Bacteriophages as Therapeutic Preparations: What Restricts Their Application in Medicine

The increasing prevalence of bacterial pathogens with multiple antibiotic resistance requires development of new approaches to control infections. Phage therapy is one of the most promising approaches. In recent years, research organizations and a number of pharmaceutical companies have intensified investigations aimed at developing bacteriophage-based therapeutics. In the United States and European countries, special centers have been established that experimentally apply phage therapy to treat patients who do not respond to antibiotic therapy. This review describes the features of bacteriophages as therapeutic tools, critically discusses the results of clinical trials of bacteriophage preparations, and assesses the prospects for using phage therapy to treat certain types of infectious diseases.

Structure of acute lethal poisonings in children: a retrospective study in the Moscow Region, Russia

Background

Poisonings are of major public health concern - they cause sickness and death in many children. The clinical case series are non-informative about the very severe intoxications. The objective of this study was to describe the spectrum of toxic substances leading to the death of children, and analyze the time trends and age differences.

Materials and Methods

We analyzed autopsy reports from the archives of the Bureau of Forensic Medical Expertise of the Moscow Region over a 10-year period.

Results

Of total children's deaths in age 0 to 19 (n = 3873), unnatural death accounted for 71% of cases (n = 2750). In the structure of unnatural deaths, poisoning accounted for 15.56%. The average age of dead children is 11.2 ± 6.10 years (X + SD). Deaths of boys dominates (at least 60% in age older one year), mostly due to the higher frequency of poisoning with chemical/technical agents (p < 0.01). Age groups are different by the causes of death (p < 0.01): higher frequency of poisoning by carbon monoxide (p = 0.036) in younger children and in older children - by illicit drugs (p = 0,026). There was significant increase in frequency of fatal poisoning by therapeutic drugs and chemical-technical agents in 2016-2018 compared with the previous time interval (p < 0.01).

Conclusions

The most common cause of Russian children's death is the exposition to the carbon monoxide. The improvement in living conditions and heating technology is a major preventive measure. In the group of therapeutic drugs, the leading toxicant is drotaverine, and among technical substances - natural gas (as a recreational self-poisoning).

Key messages

Unnatural deaths a numerous in Russian children, and intoxication is one of the leading causes. Dangerous heating of the houses is a major and preventable cause of death by CO intoxication.

Prevalence of obesity and longevity: cohort study using national statistics

Background

Obesity is a problem of major concern all around the world. On the personal level it leads not only to a decrease in life expectancy, but also increases the burden on health care. Objective of this study was to review the correlation between the longevity and prevalence of obesity in countries stratified by their economic prosperity.

Methods

We did a retrospective longitudinal analysis based on the World Bank and Global Burden of Disease data for the period from 1980 to 2015. We grouped countries by the national gross domestic product (GDP) per capita in purchasing power parity, and analyzed the correlation between life expectancy at birth, obesity prevalence for both sexes, 20+ years old, age-adjusted. For calculations and plotting we employ Python, libraries pandas, NumPy.

Results

We grouped countries at different time point during the study interval. Some countries changed their place in the range of GDP, and thus the shape of the curves describing the connection of obesity and longevity changed. In all groupings countries that are more affluent demonstrates higher longevity and higher prevalence of obesity. At all levels of GDP during the period of analysis we found the increase in obesity prevalence and increase of longevity. In poor countries the small increase in obesity prevalence is accompanied by the significant increase in longevity. Obesity-longevity tracks for individual countries suggest that they reflect the specific periods of the blossom or crisis in national economy and related aspects of life. For rich countries obesity-longevity curves suggest that the positive correlation is approaching the upper limit.

Conclusions

During the period 1980-2015 life expectancy is increasing at all levels of GDP with increase in the prevalence of obesity. Positive effect of a better nutrition, reflected by the prevalence of obesity, is powerful, but approaching its upper limit in the affluent countries.

Key messages

At all levels of economic development the life expectance is increasing with prevalence of obesity. Positive effect of a better nutrition, reflected by the prevalence of obesity, is powerful, but approaching its upper limit in the affluent countries.

