iPSC-Derived Endothelial Cells Reveal LDLR Dysfunction and Dysregulated Gene Expression Profiles in Familial Hypercholesterolemia.

Defects in the low-density lipoprotein receptor (LDLR) are associated with familial hypercholesterolemia (FH), manifested by atherosclerosis and cardiovascular disease. LDLR deficiency in hepatocytes leads to elevated blood cholesterol levels, which damage vascular cells, especially endothelial cells, through oxidative stress and inflammation. However, the distinctions between endothelial cells from individuals with normal and defective LDLR are not yet fully understood. In this study, we obtained and examined endothelial derivatives of induced pluripotent stem cells (iPSCs) generated previously from conditionally healthy donors and compound heterozygous FH patients carrying pathogenic LDLR alleles. In normal iPSC-derived endothelial cells (iPSC-ECs), we detected the LDLR protein predominantly in its mature form, whereas iPSC-ECs from FH patients have reduced levels of mature LDLR and show abolished low-density lipoprotein uptake. RNA-seq of mutant LDLR iPSC-ECs revealed a unique transcriptome profile with downregulated genes related to monocarboxylic acid transport, exocytosis, and cell adhesion, whereas upregulated signaling pathways were involved in cell secretion and leukocyte activation. Overall, these findings suggest that LDLR defects increase the susceptibility of endothelial cells to inflammation and oxidative stress. In combination with elevated extrinsic cholesterol levels, this may result in accelerated endothelial dysfunction, contributing to early progression of atherosclerosis and other cardiovascular pathologies associated with FH.

Calling and Phasing of Single-Nucleotide and Structural Variants of the LDLR Gene Using Oxford Nanopore MinION.

The LDLR locus has clinical significance for lipid metabolism, Mendelian familial hypercholesterolemia (FH), and common lipid metabolism-related diseases (coronary artery disease and Alzheimer's disease), but its intronic and structural variants are underinvestigated. The aim of this study was to design and validate a method for nearly complete sequencing of the LDLR gene using long-read Oxford Nanopore sequencing technology (ONT). Five PCR amplicons from LDLR of three patients with compound heterozygous FH were analyzed. We used standard workflows of EPI2ME Labs for variant calling. All rare missense and small deletion variants detected previously by massively parallel sequencing and Sanger sequencing were identified using ONT. One patient had a 6976 bp deletion (exons 15 and 16) that was detected by ONT with precisely located breakpoints between AluY and AluSx1. Trans-heterozygous associations between mutation c.530C>T and c.1054T>C, c.2141-966_2390-330del, and c.1327T>C, and between mutations c.1246C>T and c.940+3_940+6del of LDLR, were confirmed. We demonstrated the ability of ONT to phase variants, thereby enabling haplotype assignment for LDLR with personalized resolution. The ONT-based method was able to detect exonic variants with the additional benefit of intronic analysis in one run. This method can serve as an efficient and cost-effective tool for diagnosing FH and conducting research on extended LDLR haplotype reconstruction.

Cryptic taxonomic diversity and high-latitude melanism in the glossiphoniid leech assemblage from the Eurasian Arctic.

The family Glossiphoniidae is a diverse and widespread clade of freshwater leeches, playing a significant role in functioning of aquatic ecosystems. The taxonomy and biogeography of leeches from temperate, subtropical, and tropical regions attracted much attention of zoologists, while their taxonomic richness and distribution in the Arctic are poorly understood. Here, we present an overview of the Eurasian Arctic Glossiphoniidae based on the most comprehensive occurrence and DNA sequence datasets sampled to date. This fauna contains 14 species, belonging to five genera and three subfamilies. One genus and five species are new to science and described here. The world's northernmost occurrences of glossiphoniids are situated on the Taymyr Peninsula at 72° N, although further records at higher latitudes are expected. Most Arctic leeches are characterized by broad ranges crossing several climatic zones (e.g., Glossiphonia balcanica and G. nebulosa), although the distribution of two new species may be confined to the high-latitude areas. The Taymyr Peninsula with the nearby Putorana Plateau represents the most species-rich area (totally 9 species), while the European Arctic, Iceland, Kolyma Highland, and Chukotka Peninsula house depleted faunas (2-4 species per subregion). Finally, we show that the high-latitude melanism is a common phenomenon in glossiphoniid leeches.

