High-throughput differentiation of human blood vessel organoids reveals overlapping and distinct functions of the cerebral cavernous malformation proteins.

Cerebral cavernous malformations (CCMs) are clusters of thin-walled enlarged blood vessels in the central nervous system that are prone to recurrent hemorrhage and can occur in both sporadic and familial forms. The familial form results from loss-of-function variants in the CCM1, CCM2, or CCM3 gene. Despite a better understanding of CCM pathogenesis in recent years, it is still unclear why CCM3 mutations often lead to a more aggressive phenotype than CCM1 or CCM2 variants.

Inhibition of ceramide synthesis improves the outcome of ischemia/reperfusion injury in cardiomyocytes derived from human induced pluripotent stem cell.

Background: Ceramides are bioactive sphingolipids that have physiological effects on inflammation, apoptosis, and mitochondrial dysfunction. They may play a critical role in the harm of ischemia/reperfusion (IR). Ceramides and IR injury are not well-studied, and there is a lack of human data.

Satellite DNA Amplification in Advanced Prostate Cancer Is Largely Independent From Euchromatic and Oncogene Amplicons.

Recently, we were able to show that satellite DNA amplification (satDNA-AMP) is present in advanced prostate cancer. A chromosome microarray study provided first evidence that satDNA-AMP appears to be largely independent of centromere-near/pericentric euchromatic copy number alterations. Therefore, it might be carefully suggested that satDNA-AMP could be a new and independent marker for advanced tumor progression.

Generation of a human induced pluripotent stem cell lines (UKJi003-A) from a patient with Fabry disease and healthy donor (UKJi004-A).

Fabry disease (FD, OMIM #301500) is a rare metabolic disorder, X-linked glycosphingolipidosis that is characterized by pathogenic mutations in the GLA (Galactosidase Alpha) gene (OMIM *300644) that result in reduced α-galactosidase A (α-GAL) activity and accumulation of globotriaosylceramide (Gb3) in tissues and organs. Peripheral blood mononuclear cells (PBMCs) were used to generate human induced pluripotent stem cells (hiPSC). UKJi004-A was produced from a healthy donor, whereas UKJi003-A was produced from a patient who had FD with GLA-mutation (IVS6-10G>A).

Inter-chromosomal contacts demarcate genome topology along a spatial gradient.

Non-homologous chromosomal contacts (NHCCs) between different chromosomes participate considerably in gene and genome regulation. Due to analytical challenges, NHCCs are currently considered as singular, stochastic events, and their extent and fundamental principles across cell types remain controversial. We develop a supervised and unsupervised learning algorithm, termed Signature, to call NHCCs in Hi-C datasets to advance our understanding of genome topology.

Deletions Identified by Genome Sequencing in Two Individuals with Xia-Gibbs Syndrome.

Introduction: Xia-Gibbs syndrome (XGS) is a rare syndromic disorder characterized by developmental delay with intellectual disability, muscular hypotonia, brain anomalies, and nonspecific dysmorphic features. Different heterozygous variants in have been reported as causal for XGS, comprising mainly stop-gain and frameshift events, but also missense variants, deletions, and a duplication of the locus.

Case Presentation: We hereby report 2 patients with clinical features of XGS.

Generation of a human induced pluripotent stem cell line (UMGACBi001-A) from urine cells of a chronic kidney disease patient with hypertension, diabetic nephropathy and acute sepsis.

Chronic kidney disease is a major public health burden associated with a drastically reduced quality of living and life span that lacks suitable, individualized therapeutic strategies. Here we present a human induced pluripotent stem cell line (iPSC, UMGACBi001-A) reprogrammed from urine cells of an acute septic dialysis patient suffering from chronic kidney disease using non-integrating administration of RNAs. The generated iPSCs were positively characterized for typical morphology, pluripotency marker expression, directed differentiation potential, non-contamination, chromosomal consistency and donor identity.

Small supernumerary marker chromosomes derived from human chromosome 11.