Peptide-oligonucleotide conjugates exhibiting pyrimidine-X cleavage specificity efficiently silence miRNA target acting synergistically with RNase H

Taking into account the important role of miRNA in carcinogenesis, oncogenic miRNAs are attractive molecules for gene-targeted therapy. Here, we developed a novel series of peptide-oligonucleotide conjugates exhibiting ribonuclease activity targeted to highly oncogenic miRNAs miR-21 and miR-17. When designing the conjugates, we enhanced both nuclease resistance of the targeted oligodeoxyribonucleotide by introducing at its 3'-end mini-hairpin structure displaying high thermostability and robustness against nuclease digestion and the efficiency of its functioning by attachment of the catalytic construction (amide)NH2-Gly(ArgLeu)4-TCAA displaying ribonuclease activity to its 5'-end. Designed miRNases efficiently cleaved miRNA targets, exhibiting Pyr-X specificity, and cleavage specificity had strong dependence on the miRNA sequence in the site of peptide location. In vitro, designed miRNases do not prevent cleavage of miRNA bound with the conjugate by RNase H, and more than an 11-fold enhancement of miRNA cleavage by the conjugate is observed in the presence of RNase H. In murine melanoma cells, miRNase silences mmu-miR-17 with very high efficiency as a result of miR-17 cleavage by miRNase and by recruited RNase H. Thus, miRNases provide a system of double attack of the miRNA molecules, significantly increasing the efficiency of miRNA downregulation in the cells in comparison with antisense oligonucleotide.

[Dynamics of LINE-1 Retrotransposon Methylation Levels in Circulating DNA from Lung Cancer Patients Undergoing Antitumor Therapy]

Malignant cell transformation is accompanied with abnormal DNA methylation, such as the hypermethylation of certain gene promoters and hypomethylation of retrotransposons. In particular, the hypomethylation of the human-specific family of LINE-1 retrotransposons was observed in lung cancer tissues. It is also known that the circulating DNA (cirDNA) of blood plasma and cell-surface-bound circulating DNA (csb-cirDNA) of cancer patients accumulate tumor-specific aberrantly methylated DNA fragments, which are currently considered to be valuable cancer markers. This work compares LINE-1 retrotransposon methylation patterns in cirDNA of 16 lung cancer patients before and after treatment. CirDNA was isolated from blood plasma, and csb-cirDNA fractions were obtained by successive elution with EDTA-containing phosphate buffered saline and trypsin. Concentrations of methylated LINE-1 region 1 copies (LINE-1-met) were assayed by real-time methylation-specific PCR. LINE-1 methylation levels were normalized to the concentration of LINE-1 region 2, which was independent of the methylation status (LINE-1-Ind). The concentrations of LINE-1-met and LINE-1-Ind in csb-cirDNA of lung cancer patients exhibited correlations before treatment (r = 0.54), after chemotherapy (r = 0.72), and after surgery (r = 0.83) (P < 0.05, Spearman rank test). In the total group of patients, the level of LINE-1 methylation (determined as the LINE-1-met/LINE-1-Ind ratio) was shown to increase significantly during the follow-up after chemotherapy (P < 0.05, paired t test) and after surgery compared to the level of methylation before treatment (P < 0.05, paired t test). The revealed association between the level of LINE-1 methylation and the effect of antitumor therapy was more pronounced in squamous cell lung cancer than in adenocarcinoma (P < 0.05 and P > 0.05, respectively). These results suggest a need for the further investigation of dynamic changes in levels of LINE-1 methylation depending on the antitumor therapy.

Antitumor Vaccines Based on Dendritic Cells: From Experiments using Animal Tumor Models to Clinical Trials

The routine methods used to treat oncological diseases have a number of drawbacks, including non-specific action and severe side effects for patients. Furthermore, tumor diseases are associated with a suppression of the immune system that often leads to the inefficiency of standard treatment methods. The development of novel immunotherapeutic approaches having specific antitumor action and that activate the immune system is of crucial importance. Vaccines based on dendritic cells (DCs) loaded with tumor antigens ex vivo that can activate antitumor cytotoxic T-cell responses stand out among different antitumor immunotherapeutic approaches. This review is focused on analyzing different methods of DC-based vaccine preparation and current research in antitumor DC-based vaccines using animal tumor models and in clinical trials.

