Endothelial gene regulatory elements associated with cardiopharyngeal lineage differentiation

Endothelial cells (EC) differentiate from multiple sources, including the cardiopharyngeal mesoderm, which gives rise also to cardiac and branchiomeric muscles. The enhancers activated during endothelial differentiation within the cardiopharyngeal mesoderm are not completely known. Here, we use a cardiogenic mesoderm differentiation model that activates an endothelial transcription program to identify endothelial regulatory elements activated in early cardiogenic mesoderm. Integrating chromatin remodeling and gene expression data with available single-cell RNA-seq data from mouse embryos, we identify 101 putative regulatory elements of EC genes. We then apply a machine-learning strategy, trained on validated enhancers, to predict enhancers. Using this computational assay, we determine that 50% of these sequences are likely enhancers, some of which are already reported. We also identify a smaller set of regulatory elements of well-known EC genes and validate them using genetic and epigenetic perturbation. Finally, we integrate multiple data sources and computational tools to search for transcriptional factor binding motifs. In conclusion, we show EC regulatory sequences with a high likelihood to be enhancers, and we validate a subset of them using computational and cell culture models. Motif analyses show that the core EC transcription factors GATA/ETS/FOS is a likely driver of EC regulation in cardiopharyngeal mesoderm.

Mathematical modelling of an intermittent anoxic/aerobic MBBR: Estimation of nitrification rates and energy savings

This study aimed at modelling the performance of a novel MBBR configuration, named A/O-MBBR, comprised of a pre-anoxic reactor, with an HRT of 4.5 h, coupled with an intermittent anoxic/aerobic MBBR (HRT = 6.8 h). The lab-scale system was fed with municipal wastewater with an average influent Total Ammonia Nitrogen (TAN) and total COD (TCOD) concentrations of 46 mg of TAN-N L^-1 and 310 mg TCOD L^-1. During the whole experimental period, TAN removal efficiency was always higher than 96%; denitrification was also very effective, achieving nitrate and nitrite concentrations in the effluent both lower than 5 mg NO_x-N L^-1 on average. Moreover, TCOD average removal efficiency was equal to 85%. Modelling was performed to investigate the nitrification efficacy enhancement; to this aim, a biofilm model was developed, adopting the equations for mixed-culture biofilms and the Activated Model Sludge n°1 (ASM1) for the biological processes rates. The model allowed to determine the maximum uptake rate for autotrophic growth (μ_A was 2.5 d^-1) and the semisaturation constant (K_OA was 0.2 mg O₂ L^-1), suggesting that the nitrification process was 3-fold faster than average and very effective at low oxygen concentrations. The model estimated that about 85% of TAN was removed by the biofilm and only the remaining part by suspended biomass in the bulk liquid. Finally, it was assessed that the A/O-MBBR configuration allowed for a 45-60% savings of the energy requirement compared to a Benchmark WWTP layout.

Sewage Sludge Management at District Level: Reduction and Nutrients Recovery via Hydrothermal Carbonization

In this study, two scenarios of a municipal wastewater treatment plant (WWTP) are presented, which include the integration of the hydrothermal carbonization (HTC) process into the sludge line as a post-treatment of the anaerobic digestion (AD) process. The objective of the simulation is to investigate the performances of AD + HTC treatment to reduce sludge production and improve nutrient and energy recovery. For this purpose, the scheme of an under-construction WWTP was considered, named Trento 3 (Trento, Italy) and with a treatment capacity of 300,000 PE. In the first scenario, the HTC process was fed with thickened sludge from the Trento 3 WWTP, while in the second scenario, dewatered sludge from other local WWTPs was also used as feedstock for the HTC process. Both scenarios allowed to obtain a considerable sludge reduction ranging from 70 to 75% with a notably increase in the biogas production up to 47%, due to the recycling of HTC liquor (HTCL) to the anaerobic digester. Considering nutrients recovery, all the phosphorus and nitrogen present in the HTCL could be used for struvite precipitation with an average yearly gain of 1 million euros. Moreover, the introduction of HTC in the Trento 3 WWTP could allow a reduction in the sludge management costs of up to 2 M€/year.