With only 39 reported cases in the literature, carriers of a small supernumerary marker chromosome (sSMC) derived from chromosome 11 represent an extremely rare cytogenomic condition. Herein, we present a review of reported sSMC(11), add 18 previously unpublished cases, and closely review eight cases classified as 'centromere-near partial trisomy 11' and a further four suited cases from DECIPHER. Based on these data, we deduced the borders of the pericentric regions associated with clinical symptoms into a range of 2.

Molecular cytogenetic and phenotypic characterization of Phelan McDermid and 22q13 duplication syndrome: a case report.

Background: Phelan-McDermid syndrome (PHMDS) is a rare genetic disorder mostly caused by haploinsufficincy of SHANK3 gene, and characterized by neonatal hypotonia, developmental delay, minor dysmorphic features, seizures and behavior problems. Literature of this syndrome is scanty and confusing, and represents a challenge for pediatricians, in terms of finding the correct diagnoses.

Case Presentation: In a postnatal case with hypotonia and dysmorphic features a de novo ring chromosome r(22) leading to in parallel microdeletion and micro duplication in 22q13 was diagnosed by banding cytogenetics, and further characterized in detail by molecular cytogenetic and chromosomal microarray.

Non-Invasive Prenatal Testing in Germany.

In the short 10 years following the introduction of non-invasive prenatal testing (NIPT), it has been adapted in many countries around the world as a standard screening test. In this review, this development was analyzed with a special focus on Germany. As a result, it can be stated that all known advantages of NIPT apart from "compensating for having no access to centers offering invasive diagnostics" are valid for Germany.

Induced pluripotent stem cells and cerebral organoids from the critically endangered Sumatran rhinoceros.

Less than 80 Sumatran rhinos (SR, are left on earth. Habitat loss and limited breeding possibilities are the greatest threats to the species and lead to a continuous population decline. To stop the erosion of genetic diversity, reintroduction of genetic material is indispensable.

Using CRISPR/Cas9 genome editing in human iPSCs for deciphering the pathogenicity of a novel transcription start site deletion.

Cerebral cavernous malformations are clusters of aberrant vessels that can lead to severe neurological complications. Pathogenic loss-of-function variants in the , , or gene are associated with the autosomal dominant form of the disease. While interpretation of variants in protein-coding regions of the genes is relatively straightforward, functional analyses are often required to evaluate the impact of non-coding variants.

First Comprehensive Characterization of Phayre's Leaf-Monkey () Karyotype.

The chromosomal homologies of human (-HSA) and (TPH-Phayre's leaf-monkey, family Cercopithecidae) have previously been studied by using classical chromosome staining/banding and fluorescence hybridization (FISH) from the 1970s to 1990s. In this study, we carried out molecular cytogenetics applying human multicolor banding (MCB), locus-specific, and human heterochromatin-specific probes to establish the first detailed chromosomal map of TPH, which was not available until now. Accordingly, it was possible to precisely determine evolutionary-conserved breakpoints (ECBs) and the orientation of evolutionary-conserved segments compared to HSA.

How to Obtain High-Quality Metaphase Spreads for Molecular Cytogenetics.

Interphase or metaphase nuclei can be accessed in molecular cytogenetic analyses. Metaphase spreads are routinely studied by fluorescence in situ hybridization (FISH) to answer clinical genetic questions. Even though metaphase quality is essential for FISH studies, there is limited ability in clinical cases to improve the quality of cytogenetic preparations.

Association of Lymphatic Abnormalities with Early Complications after Fontan Operation.

Background: Increased central venous pressure is inherent in Fontan circulation but not strongly related to Fontan complication. Abnormalities of the lymphatic circulation may play a crucial role in early Fontan complications.

Methods: This was a retrospective, single-center study of patients undergoing Fontan operation from 2008 to 2015.

Sites of chromosomal instability in the context of nuclear architecture and function.

Chromosomal fragile sites are described as areas within the tightly packed mitotic chromatin that appear as breaks or gaps mostly tracing back to a loosened structure and not a real nicked break within the DNA molecule. Most facts about fragile sites result from studies in mitotic cells, mainly during metaphase and mainly in lymphocytes. Here, we synthesize facts about the genomic regions that are prone to form gaps and breaks on metaphase chromosomes in the context of interphase.