Antitumor Vaccines Based on Dendritic Cells: From Experiments using Animal Tumor Models to Clinical Trials

The routine methods used to treat oncological diseases have a number of drawbacks, including non-specific action and severe side effects for patients. Furthermore, tumor diseases are associated with a suppression of the immune system that often leads to the inefficiency of standard treatment methods. The development of novel immunotherapeutic approaches having specific antitumor action and that activate the immune system is of crucial importance. Vaccines based on dendritic cells (DCs) loaded with tumor antigens ex vivo that can activate antitumor cytotoxic T-cell responses stand out among different antitumor immunotherapeutic approaches. This review is focused on analyzing different methods of DC-based vaccine preparation and current research in antitumor DC-based vaccines using animal tumor models and in clinical trials.

Whole-Genome DNA Methylation Analysis of Peripheral Blood Mononuclear Cells in Multiple Sclerosis Patients with Different Disease Courses

Multiple sclerosis (MS) is a severe neurodegenerative disease of polygenic etiology affecting the central nervous system. In addition to genetic factors, epigenetic mechanisms, primarily DNA methylation, which regulate gene expression, play an important role in MS development and progression. In this study, we have performed the first whole-genome DNA methylation profiling of peripheral blood mononuclear cells in relapsing-remitting MS (RRMS) and primary-progressive MS (PPMS) patients and compared them to those of healthy individuals in order to identify the differentially methylated CpG-sites (DMSs) associated with these common clinical disease courses. In addition, we have performed a pairwise comparison of DNA methylation profiles in RRMS and PPMS patients. All three pairwise comparisons showed significant differences in methylation profiles. Hierarchical clustering of the identified DMS methylation levels and principal component analysis for data visualization demonstrated a clearly defined aggregation of DNA samples of the compared groups into separate clusters. Compared with the control, more DMSs were identified in PPMS patients than in RRMS patients (67 and 30, respectively). More than half of DMSs are located in genes, exceeding the expected number for random distribution of DMSs between probes. RRMS patients mostly have hypomethylated DMSs, while in PPMS patients DMSs are mostly hypermethylated. CpG-islands and CpG-shores contain 60% of DMSs, identified by pairwise comparison of RRMS and control groups, and 79% of those identified by pairwise comparison of PPMS and control groups. Pairwise comparison of patients with two clinical MS courses revealed 51 DMSs, 82% of which are hypermethylated in PPMS. Overall, it was demonstrated that there are more changes in the DNA methylation profiles in PPMS than in RRMS. The data confirm the role of DNA methylation in MS development. We have shown, for the first time, that DNA methylation as an epigenetic mechanism is involved in the formation of two distinct clinical courses of MS: namely, RRMS and PPMS.

Nucleic acids in exosomes: disease markers and intercellular communication molecules

The term "exosomes" is currently used to describe specific vesicular structures of endosomal origin produced by the majority of eukaryotic cells. These natural vesicles have been under study for more than two decades. Nevertheless, a real splash of scientific interest in studies on exosomes took place only during recent years, when the concept of the role and functions of exosomes in multicellular organisms was essentially reconsidered. The major role in this was played by the discovery of exosomal mRNA and miRNA in 2007, which stimulated the idea of regulatory and communicative role of exosomes in the organism and also encouraged considering exosomes and other vesicles as potential biomarkers. The present review summarizes the up to date knowledge on the composition and probable physiological functions of nucleic acids released by different cells as components of exosomes. We also touch upon the problem of using these data in clinical diagnosis.