Constitutive heterochromatin propagation contributes to the X chromosome inactivation.

Imprinted X chromosome inactivation (iXCI) balances the expression of X-linked genes in preimplantation embryos and extraembryonic tissues in rodents. Long noncoding Xist RNA drives iXCI, silencing genes and recruiting Xist-dependent chromatin repressors. Some domains on the inactive X chromosome include repressive modifications specific to constitutive heterochromatin, which show no direct link to Xist RNA. We explored the relationship between Xist RNA and chromatin silencing during iXCI in vole Microtus levis. We performed locus-specific activation of Xist transcription on the only active X chromosome using the dCas9-SAM system in XO vole trophoblast stem cells (TSCs), which allow modeling iXCI events to some extent. The artificially activated endogenous vole Xist transcript is truncated and restricted ~ 6.6 kb of the exon 1. Ectopic Xist RNA accumulates on the X chromosome and recruits Xist-dependent modifications during TSC differentiation, yet is incapable by itself repressing X-linked genes. Transcriptional silencing occurs upon ectopic Xist upregulation only when repressive marks spread from the massive telomeric constitutive heterochromatin to the X chromosome region containing genes. We hypothesize that the Xist RNA-induced propagation of repressive marks from the constitutive heterochromatin could be a mechanism involved in X chromosome inactivation.

Noninvasive Glioma Grading with Deep Learning: A Pilot Study.

Gliomas are the most common neuroepithelial brain tumors, different by various biological tissue types and prognosis. They could be graded with four levels according to the 2007 WHO classification. The emergence of non-invasive histological and molecular diagnostics for nervous system neoplasms can revolutionize the efficacy and safety of medical care and radically reduce healthcare costs. Our pilot study aimed to evaluate the diagnostic accuracy of deep learning (DL) in subtyping gliomas by WHO grades (I-IV) based on preoperative magnetic resonance imaging (MRI) from Burdenko Neurosurgery Center's database. A total of 707 MRI studies was included. A "3D classification" approach predicting tumor type for the entire patient's MRI data showed the best result (accuracy = 83%, ROC AUC = 0.95), consistent with that of other authors who used different methodologies. Our preliminary results proved the separability of MR T1 axial images with contrast enhancement by WHO grade using DL.

Mining Knowledge from Crystal Structures: Oxidation States of Oxygen-Coordinated Metal Atoms in Ionic and Coordination Compounds.

We propose a universal scheme for predicting the oxidation states of metal atoms in ionic and coordination compounds with a small set of structural descriptors, which include the parameters of atomic Voronoi polyhedra. The scheme has been trained and checked with more than 35,000 crystal structures containing more than 90,000 metal atoms in the oxygen environment. The accuracy of the prediction exceeded 95%; we have detected a number of wrong oxidation states and incorrect chemical compositions in the crystallographic databases using this scheme. The scheme is easily extendable to any kind of atomic environment and can be used to search for correlations between geometrical and physical properties of crystal structures.

Mitomycin-Treated Endothelial and Smooth Muscle Cells Suitable for Safe Tissue Engineering Approaches.

