Short Peptides Regulate Gene Expression

Peptides Regulating Proliferative Activity and Inflammatory Pathways in the Monocyte/Macrophage THP-1 Cell Line

This study evaluates the effects of five different peptides, the Epitalon^® tetrapeptide, the Vilon^® dipeptide, the Thymogen^® dipeptide, the Thymalin^® peptide complex, and the Chonluten^® tripeptide, as regulators of inflammatory and proliferative processes in the human monocytic THP-1, which is a human leukemia monocytic cell line capable of differentiating into macrophages by PMA in vitro. These peptides (Khavinson Peptides^®), characterized by Prof. Khavinson from 1973 onwards, were initially isolated from animal tissues and found to be organ specific. We tested the capacity of the five peptides to influence cell cultures in vitro by incubating THP-1 cells with peptides at certain concentrations known for being effective on recipient cells in culture. We found that all five peptides can modulate key proliferative patterns, increasing tyrosine phosphorylation of mitogen-activated cytoplasmic kinases. In addition, the Chonluten tripeptide, derived from bronchial epithelial cells, inhibited in vitro tumor necrosis factor (TNF) production of monocytes exposed to pro-inflammatory bacterial lipopolysaccharide (LPS). The low TNF release by monocytes is linked to a documented mechanism of TNF tolerance, promoting attenuation of inflammatory action. Therefore, all peptides inhibited the expression of TNF and pro-inflammatory IL-6 cytokine stimulated by LPS on terminally differentiated THP-1 cells. Lastly, by incubating the THP1 cells, treated with the peptides, on a layer of activated endothelial cells (HUVECs activated by LPS), we observed a reduction in cell adhesion, a typical pro-inflammatory mechanism. Overall, the results suggest that the Khavinson Peptides^® cooperate as natural inducers of TNF tolerance in monocyte, and act on macrophages as anti-inflammatory molecules during inflammatory and microbial-mediated activity.

Peptide Drug Thymalin Regulates Immune Status in Severe COVID-19 Older Patients

Peptide drug Thymalin, isolated from the calve thymus, is successfully used for the treatment of various immunopathologies, including those in older age groups. The molecular mechanism of the Thymalin immunoprotective action is due to the effects of the short peptides KE, EW, EDP in its composition. These short peptides can specifically bind to double-stranded DNA and/or histone proteins and regulate gene expression, synthesis of immune system proteins, activity of gerontogenes, and stimulate stem cell differentiation. Regulation of immunogenesis is a key factor preventing the development of the “cytokine storm” that develops in severe COVID-19. The purpose of this work is to study the effectiveness of Thymalin in severe COVID-19 in older patients. Patients administered with Thymalin against the background of a standard therapy (n = 36) manifested a more rapid clinical improvement, higher proportions of recovery from lymphopenia, faster normalization of the concentration of C-reactive protein, D-dimer, the number of lymphocytes and NK-cells in the blood, compared to patients who received a standard therapy only (n = 44). Thymalin halved hospital mortality in older patients with severe COVID-19. The results obtained showed the effectiveness of Thymalin administration in the complex therapy of patients with severe COVID-19.

Peptide KED: Molecular-Genetic Aspects of Neurogenesis Regulation in Alzheimer's Disease

Neuroprotective peptides are promising candidate molecules for the treatment of Alzheimer's disease (AD). Oral application of KED (Lys-Glu-Asp) improved memory and attention in elderly individuals with functional CNS disorders. Peptide KED also restores synaptic plasticity in in vitro model of AD. This review is focused on the analysis of the influence of KED peptide on the expression of genes and synthesis of proteins regulating apoptosis, aging, neurogenesis, and involved in AD pathogenesis. Analysis of published reports and our experimental findings suggests that KED regulates the expression of genes of cell aging and apoptosis (р16, р21), genes (NES, GAP43) and proteins (nestin, GAP43) of the neuronal differentiation, and genes involved in AD pathogenesis (SUMO, APOE, and IGF1). The study the effectiveness of neuroprotective peptide KED in animal models of AD seems to be very important.