A method for generating selective DNA probes for the analysis of C-negative regions in human chromosomes

Linker-adapter polymerase chain reaction (LA-PCR) is among the most efficient techniques for whole genome DNA amplification. The key stage in LA-PCR is the hydrolysis of a DNA sample with restriction endonucleases, and the choice of a restriction endonuclease (or several endonucleases) determines the composition of DNA probes generated in LA-PCR. Computer analysis of the localization of the restriction sites in human genome has allowed us to propose an efficient technique for generating DNA probes by LA-PCR using the restriction endonucleases HaeIII and RsaI. In silico hydrolysis of human genomic DNA with endonucleases HaeIII and RsaI demonstrate that 100- to 1,000-bp DNA fragments are more abundant in the gene-rich regions. Applying in situ hybridization to metaphase chromosomes, we demonstrated that the produced DNA probes predominantly hybridized to the C-negative chromosomal regions, whereas the FISH signal was almost absent in the C-positive regions. The described protocol for generating DNA probes may be successfully used in subsequent cytogenetic analysis of the C-negative chromosomal regions.

Circulating nucleic acids as a potential source for cancer biomarkers

Since the association of circulating DNA level changes with tumor growth was discovered many attempts have been made to develop the sensitive and robust blood-based tests for early tumor diagnostics. Both genomic as well as mitochondrial DNA quantification in the circulation have been extensively evaluated as a diagnostic and prognostic tool to monitor cancer therapy. Cell-free DNA bearing the same genetic and epigenetic changes as the tumor tissues were shown to be detectable in plasma / serum of cancer patients indicating the principal possibility to create the minimally invasive diagnostic tests based on tumor-specific DNA markers. Apart from circulating DNA, tumor-derived RNA in plasma / serum was found to be a promising approach for the development of cancer markers. Results of the last two years establish the quantification of the tumor-derived microRNAs in plasma / serum as an extremely promising approach for cancer diagnostics. The aim of this publication was to review the recently reported studies on the circulating DNA and RNA in cancer patients and to estimate their impact on making the ongoing research closer to clinical application.

[Sequence-specific interaction of pyrimidine oligonucleotides with double-stranded DNA at acidic pH complexes of different types]

The interaction of pyrimidine oligonucleotides (OLN(15) and OLN(6)) and their alkylating derivatives bearing 4-(3-amino)-N-methyl and N-2-chloroethyl (RCl) aniline residues at the 5'-phosphate with a fragment of the human gamma-interferon gene was studied. In the presence of 150 mM NaCl at pH 5.4, the yield of dsDNA alkylation was 60% for RCl-OLN(15) and 10% for RCl-OLN(6); at pH 4.0 in the presence of 150 mM NaCl and 10 mM MgCl2, the yield of the dsDNA modification product was 100% for RCl-OLN(6) and 50% for RCl-OLN(15). It was shown by native electrophoresis that OLN(15) could form with the target dsDNA complexes of two types in the presence of magnesium ions at pH 4.0. One of the complexes was stable at pH 5.4 in the presence of magnesium ions, whereas the other was not. We found that only the complex stable in 10 mM Mg(OAc)2, pH 5.4, was effectively alkylated.

New approaches for cancer treatment: antitumor drugs based on gene-targeted nucleic acids

Currently, the main way to fight cancer is still chemotherapy. This method of treatment is at the height of its capacity, so, setting aside the need for further improvements in traditional treatments for neoplasia, it is vital to develop now approaches toward treating malignant tumors. This paper reviews innovational experimental approaches to treating malignant malformations based on the use of gene-targeted drugs, such as antisense oligonucleotides (asON), small interfering RNA (siRNA), ribozymes, and DNAzymes, which can all inhibit oncogene expression. The target genes for these drugs are thoroughly characterized, and the main results from pre-clinical and first-step clinical trials of these drugs are presented. It is shown that the gene-targeted oligonucleotides show considerable variations in their effect on tumor tissue, depending on the target gene in question. The effects range from slowing and stopping the proliferation of tumor cells to suppressing their invasive capabilities. Despite their similarity, not all the antisense drugs targeting the same region of the mRNA of the target-gene were equally effective. The result is determined by the combination of the drug type used and the region of the target-gene mRNA that it complements.