In our previous study, we showed that discarded cardiac tissue from the right atrial appendage and right ventricular myocardium is an available source of functional endothelial and smooth muscle cells for regenerative medicine and tissue engineering. In the study, we aimed to find out what benefits are given by vascular cells from cardiac explants used for seeding on vascular patches engrafted to repair vascular defects in vivo. Additionally, to make the application of these cells safer in regenerative medicine we tested an in vitro approach that arrested mitotic division to avoid the potential tumorigenic effect of dividing cells. A tissue-engineered construction in the form of a patch based on a polycaprolactone-gelatin scaffold and seeded with endothelial and smooth muscle cells was implanted into the abdominal aorta of immunodeficient SCID mice. Aortic patency was assessed using ultrasound, MRI, immunohistochemical and histological staining. Endothelial and smooth muscle cells were treated with mitomycin C at a therapeutic concentration of 10 µg/ml for 2 h with subsequent analysis of cell proliferation and function. The absence of the tumorigenic effect of mitomycin C-treated cells, as well as their angiogenic potential, was examined by injecting them into immunodeficient mice. Cell-containing patches engrafted in the abdominal aorta of immunodeficient mice form the vessel wall loaded with the appropriate cells and extracellular matrix, and do not interfere with normal patency. Endothelial and smooth muscle cells treated with mitomycin C show no tumorigenic effect in the SCID immunodeficient mouse model. During in vitro experiments, we have shown that treatment with mitomycin C does not lead to a decrease in cell viability. Despite the absence of proliferation, mitomycin C-treated vascular cells retain specific cell markers, produce specific extracellular matrix, and demonstrate the ability to stimulate angiogenesis in vivo. We pioneered an approach to arresting cell division with mitomycin C in endothelial and smooth muscle cells from cardiac explant, which prevents the risk of malignancy from dividing cells in vascular surgery. We believe that this approach to the fabrication of tissue-engineered constructs based on mitotically inactivated cells from waste postoperative material may be valuable to bring closer the development of safe cell products for regenerative medicine.

Induced pluripotent stem cell line ICGi038-A, obtained by reprogramming peripheral blood mononuclear cells from a patient with familial hypercholesterolemia due to compound heterozygous c.1246C > T/c.940 + 3_940 + 6del mutations in LDLR.

The development of cellular models for familial hypercholesterolemia (FH) is an important direction for creating new approaches to atherosclerosis treatment. Pathogenic mutations in the LDLR gene are the main FH source. We generated an iPSC line from peripheral blood mononuclear cells of the patient with compound heterozygous c.1246C > T/c.940 + 3_940 + 6del LDLR mutation. The resulting iPSC line with confirmed patient-specific mutations maintains a normal karyotype and a typical undifferentiated state, including morphology, pluripotent gene expression, and in vitro differentiation potential. This iPSC line can be further differentiated toward relevant cells to better understand FH pathogenesis.

Induced pluripotent stem cell line ICGi037-A, obtained by reprogramming peripheral blood mononuclear cells from a patient with familial hypercholesterolemia due to heterozygous p.Trp443Arg mutations in LDLR.

Familial hypercholesterolemia (FH) is an autosomal dominant disorder increasing premature cardiovascular diseases risk due to atherosclerosis. Pathogenic mutations in the LDLR gene cause most FH cases. Available treatments are effective not for all LDLR mutations. Testing drugs on FH cell models help develop new efficient treatments. We obtained an iPSC line from peripheral blood mononuclear cells of the patient with heterozygous p.Trp443Arg LDLR mutation. The iPSCs with confirmed patient-specific mutations express pluripotency markers, spontaneously differentiate into three germ layers and demonstrate normal karyotype. Patient-specific iPSCs-derived hepatocyte-like and endothelial cells are promising to develop new targeted therapies for FH.

Induced pluripotent stem cell line ICGi036-A generated by reprogramming peripheral blood mononuclear cells from a patient with familial hypercholesterolemia caused due to compound heterozygous p.Ser177Leu/p.Cys352Arg mutations in LDLR.

Familial hypercholesterolemia (FH) is a monogenic disease, leading to atherosclerosis due to a high level of low-density lipoprotein cholesterol. Most cases of the disease are based on pathological variants in the LDLR gene. Hepatocyte-like and endothelial cells derived from individual iPSCs are a good model for developing new approaches to therapy. We obtained an iPSC line from peripheral blood mononuclear cells of the patient with compound heterozygous p.Ser177Leu/p.Cys352Arg mutation in LDLR using non-integrating vectors. The iPSCs with a confirmed patient-specific mutation demonstrate pluripotency markers, normal karyotype, and the ability to differentiate into derivatives of three germ layers.

Etiopathogenesis of adolescent idiopathic scoliosis: Review of the literature and new epigenetic hypothesis on altered neural crest cells migration in early embryogenesis as the key event.