COVID-19, Retroelements, and Aging

The review presents an analysis of the scientific data on the characteristics of COVID-19 from the perspective of potential interactions between the virus and the host genome retroelements. According to global statistical data, severe COVID-19 with immune-system hyperactivity is observed mainly in elderly people. At the same time, aging is characterized by a decrease in immune responses. This paradox may be resolved by the assumption that DNA regions that can move along the genome with the “copy and paste” mechanism (retroelements) may play a role in COVID-19 development; these elements are characterized by abnormal expression patterns in aging. Their interaction with SARS-CoV-2 may occur at the level of RNA interference or RNA recombination, or the virus can use retroelement proteins to integrate into the host genome. There is supporting evidence of this interaction: data indicating the efficiency of antiretroviral drugs at the early stage of COVID-19, the isolation of SARS-CoV-2 for a long time after recovery, the persistence of coronavirus infections, and changes in the L1 retrotransposon expression patterns in the lung tissues of COVID-19 patients. In additional, retroelements affect the functioning of the immune system and affect the receptors interacting with SARS-CoV-2. Recombination with retroelements and viral insertions into host genomes have been demonstrated in the case of other infections caused by nonretroviral, RNA-containing viruses. The presumable interaction between SARS-CoV-2 and retroelements may explain the differences in the severity and lethality of COVID-19 in different countries as a result of specific insertional patterns in the genomes of individuals belonging to different human populations. The possible insertion of SARS-CoV-2 cDNA into the genome should be kept in mind in the design of anti-COVID-19 vaccines. Peptide preparations are the most promising in this regard.

EDR Peptide: Possible Mechanism of Gene Expression and Protein Synthesis Regulation Involved in the Pathogenesis of Alzheimer's Disease

The EDR peptide (Glu-Asp-Arg) has been previously established to possess neuroprotective properties. It activates gene expression and synthesis of proteins, involved in maintaining the neuronal functional activity, and reduces the intensity of their apoptosis in in vitro and in vivo studies. The EDR peptide interferes with the elimination of dendritic spines in neuronal cultures obtained from mice with Alzheimer’s (AD) and Huntington’s diseases. The tripeptide promotes the activation of the antioxidant enzyme synthesis in the culture of cerebellum neurons in rats. The EDR peptide normalizes behavioral responses in animal studies and improves memory issues in elderly patients. The purpose of this review is to analyze the molecular and genetics aspects of the EDR peptide effect on gene expression and synthesis of proteins involved in the pathogenesis of AD. The EDR peptide is assumed to enter cells and bind to histone proteins and/or ribonucleic acids. Thus, the EDR peptide can change the activity of the MAPK/ERK signaling pathway, the synthesis of proapoptotic proteins (caspase-3, p53), proteins of the antioxidant system (SOD2, GPX1), transcription factors PPARA, PPARG, serotonin, calmodulin. The abovementioned signaling pathway and proteins are the components of pathogenesis in AD. The EDR peptide can be AD.

Complex Analysis of Retroposed Genes' Contribution to Human Genome, Proteome and Transcriptome

Gene duplication is a major driver of organismal evolution. One of the main mechanisms of gene duplications is retroposition, a process in which mRNA is first transcribed into DNA and then reintegrated into the genome. Most gene retrocopies are depleted of the regulatory regions. Nevertheless, examples of functional retrogenes are rapidly increasing. These functions come from the gain of new spatio-temporal expression patterns, imposed by the content of the genomic sequence surrounding inserted cDNA and/or by selectively advantageous mutations, which may lead to the switch from protein coding to regulatory RNA. As recent studies have shown, these genes may lead to new protein domain formation through fusion with other genes, new regulatory RNAs or other regulatory elements. We utilized existing data from high-throughput technologies to create a complex description of retrogenes functionality. Our analysis led to the identification of human retroposed genes that substantially contributed to transcriptome and proteome. These retrocopies demonstrated the potential to encode proteins or short peptides, act as cis- and trans- Natural Antisense Transcripts (NATs), regulate their progenitors’ expression by competing for the same microRNAs, and provide a sequence to lncRNA and novel exons to existing protein-coding genes. Our study also revealed that retrocopies, similarly to retrotransposons, may act as recombination hot spots. To our best knowledge this is the first complex analysis of these functions of retrocopies.

AEDG Peptide (Epitalon) Stimulates Gene Expression and Protein Synthesis during Neurogenesis: Possible Epigenetic Mechanism

