A Finer Print Than TADs: PRC1-Mediated Domains.

Polycomb proteins are well-known epigenetic repressors with unexplained roles in chromatin folding. In this issue of Molecular Cell, Kundu et al. (2017) investigate the structures of PRC1-mediated domains in stem cells and probe their changes upon differentiation and in PRC knockouts.

Non-VKA Oral Anticoagulants in Adult Congenital Heart Disease: a Single-Center Study.

PURPOSE: Non-VKA oral anticoagulants (NOACs) prescription is increasing in adults with congenital heart disease (ACHD). However, data on efficacy and safety in ACHD is unclear, particularly in severe CHD. The study aimed to review the safety and efficacy of NOACs in ACHD. METHODS: Retrospective evaluation of ACHD patients started on NOACs from 2014 to 2020, with the primary endpoints of bleeding or thromboembolic events (TE). CHA2DS2-VASc and HAS-BLED scores were calculated, mortality was assessed, and risk factors for bleeding were identified. RESULTS: A total of 93 patients were included, the mean age was 52 ± 15 years, 58% were female, 55.9% had moderate CHD, and 23.7% had severe CHD (3.2% Fontan). Most (66%) had a CHA2DS2-VASc score ≥ 2 and 82% HAS-BLED ≤ 2. In a median follow-up of 41 (IQR 21) months (400.4 patient-years), there were TE in two patients. The annual risk for TE was 0.49%/patient/year. The cardiovascular mortality was 2% and all-cause mortality 5%; there were no fatal TE or bleeding events. Minor (n = 6, 6.5%) and major (n = 3, 3.2%) bleeding events were observed, a median of 12 (IQR 15) months after starting NOAC therapy. The annual risk for bleeding was 2.2%/patient/year. Renal disease (HR 14.6 [95% CI 1.23-73.6], p = 0.033) and the HAS-BLED score were predictors of major (adjusted HR 6.97 [95% CI 1.69-28.78], p = 0.007) and minor (adjusted HR 3.80 [95% CI 1.48-9.78], p = 0.006) bleeding complications. CONCLUSION: In this real-life cohort of selected ACHD, the use of NOACs was safe and effective, with a low incidence of bleeding events.

Infective endocarditis in a cohort of adult CHD patients.

BACKGROUND: CHD increases the risk of infective endocarditis due to the substrate of prosthetic materials and residual lesions. However, lesion-specific and mortality risks data are lacking. We sought to analyse clinical course and mortality of infective endocarditis in a cohort of adult CHD. METHODS: Retrospective analysis of all cases of proven and probable infective endocarditis (Duke's criteria) followed in our adult CHD clinic between 1970 and August, 2021. Epidemiological, clinical and imaging data were analysed. Predictors of surgical treatment and mortality were assessed using regression analysis. RESULTS: During a mean follow-up of 15.8 ± 10.9 years, 96 patients had 105 infective endocarditis episodes, half with previous cardiac surgery (corrective or palliative). The most frequent diagnoses were: ventricular septal defect, bicuspid aortic valve, Tetralogy of Fallot and pulmonary atresia. The site of infection was identified by echocardiography in 82 episodes (91%), most frequently in aortic (n = 27), tricuspid (n = 15), and mitral (n = 13) valves. Blood cultures were positive in 79% of cases, being streptococci (n = 29) and staphylococci (n = 23) the predominant pathogens. Surgery was necessary in 40% and the in-hospital mortality was 10.5%, associated with heart failure (p < 0.001; OR 13.5) and a non-surgical approach (p = 0.003; OR 5.06). CONCLUSIONS: In an adult CHD cohort, infective endocarditis was more frequent in patients with ventricular septal defect and bicuspid aortic valves, which contradicts the current guidelines that excludes them from prophylaxis. Surgical treatment is often required and mortality remains substantial. Prevention of this serious complication should be one of the major tasks in the care of adults with CHD.

RNA polymerase II primes Polycomb-repressed developmental genes throughout terminal neuronal differentiation.

Polycomb repression in mouse embryonic stem cells (ESCs) is tightly associated with promoter co-occupancy of RNA polymerase II (RNAPII) which is thought to prime genes for activation during early development. However, it is unknown whether RNAPII poising is a general feature of Polycomb repression, or is lost during differentiation. Here, we map the genome-wide occupancy of RNAPII and Polycomb from pluripotent ESCs to non-dividing functional dopaminergic neurons. We find that poised RNAPII complexes are ubiquitously present at Polycomb-repressed genes at all stages of neuronal differentiation. We observe both loss and acquisition of RNAPII and Polycomb at specific groups of genes reflecting their silencing or activation. Strikingly, RNAPII remains poised at transcription factor genes which are silenced in neurons through Polycomb repression, and have major roles in specifying other, non-neuronal lineages. We conclude that RNAPII poising is intrinsically associated with Polycomb repression throughout differentiation. Our work suggests that the tight interplay between RNAPII poising and Polycomb repression not only instructs promoter state transitions, but also may enable promoter plasticity in differentiated cells.

Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation.

Mammalian chromosomes fold into arrays of megabase-sized topologically associating domains (TADs), which are arranged into compartments spanning multiple megabases of genomic DNA. TADs have internal substructures that are often cell type specific, but their higher-order organization remains elusive. Here, we investigate TAD higher-order interactions with Hi-C through neuronal differentiation and show that they form a hierarchy of domains-within-domains (metaTADs) extending across genomic scales up to the range of entire chromosomes. We find that TAD interactions are well captured by tree-like, hierarchical structures irrespective of cell type. metaTAD tree structures correlate with genetic, epigenomic and expression features, and structural tree rearrangements during differentiation are linked to transcriptional state changes. Using polymer modelling, we demonstrate that hierarchical folding promotes efficient chromatin packaging without the loss of contact specificity, highlighting a role far beyond the simple need for packing efficiency.

Alignment-free protein interaction network comparison.

MOTIVATION: Biological network comparison software largely relies on the concept of alignment where close matches between the nodes of two or more networks are sought. These node matches are based on sequence similarity and/or interaction patterns. However, because of the incomplete and error-prone datasets currently available, such methods have had limited success. Moreover, the results of network alignment are in general not amenable for distance-based evolutionary analysis of sets of networks. In this article, we describe Netdis, a topology-based distance measure between networks, which offers the possibility of network phylogeny reconstruction. RESULTS: We first demonstrate that Netdis is able to correctly separate different random graph model types independent of network size and density. The biological applicability of the method is then shown by its ability to build the correct phylogenetic tree of species based solely on the topology of current protein interaction networks. Our results provide new evidence that the topology of protein interaction networks contains information about evolutionary processes, despite the lack of conservation of individual interactions. As Netdis is applicable to all networks because of its speed and simplicity, we apply it to a large collection of biological and non-biological networks where it clusters diverse networks by type. AVAILABILITY AND IMPLEMENTATION: The source code of the program is freely available at http://www.stats.ox.ac.uk/research/proteins/resources. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Multiresistant Kawasaki Disease in a Young Infant with Giant Aneurysms Growing Fast.

BACKGROUND: Kawasaki disease (KD) is a type of vasculitis in which giant coronary artery aneurysms (CAAs) can occur. There are no specific guidelines for managing giant CAAs that develop quickly and are at risk of rupture. Regarding cardiovascular drugs, only beta-blockers are formally recommended in the acute phase of KD. CASE PRESENTATION: A 6-month-old male patient with multiresistant Kawasaki disease and giant CAAs that continued to enlarge after controlling systemic inflammation was examined. The patient required three doses of intravenous immunoglobulin, methylprednisolone pulses, and anakinra and infliximab to normalize systemic inflammation. Due to the rapid increment of aneurysms' dimensions and the risk of rupture, we introduced anticoagulant therapy and propranolol plus captopril, and titration doses were introduced according to a tolerated decrease in heart rate and arterial pressure. CAAs increment stabilized and slowly reduced their dimensions. CONCLUSIONS: The authors describe an atypical case of multiresistant KD with giant rapidly increasing CAAs even after controlling systemic inflammation. The introduction of a beta-blocker and an angiotensin-converting enzyme (ACE) inhibitor was demonstrated to be useful for stabilizing giant CAAs growth and reducing the potential risk of rupture.

Studying protein-protein interactions using peptide arrays.