Deoxyribonuclease activity in biological fluids of healthy donors and cancer patients

Integral activity of neutral deoxyribonucleases in the plasma and urine or donors, patients with benign prostatic hyperplasia, and patients with stomach and prostatic cancer was studied by IFA based on hydrolysis of DNA fragment modified with haptene molecules. In donors plasma deoxyribonuclease activity was 0.16+/-0.04, urinary activity 1.49+/-1.41 act. U/ml. In patients with benign prostatic hyperplasia and malignant tumors the integral activity of blood deoxyribonucleases was significantly below the normal, and in tumors it did not correlate with tumor size and disease stage. A significant correlation between blood and urinary deoxyribonuclease activities was detected.

Cleavage of RNA by an amphiphilic compound lacking traditional catalytic groups

Recently, in experiments with combinatorial libraries of amphiphilic compounds lacking groups, known as catalysts of transesterification reaction, we discovered novel RNA-cleaving compounds [N. Kovalev, E. Burakova, V. Silnikov, M. Zenkova, V. Vlassov, Bioorg. Chem. 34 (2006) 274-286]. In the present study, we investigate cleavage of RNA by the most active representative of these libraries, compound named Dp12. Sequence-specificity of RNA cleavage and influence of reaction conditions on cleavage rate suggested that Dp12 enormously accelerates spontaneous RNA cleavage. Light scattering experiments revealed that the RNA cleavage proceeds within multiplexes formed by assembles of RNA and Dp12 molecules, at Dp12 concentration far below critical concentration of micelle formation. Under these conditions, Dp12 is presented in the solution as individual molecules, but addition of RNA to this solution triggers formation of the multiplexes. The obtained data suggest a possible mechanism of RNA cleavage, which includes interaction of the compound with RNA sugar-phosphate backbone resulting in changing of ribose conformation. This leads to juxtaposition of the 2'-hydroxyl group and internucleotide phosphorus atom at a distance needed for the transesterification to occur.

RNase T1 mimicking artificial ribonuclease

Recently, artificial ribonucleases (aRNases)—conjugates of oligodeoxyribonucleotides and peptide (LR)₄-G-amide—were designed and assessed in terms of the activity and specificity of RNA cleavage. The conjugates were shown to cleave RNA at Pyr-A and G–X sequences. Variations of oligonucleotide length and sequence, peptide and linker structure led to the development of conjugates exhibiting G–X cleavage specificity only. The most efficient catalyst is built of nonadeoxyribonucleotide of unique sequence and peptide (LR)₄-G-NH₂ connected by the linker of three abasic deoxyribonucleotides (conjugate pep-9). Investigation of the cleavage specificity of conjugate pep-9 showed that the compound is the first single-stranded guanine-specific aRNase, which mimics RNase T1. Rate enhancement of RNA cleavage at G–X linkages catalysed by pep-9 is 10⁸ compared to non-catalysed reaction, pep-9 cleaves these linkages only 10⁵-fold less efficiently than RNase T1 (k_{cat_RNase T1}/k_cat__pep-9 = 10⁵).

Cell-free and cell-bound circulating DNA in breast tumours: DNA quantification and analysis of tumour-related gene methylation

Tumour development is characterised by the increased circulating DNA (cirDNA) concentration and by tumour-related changes in blood plasma DNA. Concentration of cirDNA and methylation of RARβ2, RASSF1A and HIC-1 gene promoters were investigated in cell-free and cell-surface-bound fractions from healthy donors, patients with breast cancer, and patients with breast fibroadenoma. Tumour development was shown to lead to significant changes in the distribution of cirDNA between cell-free and cell-surface-bound fractions. Analysis of RARβ2 and RASSF1A methylation in the total cirDNA provides 95% diagnostic coverage in breast cancer patients, 60% in patients with benign lesions, and is without false-positive results in healthy women. Results of the study indicate that methylation-specific PCR of RARβ2 and RASSF1A genes based on the total cirDNA combined with the quantitative analysis of cirDNA distribution between cell-bound and cell-free fractions in blood provide the sensitive and accurate detection and discrimination of malignant and benign breast tumours.