It was shown that AEDG peptide (Ala-Glu-Asp-Gly, Epitalon) regulates the function of the pineal gland, the retina, and the brain. AEDG peptide increases longevity in animals and decreases experimental cancerogenesis. AEDG peptide induces neuronal cell differentiation in retinal and human periodontal ligament stem cells. The aim of the study was to investigate the influence of AEDG peptide on neurogenic differentiation gene expression and protein synthesis in human gingival mesenchymal stem cells, and to suggest the basis for the epigenetic mechanism of this process. AEDG peptide increased the synthesis of neurogenic differentiation markers: Nestin, GAP43, β Tubulin III, Doublecortin in hGMSCs. AEDG peptide increased Nestin, GAP43, β Tubulin III and Doublecortin mRNA expression by 1.6–1.8 times in hGMSCs. Molecular modelling method showed, that AEDG peptide preferably binds with H1/6 and H1/3 histones in His-Pro-Ser-Tyr-Met-Ala-His-Pro-Ala-Arg-Lys and Tyr-Arg-Lys-Thr-Gln sites, which interact with DNA. These results correspond to previous experimental data. AEDG peptide and histones H1/3, H1/6 binding may be one of the mechanisms which provides an increase of Nestin, GAP43, β Tubulin III, and Doublecortin neuronal differentiation gene transcription. AEDG peptide can epigenetically regulate neuronal differentiation gene expression and protein synthesis in human stem cells.

Peptides as epigenetic modulators: therapeutic implications

Peptides originating from different sources (endogenous, food derived, environmental, and synthetic) are able to influence different aspects of epigenetic regulation. Endogenous short peptides, resulting from proteolytic cleavage of proteins or upon translation of non-annotated out of frame transcripts, can block DNA methylation and hereby regulate gene expression. Peptides entering the body by digestion of food-related proteins can modulate DNA methylation and/or histone acetylation while environmental peptides, synthesized by bacteria, fungi, and marine sponges, mainly inhibit histone deacetylation. In addition, synthetic peptides that reverse or inhibit different epigenetic modifications of both histones and the DNA can be developed as well. Next to these DNA and histone modifications, peptides can also influence the expression of non-coding RNAs such as lncRNAs and the maturation of miRNAs.

Seen the advantages over small molecules, the development of peptide therapeutics is an interesting approach to treat diseases with a strong epigenetic basis like cancer and Alzheimer’s disease. To date, only a limited number of drugs with a proven epigenetic mechanism of action have been approved by the FDA of which two (romidepsin and nesiritide) are peptides. A large knowledge gap concerning epigenetic effects of peptides is present, and this class of molecules deserves more attention in the development as epigenetic modulators. In addition, none of the currently approved peptide drugs are under investigation for their potential effects on epigenetics, hampering drug repositioning of these peptides to other indications with an epigenetic etiology.

Signaling TLR/RLR-mechanisms of immunomodulating action of ingavirin and thymogen preparations

Objective: to study drugs ingavirin and thymogen as activators of signal TLR and RLR reactions in a sensitive cell model of THP-1 monocytes and blood cells of donors.Materials and methods . Investigated drugs ingavirin (imidazolylethanamide pentanedioic acid – 6-[2-(1H-imidazol-4-yl)ethylami- no]-5-oxohexanoic acid; Valenta Pharmaceutics, Russia) and thymogen (alpha-glutamyl-tryptophan; Cytomed, Russia), registered in Russia as medicines. The expression of TLR/RLR receptor genes was determined under the action of ingavirin 50–300 μg/ml and thymogen 0.1–5 μg/ml (24 h, 37 °C) using quantitative RT-PCR. The level of fluid cytokines was determined using ELISA kits (Vec- tor-Best, Russia) in the culture fluid. Transfection of small inhibitory RNA (siRNA) MAVS was performed using the reagent Lipofect- amine 2000 (Invitrogen). The immunophenotype of the THP-1 cell line was determined by flow cytometry with labeled monoclonal antibodies FITC CD14 and PE CD34 (BD Biosciences) on a FACSCanto II instrument (Becton Dickinson).Results . For the first time, it has been shown that ingavirin (imidazolylethanamide) and thymogen (dipeptide Glu-Trp) preparations are activators of the immune TLR/RLR receptors and their signaling factors genes in the cultures of monocytic leukemia THP-1 and blood of healthy donors. In these cellular systems, ingavirin and thymogen preparations elicited similar immune responses and stimulated the expression of genes: endosomal TLR3/7/8/9 receptors, RIG1/MDA5 cytoplasmic sensors and NFκB1 and MAVS signaling factors. Induced cells secrete inflammatory cytokines of TNF-α and IL1-β. Ingavirin in THP-1 cell culture monocytes caused a decrease in CD34+ blast cells. Activation the genes of MAVS and co-receptor B2M of the main histocompatibility complex (MHCII) by ingavirin were interrelated. Transfection of siRNA MAVS reduced the level of homologous mRNA MAVS and heterologous mRNA B2M. Conclusion . The results obtained suggest that the antiviral and immunomodulating properties of the drugs ingavirin and thymogen are associated with the activation of a group of TLR/RLR signaling pathways of the innate and adaptive immunity and the differentiation of hematopoietic cell precursors.