Adolescent idiopathic scoliosis (AIS) affects 2-3% of children. Numerous hypotheses on etiologic/causal factors of AIS were investigated, but all failed to identify therapeutic targets and hence failed to offer a cure. Therefore, currently there are only two options to minimize morbidity of the patients suffering AIS: bracing and spinal surgery. From the beginning of 1960th, spinal surgery, both fusion and rod placement, became the standard of management for progressive adolescent idiopathic spine deformity. However, spinal surgery is often associated with complications. These circumstances motivate AIS scientific community to continue the search for new etiologic and causal factors of AIS. While the role of the genetic factors in AIS pathogenesis was investigated intensively and universally recognized, these studies failed to nominate mutation of a particular gene or genes combination responsible for AIS development. More recently epigenetic factors were suggested to play causal role in AIS pathogenesis. Sharing this new approach, we investigated scoliotic vertebral growth plates removed during vertebral fusion (anterior surgery) for AIS correction. In recent publications we showed that cells from the convex side of human scoliotic deformities undergo normal chondrogenic/osteogenic differentiation, while cells from the concave side acquire a neuronal phenotype. Based on these facts we hypothesized that altered neural crest cell migration in early embryogenesis can be the etiological factor of AIS. In particular, we suggested that neural crest cells failed to migrate through the anterior half of somites and became deposited in sclerotome, which in turn produced chondrogenic/osteogenic-insufficient vertebral growth plates. To test this hypothesis we conducted experiments on chicken embryos with arrest neural crest cell migration by inhibiting expression of Paired-box 3 (Pax3) gene, a known enhancer and promoter of neural crest cells migration and differentiation. The results showed that chicken embryos treated with Pax3 siRNA (microinjection into the neural tube, 44 h post-fertilization) progressively developed scoliotic deformity during maturation. Therefore, this analysis suggests that although adolescent idiopathic scoliosis manifests in children around puberty, the real onset of the disease is of epigenetic nature and takes place in early embryogenesis and involves altered neural crest cells migration. If these results confirmed and further elaborated, the hypothesis may shed new light on the etiology and pathogenesis of AIS.

Visualization and Quantification of Geometric Diversity in Metal-Organic Frameworks.

With ever-growing numbers of metal-organic framework (MOF) materials being reported, new computational approaches are required for a quantitative understanding of structure-property correlations in MOFs. Here, we show how structural coarse-graining and embedding ("unsupervised learning") schemes can together give new insights into the geometric diversity of MOF structures. Based on a curated data set of 1262 reported experimental structures, we automatically generate coarse-grained and rescaled representations which we couple to a kernel-based similarity metric and to widely used embedding schemes. This approach allows us to visualize the breadth of geometric diversity within individual topologies and to quantify the distributions of local and global similarities across the structural space of MOFs. The methodology is implemented in an openly available Python package and is expected to be useful in future high-throughput studies.

Topology versus porosity: what can reticular chemistry tell us about free space in metal-organic frameworks?

We present the results of a comprehensive geometrical and topological analysis of 3D coordination networks in 33 790 coordination polymers. We have found relations between topological descriptors and free space of the networks, and have revealed topological types that promote high porosity of metal-organic frameworks.

A universal algorithm for finding the shortest distance between systems of points.

Three universal algorithms for geometrical comparison of abstract sets of n points in the Euclidean space R3 are proposed. It is proved that at an accuracy ε the efficiency of all the algorithms does not exceed O(n3/ε3/2). The most effective algorithm combines the known Hungarian and Kabsch algorithms, but is free of their deficiencies and fast enough to match hundreds of points. The algorithm is applied to compare both finite (ligands) and periodic (nets) chemical objects.

Diverse developmental strategies of X chromosome dosage compensation in eutherian mammals.

In eutherian mammals, dosage compensation arose to balance X-linked gene expression between sexes and relatively to autosomal gene expression in the evolution of sex chromosomes. Dosage compensation occurs in early mammalian development and comprises X chromosome upregulation and inactivation that are tightly coordinated epigenetic processes. Despite a uniform principle of dosage compensation, mechanisms of X chromosome inactivation and upregulation demonstrate a significant variability depending on sex, developmental stage, cell type, individual, and mammalian species. The review focuses on relationships between X chromosome inactivation and upregulation in mammalian early development.

