AFM-fishing technology for protein detection in solutions

The review considers the possibility of using atomic force microscopy (AFM) as a basic method for protein detection in solutions with low protein concentrations. The demand for new bioanalytical approaches is determined by the problem of insufficient sensitivity of systems used in routine practice for protein detection. Special attention is paid to demonstration of the use in bioanalysis of a combination of AFM and fishing methods as an approach of concentrating biomolecules from a large volume of the analyzed solution on a small surface area.

[PCR analysis of the expression of chromosome 18 genes in human liver tissue: interindividual variability]

Using human chromosome 18 (Ch18) genes as an example, a PCR analysis of the interindividual variability of gene expression in liver tissue was performed. Although the quantitative profiles of the Ch18 transcriptome, expressed in the number of cDNA copies per single cell, showed a high degree of correlation between donors (Pearson correlation coefficients ranged from 0.963 to 0.966), the expression of the significant number of genes (from 13% to 19%, depending on the method of experimental data normalization) varied by more than 4-fold when comparing donors pairwise. At the same time, the proportion of differentially expressed genes increased with a decrease in the level of their expression. It is shown that the higher quantitative variability of low-abundance transcripts is mainly not technical, but biological. Bioinformatic analysis of the interindividual variability of the differential expression of chromosome 18 genes in human liver tissue did not reveal any statistically significant groups of genes related to certain biological processes that indicated a rather transient nature of the interindividual variability of their expression, probably reflecting the response of cells of an individual to specific external stimuli.

[Comparative study of the human keratinocytes proteome of the HaCaT line: identification of proteins encoded by genes of 18 chromosomes under the influence of detergents]

Using electrospray ionization tandem mass spectrometry, a comparative analysis of the HaCaT keratinocyte proteins encoded by the 18th chromosome was performed before and after exposure to sodium dodecyl sulfate (25 mg/ml) and to Triton X-100 (12.5 mg/ml) in a subtoxic dose for 48 hours. Proteins were identified using the SearchGUI platform (X!Tandem and MS-GF+ search engines). In total, 1284 proteins were found in immortalized human HaCaT keratinocytes and about 75% of them were identified by two or more peptides. Were identified, that 26 proteins were encoded by genes of chromosome 18. Among these proteins, 17 were common for control cells and HaCaT cells treated with SDS. Proteins MARE2 and CTIF were identified only in control keratinocytes. Seven identified proteins encoded by genes of chromosome 18 were found only in detergent-treated keratinocytes: LMAN1, NDUV2, SPB3, VPS4B, KDSR, ROCK1 and RHG28.

The Gene-Centric Content Management System and Its Application for Cognitive Proteomics

The Human Proteome Project is moving into the next phase of creating and/or reconsidering the functional annotations of proteins using the chromosome-centric paradigm. This challenge cannot be solved exclusively using automated means, but rather requires human intelligence for interpreting the combined data. To foster the integration between human cognition and post-genome array a number of specific tools were recently developed, among them CAPER, GenomewidePDB, and The Proteome Browser (TPB). For the purpose of tackling the task of protein functional annotating the Gene-Centric Content Management System (GenoCMS) was expanded with new features. The goal was to enable bioinformaticans to develop self-made applications and to position these applets within the generalized informational canvas supported by GenoCMS. We report the results of GenoCMS-enabled integration of the concordant informational flows in the chromosome-centric framework of the human chromosome 18 project. The workflow described in the article can be scaled to other human chromosomes, and also supplemented with new tracks created by the user. The GenoCMS is an example of a project-oriented informational system, which are important for public data sharing.

Why Are the Correlations between mRNA and Protein Levels so Low among the 275 Predicted Protein-Coding Genes on Human Chromosome 18?

In this work targeted (selected reaction monitoring, SRM, PASSEL: PASS00697) and panoramic (shotgun LC-MS/MS, PRIDE: PXD00244) mass-spectrometric methods as well as transcriptomic analysis of the same samples using RNA-Seq and PCR methods (SRA experiment IDs: SRX341198, SRX267708, SRX395473, SRX390071) were applied for quantification of chromosome 18 encoded transcripts and proteins in human liver and HepG2 cells. The obtained data was used for the estimation of quantitative mRNA-protein ratios for the 275 genes of the selected chromosome in the selected tissues. The impact of methodological limitations of existing analytical proteomic methods on gene-specific mRNA-protein ratios and possible ways of overcoming these limitations for detection of missing proteins are also discussed.