DNA isolation protocol effects on nuclear DNA analysis by microarrays, droplet digital PCR, and whole genome sequencing, and on mitochondrial DNA copy number estimation.

Potential bias introduced during DNA isolation is inadequately explored, although it could have significant impact on downstream analysis. To investigate this in human brain, we isolated DNA from cerebellum and frontal cortex using spin columns under different conditions, and salting-out. We first analysed DNA using array CGH, which revealed a striking wave pattern suggesting primarily GC-rich cerebellar losses, even against matched frontal cortex DNA, with a similar pattern on a SNP array. The aCGH changes varied with the isolation protocol. Droplet digital PCR of two genes also showed protocol-dependent losses. Whole genome sequencing showed GC-dependent variation in coverage with spin column isolation from cerebellum. We also extracted and sequenced DNA from substantia nigra using salting-out and phenol / chloroform. The mtDNA copy number, assessed by reads mapping to the mitochondrial genome, was higher in substantia nigra when using phenol / chloroform. We thus provide evidence for significant method-dependent bias in DNA isolation from human brain, as reported in rat tissues. This may contribute to array "waves", and could affect copy number determination, particularly if mosaicism is being sought, and sequencing coverage. Variations in isolation protocol may also affect apparent mtDNA abundance

Preparation of polyclonal and monoclonal anti-idiotypic antibodies against morphine-specific immunoglobulins

The preparation and study of anti-idiotypic (secondary) antibodies (Ab2) against monoclonal primary antibodies (Ab1) specific to biologically active molecules with a known structure is of great scientific and practical importance. Due to partial antigenic similarity of Ab2 and the initial antigen structures, these antibodies can be the basis of the vaccine, if the antigen usage is not possible, or is limited by law. In particular, one may create Ab2-based preparations, designed for immunization, in order to prevent and treat the drug addiction. The value of Ab2 properties increases even more if Ab1, used to obtain them, recognize different parts of the antigen molecule, which makes it possible to obtain second-generation antibodies with a wide range of specificity. In this work, the morphine-like polyclonal and monoclonal Ab2 were obtained. In each case, as the first-generation immunoglobulins for immunization, we used two murine monoclonal antibodies (mAbs) specific to different morphine derivatives: 3K11 antibodies to 3-0-carboxymethyl (CMM) and 2-p-carboxyphenylazomethyl (FAM) derivatives, as well as 6G1 antibodies to 6-hemisuccinyl derivative (GSM). After immunization of the horse with Ab1 and development of immune response, three pools of specific polyclonal antibodies were isolated from the animal blood serum: horse anti-species antibodies to the total mouse immunoglobulins (HAM); horse anti-idiotypic antibodies against 3K11 antibodies (HAM-K11), and against 6G1 antibodies (HAM-G1). In parallel, immunization of mice with 3K11 and 6G1 antibodies and fusion of obtained lymphocytes with Sp2/0 mouse myeloma cells by the Milstein-Köhler method resulted in three producers of anti-idiotypic antibodies: a clone producing mouse monoclonal Ab2 specific for mAb-6G1 (AIG1), as well as clones producing anti-mAb-3K11 antibodies (AI-K11A and AI-K11B). The physico-chemical and antigenic properties of all the Ab2 obtained were characterized. It was shown that the horse anti-idiotypic immunoglobulins not only belong to different classes, but are also polyvalent, while all monoclonal Ab2 obtained are represented by IgM immunoglobulins, being also strictly specific to the corresponding first-generation antibodies. Subsequently, the morphine-like properties of the first domestic polyclonal and monoclonal Ab2 obtained in the work will be investigated in a cellular model. Likewise, we shall study their ability to induce Ab3 as well as morphine-specific Ab1

Copy number evolution and its relationship with patient outcome—an analysis of 178 matched presentation-relapse tumor pairs from the Myeloma XI trial