Screening of arrays and libraries of compounds is well-established as a high-throughput method for detecting and analyzing interactions in both biological and chemical systems. Arrays and libraries can be composed from various types of molecules, ranging from small organic compounds to DNA, proteins and peptides. The applications of libraries for detecting and characterizing biological interactions are wide and diverse, including for example epitope mapping, carbohydrate arrays, enzyme binding and protein-protein interactions. Here, we will focus on the use of peptide arrays to study protein-protein interactions. Characterization of protein-protein interactions is crucial for understanding cell functionality. Using peptides, it is possible to map the precise binding sites in such complexes. Peptide array libraries usually contain partly overlapping peptides derived from the sequence of one protein from the complex of interest. The peptides are attached to a solid support using various techniques such as SPOT-synthesis and photolithography. Then, the array is incubated with the partner protein from the complex of interest. Finally, the detection of the protein-bound peptides is carried out by using immunodetection assays. Peptide array screening is semi-quantitative, and quantitative studies with selected peptides in solution are required to validate and complement the screening results. These studies can improve our fundamental understanding of cellular processes by characterizing amino acid patterns of protein-protein interactions, which may even develop into prediction algorithms. The binding peptides can then serve as a basis for the design of drugs that inhibit or activate the target protein-protein interactions. In the current review, we will introduce the recent work on this subject performed in our and in other laboratories. We will discuss the applications, advantages and disadvantages of using peptide arrays as a tool to study protein-protein interactions.

Long term follow-up of Marfan Syndrome - experience of an adult congenital heart disease centre.

BACKGROUND: Marfan Syndrome (MFS) is one of the most common connective tissue disorders. The aim of this study was to characterize an adult population with MFS and evaluate its long-term prognosis. METHODS: A retrospective analysis of adult patients with MFS followed up during the past 40 years in a tertiary congenital heart disease outpatient clinic was performed. Survival analysis was performed according to different parameters, and survival curves were compared using the log-rank test. RESULTS: A total of 62 MFS patients were followed up for a mean period of 12 years (47% male; mean age, 39 years). The baseline mean aortic root diameter (ARD) at the Valsalva sinus was 42.4 ± 10.3 mm, with 15% of patients having moderate-to-severe aortic regurgitation and seven patients with acute aortic syndrome. The Bentall procedure was the most commonly performed surgical technique, and five patients required re-operation. Of the 17 pregnancies, 29% developed fetal complications; however, there was no maternal morbidity or mortality. A total of ten deaths occurred at a mean age of 52 years. Patients with an ARD ≤ 45 mm had a significantly lower all-cause mortality rate than patients with 45 < ARD ≤ 50 mm or with ARD > 50 mm (P = 0.004 and P < 0.001, respectively). Heart failure symptoms were associated with a worse outcome (P = 0.041), while the presence of extracardiac involvement had a protective effect (P < 0.001). CONCLUSION: MFS-related aortopathy is associated with high morbidity rates. In the overall population, an ARD > 45 mm at the time of diagnosis was associated with higher mortality during follow-up.

How threshold behaviour affects the use of subgraphs for network comparison.

MOTIVATION: A wealth of protein-protein interaction (PPI) data has recently become available. These data are organized as PPI networks and an efficient and biologically meaningful method to compare such PPI networks is needed. As a first step, we would like to compare observed networks to established network models, under the aspect of small subgraph counts, as these are conjectured to relate to functional modules in the PPI network. We employ the software tool GraphCrunch with the Graphlet Degree Distribution Agreement (GDDA) score to examine the use of such counts for network comparison. RESULTS: Our results show that the GDDA score has a pronounced dependency on the number of edges and vertices of the networks being considered. This should be taken into account when testing the fit of models. We provide a method for assessing the statistical significance of the fit between random graph models and biological networks based on non-parametric tests. Using this method we examine the fit of Erdös-Rényi (ER), ER with fixed degree distribution and geometric (3D) models to PPI networks. Under these rigorous tests none of these models fit to the PPI networks. The GDDA score is not stable in the region of graph density relevant to current PPI networks. We hypothesize that this score instability is due to the networks under consideration having a graph density in the threshold region for the appearance of small subgraphs. This is true for both geometric (3D) and ER random graph models. Such threshold behaviour may be linked to the robustness and efficiency properties of the PPI networks.

Depletion of aneuploid cells in human embryos and gastruloids.

Chromosomal instability leading to aneuploidy is pervasive in early human embryos1-3 and is considered as a major cause of infertility and pregnancy wastage4,5. Here we provide several lines of evidence that blastocysts containing aneuploid cells are worthy of in vitro fertilization transfer. First, we show clinically that aneuploid embryos can lead to healthy births, suggesting the presence of an in vivo mechanism to eliminate aneuploidy. Second, early development and cell specification modelled in micropatterned human 'gastruloids' grown in confined geometry show that aneuploid cells are depleted from embryonic germ layers, but not from extraembryonic tissue, by apoptosis in a bone morphogenetic protein 4 (BMP4)-dependent manner. Third, a small percentage of euploid cells rescues embryonic tissue in mosaic gastruloids when mixed with aneuploid cells. Finally, single-cell RNA-sequencing analysis of early human embryos revealed a decline of aneuploidy beginning on day 3. Our findings challenge two current dogmas: that a single trophectoderm biopsy at blastocyst stage to perform prenatal genetic testing can accurately determine the chromosomal make-up of a human embryo, and that aneuploid embryos should be withheld from embryo transfer in association with in vitro fertilization.

