Statistical Dissection of the Genetic Determinants of Phenotypic Heterogeneity in Genes with Multiple Associated Rare Diseases.

Phenotypicheterogeneity is a phenomenon in which distinct phenotypes can develop in individuals bearing pathogenic variants in the same gene. Genetic factors, gene interactions, and environmental factors are usually considered the key mechanisms of this phenomenon. Phenotypic heterogeneity may impact the prognosis of the disease severity and symptoms. In our work, we used publicly available data on the association between genetic variants and Mendelian disease to investigate the genetic factors (such as the intragenic localization and type of a variant) driving the heterogeneity of gene-disease relationships. First, we showed that genes linked to multiple rare diseases (GMDs) are more constrained and tend to encode more transcripts with high levels of expression across tissues. Next, we assessed the role of variant localization and variant types in specifying the exact phenotype for GMD variants. We discovered that none of these factors is sufficient to explain the phenomenon of such heterogeneous gene-disease relationships. In total, we identified only 38 genes with a weak trend towards significant differences in variant localization and 30 genes with nominal significant differences in variant type for the two associated disorders. Remarkably, four of these genes showed significant differences in both tests. At the same time, our analysis suggests that variant localization and type are more important for genes linked to autosomal dominant disease. Taken together, our results emphasize the gene-level factors dissecting distinct Mendelian diseases linked to one common gene based on open-access genetic data and highlight the importance of exploring other factors that contributed to phenotypic heterogeneity.

Bone calcification rate as a factor of craniofacial transformations in salmonid fish: Insights from an experiment with hormonal treatment of calcium metabolism.

Adaptation to different environments can be achieved by physiological shifts throughout development. Hormonal regulators shape the physiological and morphological traits of the evolving animals making them fit for the particular ecological surroundings. We hypothesized that the artificially induced hypersynthesis of calcitonin and parathyroid hormone mutually influencing calcium metabolism could affect bone formation during early ontogeny in fish imitating the heterochrony in craniofacial ossification in natural adaptive morphs. Conducting an experiment, we found that the long-standing treatment of salmonid juveniles with high doses of both hormones irreversibly shifts the corresponding hormone status for a period well beyond the time scale for total degradation of the injected hormone. The hormones program the ossification of the jaw suspension bones and neurocranial elements in a specific manner affecting the jaws position and pharingo-branchial area stretching. These morphological shifts resemble the adaptive variants found in sympatric pelagic and demersal morphs of salmonids. We conclude that solitary deviations in the regulators of calcium metabolism could determine functional morphological traits via transformations in skeletal development.

The variability of PNPLA3 gene as a potential marker of cold adaptation in Yakuts.

Nonalcoholic fatty liver disease (NAFLD) is one of the most common chronic liver diseases. It has been reported that specific variants of patatin-like phospholipase domain-containing 3 (PNPLA3) gene, notably SNPs rs738409 and rs2294918 are associated with high risks of liver disease. PNPLA3 rs738409 polymorphism is the main determinant of fatty liver and affects development and progression of NAFLD. rs2294918 is another SNP localised in PNPLA3 gene, it is associated with reduced expression of the PNPLA3 protein, lowering the effect of the rs738409:G variant on predisposition to steatosis and liver damage. The frequencies of alleles, genotypes, haplotypes and diplotypes (combinations of genotypes at two loci) of polymorphic variants of the PNPLA3 gene (rs2294918 and rs738409) were studied in the cohort of Yakuts (n = 150) living in the Republic of Sakha (Yakutia). Genotyping of PNPLA3 (rs738409 and rs2294918) was performed by PCR-PDRF method. The single nucleotide polymorphism rs738409 (I148M) of the PNPLA3 gene in the Yakut population is characterised by a high frequency of the risk allele G (72%). Analysis of the distribution frequency of the rs2294918 polymorphism genotypes showed that the allele G was predominant in 89.3% of individuals of the studied group of Yakuts. In this study, we identified two major diplotypes [GG][GG] and [CG][GG]. The high frequency of the mutant rs738409: G variant in Yakuts may be an adaptation of the organism to low temperatures. The study of the adiponutringene may be an important key to understanding the mechanisms of adaptation to low temperatures and metabolic processes in the indigenous population of the North.

Fear memory in humans is consolidated over time independently of sleep.

