Challenges of the Human Proteome Project: 10-Year Experience of the Russian Consortium

Archakov, Alexander I.; Aseev, A. L.; Быков, В. А.; Grigoriev, Anatoly I.; Govorun, Vadim M.; Ilgisonis, Ekaterina V.; Ivanov, Yuri D.; Иванов, В. Т.; Kiseleva, Olga I.; Kopylov, Arthur T.; Лисица, А. В.; Mazurenko, Sergey N.; Makarov, Alexander А.; Naryzhny, Stanislav N.; Pleshakova, Tatyana O.; Ponomarenko, Elena A.; Poverennaya, Ekaterina V.; Pyatnitskii, M A; Sagdeev, R. Z.; Skryabin, K. G.; Zgoda, Victor G.

doi:10.1021/acs.jproteome.9b00358

Cited by 8 publications

(3 citation statements)

References 62 publications

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“…It is necessary to specify, that our study deals only with RNA transcriptome data. Datasets were previously published in the Russian Proteomic Consortium annual reports (Ponomarenko et al, 2014;Poverennaya et al, 2016;Archakov et al, 2019).…”

Section: Datamentioning

confidence: 99%

Genome of the Single Human Chromosome 18 as a “Gold Standard” for Its Transcriptome

et al. 2021

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The cutoff level applied in sequencing analysis varies according to the sequencing technology, sample type, and study purpose, which can largely affect the coverage and reliability of the data obtained. In this study, we aimed to determine the optimal combination of parameters for reliable RNA transcriptome data analysis. Toward this end, we compared the results obtained from different transcriptome analysis platforms (quantitative polymerase chain reaction, Illumina RNASeq, and Oxford Nanopore Technologies MinION) for the transcriptome encoded by human chromosome 18 (Chr 18) using the same sample types (HepG2 cells and liver tissue). A total of 275 protein-coding genes encoded by Chr 18 was taken as the gene set for evaluation. The combination of Illumina RNASeq and MinION nanopore technologies enabled the detection of at least one transcript for each protein-coding gene encoded by Chr 18. This combination also reduced the probability of false-positive detection of low-copy transcripts due to the simultaneous confirmation of the presence of a transcript by the two fundamentally different technologies: short reads essential for reliable detection (Illumina RNASeq) and long-read sequencing data (MinION). The combination of these technologies achieved complete coverage of all 275 protein-coding genes on Chr 18, identifying transcripts with non-zero expression levels. This approach can improve distinguishing the biological and technical reasons for the absence of mRNA detection for a given gene in transcriptomics.

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Section: Datamentioning

confidence: 99%

Genome of the Single Human Chromosome 18 as a “Gold Standard” for Its Transcriptome

et al. 2021

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“…At present, there is practically no area of life sciences left where the CRISPR-Cas technology has not been used. One of the most topical areas in modern biology is the width and depth of human proteome [165]. Many proteins that can have important or even vital functions are not yet comprehensively studied.…”

Section: Discussionmentioning

confidence: 99%

Applications of CRISPR-Cas Technologies to Proteomics

Dolgalev

Poverennaya

2021

Genes

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CRISPR-Cas-based genome editing is a revolutionary approach that has provided an unprecedented investigational power for the life sciences. Rapid and efficient, CRISPR-Cas technologies facilitate the generation of complex biological models and at the same time provide the necessary methods required to study these models in depth. The field of proteomics has already significantly benefited from leveraging the power of CRISPR-Cas technologies, however, many potential applications of these technologies in the context of proteomics remain unexplored. In this review, we intend to provide an introduction to the CRISPR-Cas technologies and demonstrate how they can be applied to solving proteome-centric questions. To achieve this goal, we begin with the description of the modern suite of CRISPR-Cas-based tools, focusing on the more mature CRISPR-Cas9 system. In the second part of this review, we highlight both established and potential applications of the CRISPR-Cas technologies to proteomics.

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“…Thus, some lincRNAs involved in the pathogenesis of various cancer or non-cancer diseases may be considered as potential molecular targets or prognostic, predictive, and diagnostic biomarkers. Recent studies of human chromosome 18 within the framework of the Russian segment of the international program ‘The Human Proteome Project’ have investigated a detailed proteogenomic landscape of human chromosome 18 genes in the HepG2 cell line and liver tissue [ 18 , 19 , 20 ]. Taken together, literature data speak in favor of the associations between some lincRNAs of human chromosome 18 and cancers.…”

Section: Introductionmentioning

confidence: 99%

Long Intergenic Non-Coding RNAs of Human Chromosome 18: Focus on Cancers

Ershov,

Yablokov,

Mezentsev

et al. 2024

Biomedicines

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Malignant neoplasms are characterized by high molecular heterogeneity due to multilevel deregulation of gene expression and cellular functions. It is known that non-coding RNAs, including long intergenic non-coding RNAs (lincRNAs), can play significant roles in cancer biology. The current review focuses on a systematical analysis of genomic, transcriptomic, epigenomic, interactomic, and literature data on 65 lincRNAs of human chromosome 18 in the context of pan-cancer studies. The entire group of lincRNAs can be conditionally divided into 4 subgroups depending on experimental evidence on direct or indirect involvement in cancers and the biological associations with cancers, which we found during the data-mining process: the most studied (5 lincRNAs), moderately or poorly studied (11 lincRNAs), and understudied (31 lincRNAs). For the remaining 18 lincRNAs, data for analysis were fragmentary or missing. Among the key findings were the following: Of the lincRNAs of human chromosome 18, 40% have tissue-specific expression patterns, 22% of lincRNAs are known to have gene fusions, 40% of lincRNAs are prone to gene amplifications and/or deletions in cancers at a frequency greater than 3%, and 23% of lincRNAs are differentially expressed across cancer types, whereas 7% have subtype-specific expression patterns. LincRNAs’ interactomes consist of ‘master’ microRNAs and 47 proteins (including cancer-associated proteins and microRNAs) that can interact with 3 or more lincRNAs. Functional enrichment analysis of a set of highly co-expressed genes retrieved for 17 lincRNAs in different cancer types indicated the potential associations of these lincRNAs with cellular signaling pathways. Six lincRNAs encoded small open-reading frame (smORF) proteins with emerging roles in cancers, and microRNAs as well as proteins with known functions in molecular carcinogenesis can bind to coding regions of smORFs. We identified seven transcriptomic signatures with potential prognostic value, consisting of two to seven different lincRNAs only. Taken together, the literature, biomedical, and molecular biology data analyzed indicated that only five of all lincRNAs of human chromosome 18 are cancer-associated, while eleven other lincRNAs have the tendency to be associated with cancers.

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Challenges of the Human Proteome Project: 10-Year Experience of the Russian Consortium

Cited by 8 publications

References 62 publications

Genome of the Single Human Chromosome 18 as a “Gold Standard” for Its Transcriptome

Genome of the Single Human Chromosome 18 as a “Gold Standard” for Its Transcriptome

Applications of CRISPR-Cas Technologies to Proteomics

Long Intergenic Non-Coding RNAs of Human Chromosome 18: Focus on Cancers

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