in comparison with the HepG2 cell line. The data mining of the Expression Atlas (EMBL-EBI) and the profiling of biopsy samples by using orthogonal methods of transcriptome analysis have shown that in HepG2 cells and the liver, the genes encoding functionally uncharacterized proteins (uPE1) are expressed as low as for the missing proteins (less than 1 copy per cell), except the selected cases of HSBP1L1, TMEM241, C18orf21, and KLHL14. The initial expectation that uPE1 genes might be expressed at higher levels than MP genes, was compromised by severe discrepancies in our semi-quantitative gene expression data and in public databanks. Such discrepancy forced us to revisit the transcriptome of Chr18, the target of the Russian C-HPP Consortium. Tanglegram of highly expressed genes and further correlation analysis have shown the severe dependencies on the mRNA extraction method and the analytical platform. Targeted gene expression analysis by quantitative PCR (qPCR) and high-throughput transcriptome profiling (Illumina HiSeq and ONT MinION) for the same set of samples from normal liver tissue and HepG2 cells revealed the detectable expression of 250+ (92%) protein-coding genes of Chr18 (at least one method). The expression of slightly more than 50% protein-coding genes was detected simultaneously by all three methods. Correlation analysis of the gene expression profiles showed that the grouping of the datasets depended almost equally on both the type of biological material and the experimental method, particularly cDNA/mRNA isolation and library preparation.

No abstract

A review of the second edition of the collective monograph by V.A. Klevno, S.N. Kulikova, A.V. Kopylov Atlas of medical criteria for harm to health (under the general editorship of V.A. Klevno). The first edition of the Atlas was well received by the medical community, as evidenced by the fact that it has become a bibliographic rarity. During the time that has passed since the publication of the first edition, the author and his colleagues have carried out a large number of scientific research and development, among which the most significant are doctoral and candidate dissertations, published monographs, scientific and practical manuals, and other scientific publications. With this in mind, the release of the second edition of the collective monograph should be recognized as extremely timely and relevant. Assessing the peer-reviewed work, it should be stated that the head of the team of authors, Professor V.A. Klevno a colossal work has been done to create a team of like-minded people, and this work has been crowned with a well-deserved success: it is distinguished by novelty and theoretical and applied significance, thoroughness, completeness and relative sufficiency. Among the undoubted advantages of the Atlas, it is necessary to note the concise scientific and literary style of presenting the material, its clear structuredness, and the uniformity of the approach to the choice and sequence of presentation for each chapter and each subsection within it, which facilitate the perception of the material by the user; the high quality of illustrative material, an exhaustive selection of recommended scientific literature on the topic under consideration. The use of the definitions and illustrations given in the Atlas in the practice of doctors, most of all forensic doctors, will facilitate and increase the objectivity of the choice in each specific case of the type and localization of damage and, in general, will positively affect the production of one of the most frequently prescribed forensic medical examinations to determine the severity of harm caused to human health. The monograph has an important theoretical, cognitive, and practical value makes a significant contribution to the training of highly qualified medical personnel, primarily forensic medical experts. The publication can be recommended to forensic experts, researchers, graduate students, and students of medical specialties, as well as to a wide range of readers.

Missing (MP) and functionally uncharacterized proteins (uPE1) comprise less than 5% of the total number of human Chr18 genes. Within half a year, since the January 2020 version of NextProt, the number of entries in the MP+uPE1 datasets has changed, mainly due to the achievements of antibody-based proteomics. Assuming that the proteome is closely related to the transcriptome scaffold, quantitative PCR, Illumina HiSeq, and Oxford Nanopore Technology were applied to characterize the liver samples of three male donors compared with the HepG2 cell line. The data mining of Expression Atlas (EMBL-EBI) and the profiling of our biospecimens using orthogonal methods of transcriptome analysis have shown that in HepG2 cells and the liver, the genes encoding functionally uncharacterized proteins (uPE1) are expressed as low as for the missing proteins (less than 1 copy per cell), except for selected cases of HSBP1L1, TMEM241, C18orf21, and KLHL14. The initial expectation that uPE1 genes might be expressed at higher levels than MP genes, was compromised by severe discrepancies in our semi-quantitative gene expression data and in public databanks. Such discrepancy forced us to revisit the transcriptome of Chr18, the target of Russian C-HPP Consortia. Tanglegram of highly expressed genes and further correlation analysis have shown the severe dependencies on the mRNA extraction method and analytical platform. Targeted gene expression analysis by quantitative PCR (qPCR) and high-throughput transcriptome profiling (Illumina HiSeq and ONT MinION) for the same set of samples from normal liver tissue and HepG2 cells revealed the detectable expression of 250+ (92%) protein-coding genes of Chr18 (at least one method). The expression of slightly more than 50% protein-coding genes was detected simultaneously by all three methods. Correlation analysis of the gene expression profiles showed that the grouping of the datasets depended almost equally on both the type of biological material and the experimental method, particularly cDNA/mRNA isolation and library preparation. The dependence on the choice of bioinformatics analysis pipeline was also noticeable but significantly less. Furthermore, the combination of Illumina HiSeq and ONT MinION sequencing to validate proteotypic peptides of missing and uPE1 proteins was performed for the heat-shock factor binding protein HSBP1L1 (missing protein, recently transferred to PE1 category) and uncharacterized protein C18orf21 (uPE1). We observed that a nonsynonymous SNP led to the loss of the site of trypsinolysis in HSBP1L1. The modified version of HSBP1L1 was included in the sequence database and searched against the MS/MS dataset from Kulak, Geyer & Mann (2017), but delivered no significant identification. Thus, HSBP1L1 is still missing for the MS-pillar of C-HPP, although its existence at the protein level has been confirmed.