Fear memories can be altered after acquisition by processes, such as fear memory consolidation or fear extinction, even without further exposure to the fear-eliciting stimuli, but factors contributing to these processes are not well understood. Sleep is known to consolidate, strengthen, and change newly acquired declarative and procedural memories. However, evidence on the role of time and sleep in the consolidation of fear memories is inconclusive. We used highly sensitive electrophysiological measures to examine the development of fear-conditioned responses over time and sleep in humans. We assessed event-related brain potentials (ERP) in 18 healthy, young individuals during fear conditioning before and after a 2-hour afternoon nap or a corresponding wake interval in a counterbalanced within-subject design. The procedure involved pairing a neutral tone (CS+) with a highly unpleasant sound. As a control, another neutral tone (CS-) was paired with a neutral sound. Fear responses were examined before the interval during a habituation phase and an acquisition phase as well as after the interval during an extinction phase and a reacquisition phase. Differential fear conditioning during acquisition was evidenced by a more negative slow ERP component (stimulus-preceding negativity) developing before the unconditioned stimulus (loud noise). This differential fear response was even stronger after the interval during reacquisition compared with initial acquisition, but this effect was similarly pronounced after sleep and wakefulness. These findings suggest that fear memories are consolidated over time, with this effect being independent of intervening sleep.

The Modifying Effect of Obesity on the Association of Matrix Metalloproteinase Gene Polymorphisms with Breast Cancer Risk.

Objective: We investigated the possible modifying effect of obesity on the association of matrix metalloproteinase (MMP) gene polymorphisms with breast cancer (BC) risk. Methods: A total of 1104 women divided into two groups according to their body mass index (BMI): BMI ≥ 30 (119 BC, and 190 control) and BMI < 30 (239 BC, and 556 control) were genotyped for specially selected (according to their association with BC in the previous study) 10 single-nucleotide polymorphisms (SNP) of MMP1, 2, 3, 8, and 9 genes. Logistic regression association analysis was performed in each studied group of women (with/without obesity). Functional annotation of BC-correlated MMP polymorphic variants was analyzed by in silico bioinformatics. Results: We observed significant differences in the involvement of MMP SNPs in BC in obese and non-obese women. Polymorphic loci MMP9 (c.836 A > G (rs17576) and c. 1721 C > G (rs2250889)) were BC-protective factors in obese women (OR 0.71, allelic model, and OR 0.55, additive model, respectively). Genotypes TT MMP2 (c.-1306 C > T,rs243865) and AA MMP9 (c. 1331-163 G > A,rs3787268) determined BC susceptibility in non-obese women (OR 0.31, and OR 2.36, respectively). We found in silico substantial multidirectional influences on gene expression in adipose tissue BC-related polymorphic loci: BC risk allele A-rs3787268 in non-obese women is associated with low expression NEURL2, PLTP, RP3-337O18.9, SPATA25, and ZSWIM1, whereas BC risk allele A-rs17576 in obese women is associated with high expression in the same genes in visceral and/or subcutaneous adipose. Conclusions: our study indicated that obesity has a significant modifying effect on the association of MMP genes with BC risk in postmenopausal women.

Matrix Metalloproteinase Gene Polymorphisms Are Associated with Breast Cancer in the Caucasian Women of Russia.

We conducted this study to explore the association between matrix metalloproteinase (MMP) gene polymorphisms and breast cancer (BC) risk in the Caucasian women of Russia. In total, 358 affected (BC) and 746 unaffected (cancer-free) women were included in this case-control retrospective study. From BC-related genes in previous studies, ten single nucleotide polymorphisms (SNPs) in five MMP genes (MMP1, 2, 3, 8, 9) were genotyped. The BC risk was calculated by logistic regression (to evaluate the SNPs' independent effects) and model-based multifactor dimensionality reduction (MB-MDR) (to identify SNP−SNP interactions) methods. The allelic variants' distribution of c.836 A > G (rs17576) and c. 1721 C > G (rs2250889) MMP9 was significantly different between BC and cancer-free women: for G minor alleles, these SNPs manifested disorder protective effects (OR 0.82 and OR 0.67−0.71, respectively, pperm ≤ 0.035). Eleven haplotypes of six SNPs MMP9 were involved in BC risk (nine haplotypes) and protective (two haplotypes) effects. All 10 SNPs of the MMP genes examined were associated with BC within the 13 SNP−SNP interaction simulated models, with a pivotal role of the two-locus (rs17577 × rs3918242) MMP9 epistatic interaction (defined as 1.81% BC entropy within more than 60% of the genetic models). Under in silico bioinformatics, BC susceptibility MMP polymorphic loci are located in functionally active genome regions and impact genes expression and splicing "regulators" in the mammary gland. The biological pathways of BC MMP candidate genes are mainly realized due to metalloendopeptidase activity and extracellular matrix organization (structure, disassembly, metabolic process, etc.). In conclusion, our data show that MMP gene polymorphisms are related to BC susceptibility in the Caucasian women of Russia.