Self-organizing neuruloids model developmental aspects of Huntington's disease in the ectodermal compartment.

Harnessing the potential of human embryonic stem cells to mimic normal and aberrant development with standardized models is a pressing challenge. Here we use micropattern technology to recapitulate early human neurulation in large numbers of nearly identical structures called neuruloids. Dual-SMAD inhibition followed by bone morphogenic protein 4 stimulation induced self-organization of neuruloids harboring neural progenitors, neural crest, sensory placode and epidermis. Single-cell transcriptomics unveiled the precise identities and timing of fate specification. Investigation of the molecular mechanism of neuruloid self-organization revealed a pulse of pSMAD1 at the edge that induced epidermis, whose juxtaposition to central neural fates specifies neural crest and placodes, modulated by fibroblast growth factor and Wnt. Neuruloids provide a unique opportunity to study the developmental aspects of human diseases. Using isogenic Huntington's disease human embryonic stem cells and deep neural network analysis, we show how specific phenotypic signatures arise in our model of early human development as a consequence of mutant huntingtin protein, outlining an approach for phenotypic drug screening.

hPSC Modeling Reveals that Fate Selection of Cortical Deep Projection Neurons Occurs in the Subplate.

Cortical deep projection neurons (DPNs) are implicated in neurodevelopmental disorders. Although recent findings emphasize post-mitotic programs in projection neuron fate selection, the establishment of primate DPN identity during layer formation is not well understood. The subplate lies underneath the developing cortex and is a post-mitotic compartment that is transiently and disproportionately enlarged in primates in the second trimester. The evolutionary significance of subplate expansion, the molecular identity of its neurons, and its contribution to primate corticogenesis remain open questions. By modeling subplate formation with human pluripotent stem cells (hPSCs), we show that all classes of cortical DPNs can be specified from subplate neurons (SPNs). Post-mitotic WNT signaling regulates DPN class selection, and DPNs in the caudal fetal cortex appear to exclusively derive from SPNs. Our findings indicate that SPNs have evolved in primates as an important source of DPNs that contribute to cortical lamination prior to their known role in circuit formation.

Methylation of RNA polymerase II non-consensus Lysine residues marks early transcription in mammalian cells.

Dynamic post-translational modification of RNA polymerase II (RNAPII) coordinates the co-transcriptional recruitment of enzymatic complexes that regulate chromatin states and processing of nascent RNA. Extensive phosphorylation of serine residues at the largest RNAPII subunit occurs at its structurally-disordered C-terminal domain (CTD), which is composed of multiple heptapeptide repeats with consensus sequence Y1-S2-P3-T4-S5-P6-S7. Serine-5 and Serine-7 phosphorylation mark transcription initiation, whereas Serine-2 phosphorylation coincides with productive elongation. In vertebrates, the CTD has eight non-canonical substitutions of Serine-7 into Lysine-7, which can be acetylated (K7ac). Here, we describe mono- and di-methylation of CTD Lysine-7 residues (K7me1 and K7me2). K7me1 and K7me2 are observed during the earliest transcription stages and precede or accompany Serine-5 and Serine-7 phosphorylation. In contrast, K7ac is associated with RNAPII elongation, Serine-2 phosphorylation and mRNA expression. We identify an unexpected balance between RNAPII K7 methylation and acetylation at gene promoters, which fine-tunes gene expression levels.

The importance of age and high degree, in protein-protein interaction networks.

Here we present an in-depth analysis of the protein age patterns found in the edge and triangle subgraphs of the yeast protein-protein interaction network (PIN). We assess their statistical significance both according to what would be expected by chance given the node frequencies found in the yeast PIN, and also, for the case of triangles, given the age frequencies observed in the currently available pairwise data. We find that pairwise interactions between Old proteins are over-represented even when controlling for high degree, and triangle interactions between Old proteins are over-represented even when controlling for pairwise interaction frequencies. There is evidence for negative selection of interactions between Middle-aged and Old proteins within triangles, despite pairwise Middle-Old interactions being common. Most triangles consist solely of vertices with high degree. Our findings point towards an architecture of the yeast PIN that is highly heterogeneous, having connected clumps which contain a large number of interacting Old proteins along with selective age-dependent interaction patterns. Supplementary Material is available online (www.liebertonline.com/cmb).