Structural chromosomal changes including copy number aberrations (CNAs) are a major feature of multiple myeloma (MM), however their evolution in context of modern biological therapy is not well characterized. To investigate acquisition of CNAs and their prognostic relevance in context of first-line therapy, we profiled tumor diagnosis–relapse pairs from 178 NCRI Myeloma XI (ISRCTN49407852) trial patients using digital multiplex ligation-dependent probe amplification. CNA profiles acquired at relapse differed substantially between MM subtypes: hyperdiploid (HRD) tumors evolved predominantly in branching pattern vs. linear pattern in t(4;14) vs. stable pattern in t(11;14). CNA acquisition also differed between subtypes based on CCND expression, with a marked enrichment of acquired del(17p) in CCND2 over CCND1 tumors. Acquired CNAs were not influenced by high-dose melphalan or lenalidomide maintenance randomization. A branching evolution pattern was significantly associated with inferior overall survival (OS; hazard ratio (HR) 2.61, P = 0.0048). As an individual lesion, acquisition of gain(1q) at relapse was associated with shorter OS, independent of other risk markers or time of relapse (HR = 2.00; P = 0.021). There is an increasing need for rational therapy sequencing in MM. Our data supports the value of repeat molecular profiling to characterize disease evolution and inform management of MM relapse

Polyglutamine tracts as modulators of transcriptional activation from yeast to mammals

Abstract Microsatellite repeats are genetically unstable and subject to expansion and shrinkage. A subset of them, triplet repeats, can occur within the coding region and specify homomeric tracts of amino acids. Polyglutamine (polyQ) tracts are enriched in eukaryotic regulatory proteins, notably transcription factors, and we had shown before that they can contribute to transcriptional activation in mammalian cells. Here we generalize this finding by also including evolutionarily divergent organisms, namely, Drosophila and baker's yeast. In all three systems, Gal4-based model transcription factors were more active if they harbored a polyQ tract, and the activity depended on the length of the tract. By contrast, a polyserine tract was inactive. PolyQs acted from either an internal or a C-terminal position, thus ruling out a merely structural "linker" effect. Finally, a two-hybrid assay in mammalian cells showed that polyQ tracts can interact with each other, supporting the concept that a polyQ-containing transcription factor can recruit other factors with polyQ tracts or glutamine-rich activation domains. The widespread occurrence of polyglutamine repeats in regulatory proteins suggests a beneficial role; in addition to the contribution to transcriptional activity, their genetic instability might help a species to adapt to changing environmental conditions in a potentially reversible manner

Characterization of MtnE, the fifth metallothionein member in Drosophila

Metallothioneins (MTs) constitute a family of cysteine-rich, low molecular weight metal-binding proteins which occur in almost all forms of life. They bind physiological metals, such as zinc and copper, as well as nonessential, toxic heavy metals, such as cadmium, mercury, and silver. MT expression is regulated at the transcriptional level by metal-regulatory transcription factor 1 (MTF-1), which binds to the metal-response elements (MREs) in the enhancer/promoter regions of MT genes. Drosophila was thought to have four MT genes, namely, MtnA, MtnB, MtnC, and MtnD. Here we characterize a new fifth member of Drosophila MT gene family, coding for metallothionein E (MtnE). The MtnE transcription unit is located head-to-head with the one of MtnD. The intervening sequence contains four MREs which bind, with different affinities, to MTF-1. Both of the divergently transcribed MT genes are completely dependent on MTF-1, whereby MtnE is consistently more strongly transcribed. MtnE expression is induced in response to heavy metals, notably copper, mercury, and silver, and is upregulated in a genetic background where the other four MTs are missing

High-Throughput Molecular Cancer Cell Line Characterization Using Digital Multiplex Ligation-Dependent Probe Amplification for Improved Standardization of in Vitro Research.

Tumor cell lines are widely used for cancer research, but challenges regarding quality control of cell line identity, cross contamination, and tumor somatic molecular stability remain, demanding novel approaches beyond conventional short tandem repeat profiling. A total of 21 commonly used multiple myeloma cell lines obtained from public repositories were analyzed by digital multiplex ligation-dependent probe amplification (digitalMLPA) to characterize germline single-nucleotide polymorphisms, insertions/deletions, and somatic copy number aberrations (CNAs). Using generated profiles and an in-house developed analytical pipeline, blinded experiments were performed to determine capability of digitalMLPA to predict cell line identity and potential spike-in DNA contamination in 41 anonymized cell line samples. The dominant cell line was correctly identified in all cases, and cross contamination was correctly detected in 33 of 37 samples with spike-in DNA; there were no false-positive predictions. The four samples in which spike in was not detected all carried low levels of contamination (1%), whereas levels of contamination ≥5% were correctly identified in all cases. Unsupervised clustering of CNA profiles identified shared commonalities that correlated with initiating Ig heavy locus translocation events. Longitudinal CNA assessment of nine cell lines revealed changes under standard culturing conditions not detected by insertion/deletion profiling alone. Results suggest that digitalMLPA can be utilized as a high-throughput tool for advanced quality assurance for in vitro cancer research