Expression of Opsin Genes in the Retina of Female and Male Three-Spined Sticklebacks Gasterosteus aculeatus L.: Effect of Freshwater Adaptation and Prolactin Administration.

Color vision sensitivity is crucial for fish adaptation during migration and reproduction. Prolactin and prolactin-like hormone are important regulators in both these processes. We hypothesized that prolactin influences the color vision sensitivity during freshwater migrations in fish. We studied the effects of prolactin and freshwater adaptation during the spawning period on the expression of opsin genes (SWS1, SWS2, RH2, LWS) in the retina of female and male three-spined sticklebacks Gasterosteus aculeatus L. Expression of the prolactin gene increased in the brain of females, but not males, while expression of the prolactin-like hormone decreased in the brain of both male and female sticklebacks during freshwater adaptation. Expression of the SWS2 gene decreased in the retina of females and males during freshwater adaptation and after prolactin administration. Expression of the SWS1 gene decreased in the retina of male sticklebacks after prolactin administration, but not during freshwater adaptation. Expression of the RH2 and LWS genes did not depend on prolactin administration in male and female sticklebacks. We conclude that expression of some opsin genes in the retina of sticklebacks is regulated by prolactin and depends on sex and freshwater adaptation. This expands our knowledge of the adaptive effects of prolactin on fish during freshwater migrations.

Multidecadal declines in particulate mercury and sediment export from Russian rivers in the pan-Arctic basin.

SignificanceRussian rivers are the predominant source of riverine mercury to the Arctic Ocean, where methylmercury biomagnifies to high levels in food webs. Pollution controls are thought to have decreased late-20th-century mercury loading to Arctic watersheds, but there are no published long-term observations on mercury in Russian rivers. Here, we present a unique hydrochemistry dataset to determine trends in Russian river particulate mercury concentrations and fluxes in recent decades. Using hydrologic and mercury deposition modeling together with multivariate time series analysis, we determine that 70 to 90% declines in particulate mercury fluxes were driven by pollution reductions and sedimentation in reservoirs. Results suggest that Russian rivers likely dominated over all other sources of mercury to the Arctic Ocean until recently.

Repolarizing potassium currents in working myocardium of Japanese quail: a novel translational model for cardiac electrophysiology.

Birds developed endothermy and four-chambered high-performance heart independently from mammals. Though avian embryos are extensively studied and widely used as various models for heart research, little is known about cardiac physiology of adult birds. Meanwhile, cardiac electrophysiology is in search for easily accessible and relevant model objects which resemble human myocardium in the pattern of repolarizing currents (IKr, IKs, IKur and Ito). This study focuses on the configuration of electrical activity and electrophysiological phenotype of working myocardium in adult Japanese quails (Coturnix japonica). The resting membrane potential and action potential (AP) waveform in quail atrial myocardium were similar to that in working myocardium of rodents. Using whole-cell patch clamp and sharp glass microelectrodes, we demonstrated that the repolarization of quail atrial and ventricular myocardium is determined by voltage-dependent potassium currents IKr, IKs and Ito - the latter was previously considered as an exclusive evolutionary feature of mammals. The specific blockers of these currents, dofetilide (3 µmol l-1), HMR 1556 (30 µmol l-1) and 4-aminopyridine (3 mmol l-1), prolonged AP in both ventricular and atrial myocardial preparations. The expression of the corresponding channels responsible for these currents in quail myocardium was investigated with quantitative RT-PCR and western blotting. In conclusion, the described pattern of repolarizing ionic currents and channels in quail myocardium makes this species a novel and suitable experimental model for translational cardiac research and reveals new information related to the evolution of cardiac electrophysiology in vertebrates.

LPDs - «Linked to penumbra¼ discharges or EEG correlate of excitotoxicity: A review based hypothesis.

Periodic lateralized epileptiform discharges (PLEDs) or lateralized periodic discharges (LPDs) are a well-known variant of pathological EEG activity. However, the mechanisms underpinning the appearance of this pattern are not completely understood. The heterogeneity of the features derived from LPDs patterns, and the wide range of pathological conditions in which they occur, raise a question about the unifying mechanisms underlying these phenomena. This paper reassesses the current opinion surrounding LPDs which considers glutamate excitotoxicity to be the primary pathophysiological basis, and the penumbral region to be the main morphological substrate. Arguments in favour of this hypothesis are presented, with interpretations supported by evidence from recent literature involving clinical and experimental data. Presently, no single hypothesis places considerable emphasis on the pathochemical properties of LPDs, which are implicitly meaningful towards better understanding of the clinical significance of this pattern.