Novel Heterometallic Uranyl-Transition Metal Materials: Structure, Topology, and Solid State Photoluminescence Properties.

Six new uranyl hybrid materials have been synthesized solvothermally utilizing the ligands 2,2'-bipyridine-3,3'-dicarboxylic acid (H2L) and 2,2':6',2''-terpyridine (TPY). The six compounds are classified as either molecular complexes (I0O0 connectivity), [(UO2)(L)(TPY)]·H2O (1), [Ni(TPY)2][(UO2)(L)2]·3H2O (2), and [Cu(TPY)2][(UO2)(L)2]·3H2O (3), or 3D metal-organic frameworks (MOFs, I0O3 connectivity), [Cu2(UO2)2(OH)(C2H3O2)(L)3(TPY)2]·6H2O (4), [Zn2(UO2)2(OH)(NO3)(C2H3O2)(L)3(TPY)2]·4H2O (5), and Na[Ni(UO2)3(OH)(O)(L)3]·9H2O (6). A discussion of the influence of transition metal incorporation, chelating effects of the ligand, and synthesis conditions on the formation of uranyl materials is presented. The structure of compound 6 is of particular note due to large channel-like voids with a diameter of approximately 19.6 Å. A topological analysis of 6 reveals a new topology with a 9-nodal 3,3,3,3,3,3,3,4,5-connected network, designated geg1 hereafter. Further, solid state photoluminescence experiments show emission and lifetimes values consistent with related uranyl compounds.

A New Look at Causal Factors of Idiopathic Scoliosis: Altered Expression of Genes Controlling Chondroitin Sulfate Sulfation and Corresponding Changes in Protein Synthesis in Vertebral Body Growth Plates.

Background: In a previous report, we demonstrated the presence of cells with a neural/glial phenotype on the concave side of the vertebral body growth plate in Idiopathic Scoliosis (IS) and proposed this phenotype alteration as the main etiological factor of IS. In the present study, we utilized the same specimens of vertebral body growth plates removed during surgery for Grade III-IV IS to analyse gene expression. We suggested that phenotype changes observed on the concave side of the vertebral body growth plate can be associated with altered expression of particular genes, which in turn compromise mechanical properties of the concave side. Methods: We used a Real-Time SYBR Green PCR assay to investigate gene expression in vertebral body growth plates removed during surgery for Grade III-IV IS; cartilage tissues from human fetal spine were used as a surrogate control. Special attention was given to genes responsible for growth regulation, chondrocyte differentiation, matrix synthesis, sulfation and transmembrane transport of sulfates. We performed morphological, histochemical, biochemical, and ultrastructural analysis of vertebral body growth plates. Results: Expression of genes that control chondroitin sulfate sulfation and corresponding protein synthesis was significantly lower in scoliotic specimens compared to controls. Biochemical analysis showed 1) a decrease in diffused proteoglycans in the total pool of proteoglycans; 2) a reduced level of their sulfation; 3) a reduction in the amount of chondroitin sulfate coinciding with raising the amount of keratan sulfate; and 4) reduced levels of sulfation on the concave side of the scoliotic deformity. Conclusion: The results suggested that altered expression of genes that control chondroitin sulfate sulfation and corresponding changes in protein synthesis on the concave side of vertebral body growth plates could be causal agents of the scoliotic deformity.

A New Look at Etiological Factors of Idiopathic Scoliosis: Neural Crest Cells.

Idiopathic scoliosis is one of the most common disabling pathologies of children and adolescents. Etiology and pathogenesis of idiopathic scoliosis remain unknown. To study the etiology of this disease we identified the cells' phenotypes in the vertebral body growth plates in patients with idiopathic scoliosis. Materials and methods: The cells were isolated from vertebral body growth plates of the convex and concave sides of the deformity harvested intraoperatively in 50 patients with scoliosis. Cells were cultured and identified by methods of common morphology, neuromorphology, electron microscopy, immunohistochemistry and PCR analysis. Results: Cultured cells of convex side of deformation were identified as chondroblasts. Cells isolated from the growth plates of the concave side of the deformation showed numerous features of neuro- and glioblasts. These cells formed synapses, contain neurofilaments, and expressed neural and glial proteins. Conclusion: For the first time we demonstrated the presence of cells with neural/glial phenotype in the concave side of the vertebral body growth plate in scoliotic deformity. We hypothesized that neural and glial cells observed in the growth plates of the vertebral bodies represent derivatives of neural crest cells deposited in somites due to alterations in their migratory pathway during embryogenesis. We also propose that ectopic localization of cells derived from neural crest in the growth plate of the vertebral bodies is the main etiological factor of the scoliotic disease.

