Biology subjects

Kovalenko, E.

Publications and source records attributed to Kovalenko, E..

2 recordsLinked to original sources

bioRxiv2026

Towards understanding of NK cell antigenic specificity

NK cells can form clonal populations demonstrating features of adaptive immunity, including long-term memory and at least partial antigenic specificity. Given the limited individual diversity of activating receptors, the nature of NK cell antigenic specificity remains elusive. To explore this riddle, we combined scRNA-Seq of ex vivo FACS-sorted NK cell subsets expressing specific KIR receptors, single-cell cloning and bulk RNA-Seq of in vitro cultured KIR2DS4 NK cell clones, transcriptomic profiling of antigen-stimulated NK cells, and in silico modeling of glycosylated KIR2DS4-peptide-HLA complexes. scRNA-Seq resolved 12-15 clusters per KIR subset with highly heterogeneous KIR, KLRC and NCR expression patterns, consistent with clonal lineages. Notably, those clusters demonstrated over 30 differentially expressed glycosyltransferase genes, potentially involved in post-translational modification of NK cell receptors. Single-cell-derived KIR2DS4 cultures exhibited clone-specific cytotoxic, chemokine and KIR receptor genes, and transcriptional differences in > 40 glycosyltransferases. In peptide culturing autologous assays, SARS-CoV-2 (KTFPPTEPK) and EBV (CRAKFKHLL) peptides elicited NK cell proliferation and distinct transcriptional programs linking cytotoxicity genes, KIR2DS4 and glycosyltransferases. Structural modeling revealed that N-linked glycosyl residues in specific regions of KIR2DS4 may alter its contacts and interaction with MHCI and the presented peptide. We conclude that KIR human NK cells comprise clonally imprinted populations with distinct glycosyltransferase expression profiles, and site-specific KIR2DS4 glycosylation may modulate interaction with peptide-MHCI complexes, suggesting a post-translational layer of clonal NK cell diversification as a clue to their antigenic specificity.

immunology↗

bioRxiv2025

Peptidome and Metabolome profiling of the fermented milk products revealed accumulation of bioactive compounds during two weeks of cold storage

This study assessed the metabolome and peptidome profiles of various fermented milk products produced using different starter cultures. Milk fermentation involves a set of macromolecular decomposition reactions performed by microorganisms under controlled conditions. Biotransformation of fats, proteins, and carbohydrates shapes the metabolome profile of each fermented product. Many of these microbe-generated molecules exhibit biological activities that can affect human health. The resulting profile is unique for every fermented product and depends on technology, raw materials, and starter culture composition. We used four non-targeted metabolomic methods to assess semi-quantified concentrations of four types of molecules in the final products: peptides; amino acids; long-, medium-, and short-chain fatty acids; mono- and disaccharides and their derivatives. Ultra-performance liquid chromatography-mass spectrometry (UPLC-MS/MS) was performed on the peptidome. For all other fractions, we used gas chromatography-mass spectrometry (GC-MS), with a method adapted to specific metabolite conditions. Metabolome and peptidome of four groups of 15 dairy cow milk products including yogurt (Y), fermented milk (FM), kefir made with commercial cultures (K) and kefir made with grains (KG) was performed on days 7 and 14 of shelf life at 4{degrees}C, and milk (M) was used as a control. Peptides, amino acids, fatty acids, mono- and disaccharides, and their low molecular weight derivatives were evaluated. In total, 348 peptides, 37 amino acids, 25 fatty acids, and 23 mono- and disaccharides were identified in the products. Among them, 41 functional peptides, branch-chained amino acids (BCAA), orotic acid (vitamin B13), d-phenyllactic acid, 5-phenylvaleric acid and myo-inositol (vitamin B8) accumulated in fermented products during storage.

biochemistry↗