Role of the endocrine disorders in pregnancy in the pathogenesis of intrauterine and postnatal developmental disorders in children: modern view within the concept of nutritional programming (literature review)

Due to the growth of non-infectious morbidity of the world’s child and adult population, the concept of nutritional programming connecting cardiovascular and certain endocrine diseases with the fetoplacental complex disorders in the antenatal period has been developed over the past 25 years. An increase in the prevalence of obesity and gestational diabetes in pregnant women lays the groundwork for an increase in the prevalence of glucose metabolism disorders and the risk of endocrine pathology in children. Both low weight and overweight at birth evidence the unfavourable course of the intrauterine period. The review discusses the factors contributing to the fetal organs and systems growth retardation, hypovitaminosis D, insulin resistance and possible mechanisms for their development. The authors present the analysis of the data available in the modern literature on the mechanism of the obesity and GDM programming effect on the diseases in new-borns and children

Effectiveness of nutritional supplementation for children with coeliac disease who are on a gluten-free diet

Patients on a gluten-free diet are at risk of developing polyhypoavitaminosis and deficiency states, which requires the supplementation of their diet to prevent nutrient deficiencies. The aim of the study: to analyze the dynamics of anthropometric and laboratory parameters, components of the quality of life in children with coeliac disease on the background of a month-long course of administration of hypercaloric mixture for enteric nutrition. Materials and methods: 45 children with coeliac disease aged 2-10 years (mean age 6.3 ± 0.3 years) on a strict gluten-free diet for more than one year. All patients received additional enteric nutrition with a hypercaloric mixture in the volume of 200 ml/day (300 kcal/day) for 1 month as a supplement to the main food ration. Two groups of patients receiving the supplement in 2012-2013 and 2017-2018 were identified. Physical development was assessed under the WHO AnthroPlus programme. The quality of life indicators were assessed using the PedQL 4.0 questionnaire. Results: the total frequency of protein-сalorie deficiency (PCD) before the course of nutritional supplementation was 13 (28.9%) cases, while acute PCD was diagnosed in 6 (13.3%) and chronic PCD in 7 (15.6%) patients. Against the background of the course of nutritious supplementation in children with coeliac disease, there was a significant reduction in weight, height and BMI in both groups. Patients in 2012-2013 initially had a greater gap in weight and height compared to children in 2017-2018. There was an improvement in the sum of the quality of life indicators by 6.3% for children in the first group and by 4.3% for children in the second group against the background of nutritional supplementation. Conclusions: Enrichment of children’s diets with a hypercaloric blend of dietary fiber helps to accelerate the pace of physical development, reduce the number of children with diabetes mellitus, improve hemogram rates and most components of quality of life

VITAMIN D DEFICIENCY AND OBESITY IN CHILDREN AND ADOLESCENTS: HOW THE TWO GLOBAL PANDEMIAS ARE INTERCONNECTED. VITAMIN D ROLE IN PATHOGENESIS OF OBESITY AND INSULIN RESISTANCE (PART 1)

The prevalence of the excessive weight and obesity increasing in the human population is a significant concern to the public health. The article provides a literature review devoted to pathophysiologic aspects of the obesity and vitamin D deficiency interconnection. A role of adipokines (leptin, adiponectin), cells of the immune system, proinflammatory cytokines in the pathogenesis of obesity and place of vitamin D as an endocrine and paracrine regulator of inflammatory processes in the fatty tissue. An important role of the vitamin D deficiency in the genesis of the insulin resistance is shown that underlies the fatty tissue accumulation and formation of the metabolic profile characteristic of obesity. Direct and indirect vitamin D effect on the insulin synthesis in the pancreatic gland and sensitivity to it of insulin receptors in the body tissues is demonstrated