OCT-elastography-based optical biopsy for breast cancer delineation and express assessment of morphological/molecular subtypes.

Application of compressional optical coherence elastography (OCE) for delineation of tumor and peri-tumoral tissue with simultaneous assessment of morphological/molecular subtypes of breast cancer is reported. The approach is based on the ability of OCE to quantitatively visualize stiffness of studied samples and then to perform a kind of OCE-based biopsy by analyzing elastographic B-scans that have sizes ~several millimeters similarly to bioptates used for "gold-standard" histological examinations. The method relies on identification of several main tissue constituents differing in their stiffness in the OCE scans. Initially the specific stiffness ranges for the analyzed tissue components (adipose tissue, fibrous and hyalinized tumor stroma, lymphocytic infiltrate and agglomerates of tumor cells) are determined via comparison of OCE and morphological/molecular data. Then assessment of non-tumor/tumor regions and tumor subtypes is made based on percentage of pixels with different characteristic stiffness ("stiffness spectrum") in the OCE image, also taking into account spatial localization of different-stiffness regions. Examples of high contrast among benign (or non-invasive) and several subtypes of invasive breast tumors in terms of their stiffness spectra are given.

Quantitative nontumorous and tumorous human brain tissue assessment using microstructural co- and cross-polarized optical coherence tomography.

Optical coherence tomography (OCT) is a promising method for detecting cancer margins during tumor resection. This study focused on differentiating tumorous from nontumorous tissues in human brain tissues using cross-polarization OCT (CP OCT). The study was performed on fresh ex vivo human brain tissues from 30 patients with high- and low-grade gliomas. Different tissue types that neurosurgeons should clearly distinguish during surgery, such as the cortex, white matter, necrosis and tumorous tissue, were separately analyzed. Based on volumetric CP OCT data, tumorous and normal brain tissue were differentiated using two optical coefficients - attenuation and forward cross-scattering. Compared with white matter, tumorous tissue without necrotic areas had significantly lower optical attenuation and forward cross-scattering values. The presence of particular morphological patterns, such as necrosis and injured myelinated fibers, can lead to dramatic changes in coefficient values and create some difficulties in differentiating between tissues. Color-coded CP OCT maps based on optical coefficients provided a visual assessment of the tissue. This study demonstrated the high translational potential of CP OCT in differentiating tumorous tissue from white matter. The clinical use of CP OCT during surgery in patients with gliomas could increase the extent of tumor resection and improve overall and progression-free survival.

Can "Indirect" Contact Laser Surgery be Used for Fluorescence-Image Guided Tumor Resections? Preliminary Results.

Ensuring the complete removal of tumor tissue is the main challenge during resection operations. Recently, a technique of "indirect" contact laser surgery has been developed. In this study we assess the possibility of using such surgery for fluorescence image-guided tumor resection. Mouse colon adenocarcinoma CT-26 cells stably expressing the fluorescent protein mKate-2 was used as the tumor model. Resections of the tumor nodes were performed with either a scalpel blade, a laser scalpel with a bare tip, or a laser scalpel with a strongly absorbing coating on the fiber tip. Tumor-positive resection margins were detected using an IVIS Spectrum fluorescence imaging system. After tumor resection with the scalpel blade over half of the animals needed one additional resection to remove residual tumor cells. Animals in this group showed tumor recurrence within 7 days. Fluorescence imaging of the tumor bed, performed after resection to assess the presence of tumor cell clusters, was sufficiently effective only with a bloodless resection. The laser scalpels both with the bare tip and with the strongly absorbing coating on the tip provided such bloodless tumor resection in contact mode. Fewer animals required additional resections when the bare tipped scalpel was used and this also resulted in a reduction in tumor recurrence. After resections were carried out with the laser scalpel with the strongly absorbing coating on the tip, fluorescence was detected in the operative field and this led to undertaking additional resections, although subsequent investigation suggested that this was "false" fluorescence, resulting from the effects of the scalpel rather than the presence of residual tumor cells. The method of laser resection with a strongly absorbing coating on the tip therefore did not appear to demonstrate definite advantages over laser resection with a bare tip when removing tumors.