Topology of Intermetallic Structures: From Statistics to Rational Design.

More than 38 000 substances made only of metal atoms are collected in modern structural databases; we may call them intermetallic compounds. They have important industrial applications, and yet they are terra incognita for most of our undergraduate students. Their structural complexity and synthesis are not easily adaptable to first years laboratories, keeping them away from the standard curricula. They have been described over the years following alternative and complementary views such as coordination polyhedra, atomic layers, and polyatomic clusters. All of these descriptions, albeit relying on grounded principles, have been applied on a subjective basis and never implemented as a strict computational algorithm. Sometimes, the authors generated multiple views of the same structure reported with beautifully drawn figures and/or photos of hand-crafted models in seminal works of the precomputer age. With the use of our multipurpose crystallochemical program package ToposPro, we explored the structural chemistry of intermetallics with objective and reproducible topological methods that allow us to reconcile different structure descriptions. After computing the connectivity patterns between the metal atoms on the basis of Voronoi partitioning of the crystal space, we were able to group the 38 000 intermetallic compounds into 3700 sets of crystal structures with the same topology of atomic net. We have described the different views used in the literature and shown that 12-vertex polyhedra are the most frequent (33%) and that almost half of them are icosahedron-like (46%), followed by cuboctahedron (25%) and, unexpectedly, by bicapped pentagonal prism (13%). Looking for layers, we have found that the hexagonal lattice, which corresponds to the closest packing of spheres on a plane, exists in more than 11 000 crystal structures, confirming the close-packed nature of intermetallics. We have also applied the nanocluster approach, which goes beyond the first coordination sphere and looks for structural units as multishell clusters that assemble the whole structure. This approach shows that 41% of intermetallics can be assembled with a single nanocluster and that 22.4% of these are packed according to the face-centered cubic motif of the closest packing of spheres in three-dimensional space. We have shown that our approach can easily adopt any other building model and hence could become a platform for a universal predictive scheme. Within this scheme, all of the structural descriptors can be related to experimental data and theoretical modeling results and then can be used to synthesize new intermetallic compounds and to foresee novel materials.

Impact of Xist RNA on chromatin modifications and transcriptional silencing maintenance at different stages of imprinted X chromosome inactivation in vole Microtus levis.

In vole Microtus levis, cells of preimplantation embryo and extraembryonic tissues undergo imprinted X chromosome inactivation (iXCI) which is triggered by a long non-coding nuclear RNA, Xist. At early stages of iXCI, chromatin of vole inactive X chromosome is enriched with the HP1 heterochromatin-specific protein, trimethylated H3K9 and H4K20 attributable to constitutive heterochromatin. In the study, using vole trophoblast stem (TS) cells as a model of iXCI, we further investigated chromatin of the inactive X chromosome of M. levis and tried to find out the role of Xist RNA. We demonstrated that chromatin of the inactive X chromosome in vole TS cells also contained the SETDB1 histone methyltransferase and KAP1 protein. In addition, we observed that Xist RNA did not contribute significantly to maintenance of X chromosome inactive state during iXCI in vole TS cells. Xist repression affected neither transcriptional silencing caused by iXCI nor maintenance of trimethylated H3K9 and H4K20 as well as HP1, KAP1, and SETDB1 on the inactive X chromosome. Moreover, the unique repertoire of chromatin modifications on the inactive X chromosome in vole TS cells could be disrupted by a chemical compound, DZNep, and then restored even in the absence of Xist RNA. However, Xist transcript was necessary for recruitment of an additional repressive histone modification, trimethylated H3K27, to the inactive X chromosome during vole TS cell differentiation.