Cytogenomics of six human trophoblastic cell lines.

Trophoblastic cell lines are established models used to examine human placenta physiology and disease. We performed concurrent cytogenetic analyses of six established and well-studied trophoblastic cell lines including JAR, BeWo, JEG-3, AC-1M59, HTR8/SVneo, and ACH-3P. All cell lines showed near triploid or tetraploid karyotypes with unique inter- and intra-clonal aberrations, which result possibly from long-term culture or defects in the placenta or its malignant choriocarcinoma origin.

First interchromosomal insertion in a patient with cerebral and spinal cavernous malformations.

Autosomal dominant cerebral cavernous malformations (CCM) are leaky vascular lesions that can cause epileptic seizures and stroke-like symptoms. Germline mutations in either CCM1, CCM2 or CCM3 are found in the majority of patients with multiple CCMs or a positive family history. Recently, the first copy number neutral inversion in CCM2 has been identified by whole genome sequencing in an apparently mutation-negative CCM family.

Molecular cytogenetic pilot study on pleomorphic adenomas of salivary glands.

Pleomorphic adenomas (PAs) of salivary glands are the most frequent entity of solid parotid tumors. Nonetheless, their genetics is not yet well understood. Thus, the current study characterized 14 PAs using a unique combination of cytogenetic, molecular cytogenetic and/or molecular karyotyping based approaches.

Recombinant Chromosomes Resulting From Parental Pericentric Inversions-Two New Cases and a Review of the Literature.

A balanced pericentric inversion is normally without any clinical consequences for its carrier. However, there is a well-known risk of such inversions to lead to unbalanced offspring. Inversion-loop formation is the mechanism which may lead to duplication or deletion of the entire or parts of the inverted segment in the offspring.

Analysis of copy number variations induced by ultrashort electron beam radiation in human leukocytes in vitro.

Background: Environmental risk factors have been shown to alter DNA copy number variations (CNVs). Recently, CNVs have been described to arise after low-dose ionizing radiation in vitro and in vivo. Development of cost- and size-effective laser-driven electron accelerators (LDEAs), capable to deliver high energy beams in pico- or femtosecond durations requires examination of their biological effects.

Rapid Prenatal Aneuploidy Screening by Fluorescence In Situ Hybridization (FISH).

The most common aneuploidies observed in prenatal diagnostics in the second trimester are trisomies of the chromosomes 13, 18 or 21 and gonosomal abnormalities. Rapid detection of these aneuploidies after amniocentesis is possible by fluorescence in situ hybridization (FISH) utilizing centromeric or locus-specific probes. FISH aneuploidy screening results in uncultured amniocytes are available within 24 h or less.

Assessing Skewed X-Chromosome Inactivation.

We describe a simple and straightforward method for detection and characterization of X-chromosome inactivation in females and/or individuals with more than one X chromosome. The X-chromosome inactivation pattern is visualized on a single-cell level using 5-ethynyl-2-deoxyuridine (EdU) instead of the previously widely applied 5-bromo-2'-deoxyuridine (BUdR). The fluorochrome-labeled nucleoside analog EdU is incorporated into late-replication chromosomal regions of living blood cells in vitro; thus, it can also be used to specifically highlight the inactive X chromosome within a cytogenetic preparation.

Reorganization of chromosomal interactions in the 2q37-deletion syndrome.

Chromosomes occupy distinct interphase territories in the three-dimensional nucleus. However, how these chromosome territories are arranged relative to one another is poorly understood. Here, we investigated the chromosomal interactions between chromosomes 2q, 12, and 17 in human mesenchymal stem cells (MSCs) and MSC-derived cell types by DNA-FISH We compared our findings in normal karyotypes with a three-generation family harboring a 2q37-deletion syndrome, featuring a heterozygous partial deletion of histone deacetylase 4 () on chr2q37.