Graphical Abstract

EZH2 is required for parathyroid and thymic development through differentiation of the third pharyngeal pouch endoderm

The Ezh2 gene encodes a histone methyltransferase of the polycomb repressive complex 2 that methylates histone H3 lysine 27. In this study, we investigated whether EZH2 has a role in the development of the pharyngeal apparatus and whether it regulates the expression of the Tbx1 gene, which encodes a key transcription factor required in pharyngeal development. To these ends, we performed genetic in vivo experiments with mouse embryos and used mouse embryonic stem cell (ESC)-based protocols to probe endoderm and cardiogenic mesoderm differentiation. Results showed that EZH2 occupies the Tbx1 gene locus in mouse embryos, and that suppression of EZH2 was associated with reduced expression of Tbx1 in differentiated mouse ESCs. Conditional deletion of Ezh2 in the Tbx1 expression domain, which includes the pharyngeal endoderm, did not cause cardiac defects but revealed that the gene has an important role in the morphogenesis of the third pharyngeal pouch (PP). We found that in conditionally deleted embryos the third PP was hypoplastic, had reduced expression of Tbx1, lacked the expression of Gcm2, a gene that marks the parathyroid domain, but expressed FoxN1, a gene marking the thymic domain. Consistently, the parathyroids did not develop, and the thymus was hypoplastic. Thus, Ezh2 is required for parathyroid and thymic development, probably through a function in the pouch endoderm. This discovery also provides a novel interpretational key for the finding of Ezh2 activating mutations in hyperparathyroidism and parathyroid cancer.

Summary: EZH2 in the pharyngeal apparatus is required in the endoderm for the development of the parathyroids and thymus, and positively regulates the expression of the Tbx1 gene.

Chromatin and Transcriptional Response to Loss of TBX1 in Early Differentiation of Mouse Cells

The T-box transcription factor TBX1 has critical roles in the cardiopharyngeal lineage and the gene is haploinsufficient in DiGeorge syndrome, a typical developmental anomaly of the pharyngeal apparatus. Despite almost two decades of research, if and how TBX1 function triggers chromatin remodeling is not known. Here, we explored genome-wide gene expression and chromatin remodeling in two independent cellular models of Tbx1 loss of function, mouse embryonic carcinoma cells P19Cl6, and mouse embryonic stem cells (mESCs). The results of our study revealed that the loss or knockdown of TBX1 caused extensive transcriptional changes, some of which were cell type-specific, some were in common between the two models. However, unexpectedly we observed only limited chromatin changes in both systems. In P19Cl6 cells, differentially accessible regions (DARs) were not enriched in T-BOX binding motifs; in contrast, in mESCs, 34% (n = 47) of all DARs included a T-BOX binding motif and almost all of them gained accessibility in Tbx1 -/- cells. In conclusion, despite a clear transcriptional response of our cell models to loss of TBX1 in early cell differentiation, chromatin changes were relatively modest.

Application of real-time nitrogen measurement for intermittent aeration implementation in a biological nitrogen removal system: performances and efficiencies

Several automatic strategies for aeration control have been investigated so far to favor a significant decrement of energy consumptions in biological processes in wastewater treatment plants (WWTPs). Above all, the intermittent aeration process has demonstrated to have several advantages. This work reports the results of a case study made in a small municipal WWTP where an intermittent aeration control strategy based on the online measurement of real-time nitrogen forms has been implemented to optimize the nitrogen removal and the energy consumption in an activated process. High organic removal efficiency was achieved during the whole experimental period. Results indicated that nitrogen removal efficiency has been improved, especially during winter months, by the control strategy adopted that helped to determine the perfect length for the nitrification and denitrification phases. The intermittent aeration process increased the activity of the biomass, further selecting phosphate-accumulating bacteria and improving the growth of bacteria able to internally store carbon source. Excellent effects were achieved on energy and chemical consumption, with a reduction of about 15% and 23%, respectively. Finally, a 12% reduction of sludge production was also detected.

Progress toward full scale application of the anaerobic side-stream reactor (ASSR) process

In order to reduce the investment costs of the anaerobic side-stream reactor (ASSR) process coupled with an activated sludge system and promote the full scale application, the impact of 1 d anaerobic solid retention time (SRT_ASSR) and 100% interchange ratio (IR) has been investigated on sludge reduction, carbon and nutrient removal efficiency and microbial community, in a sequencing batch reactor (SBR)-ASSR system. The SBR-ASSR achieved good removal efficiencies in COD (91.5 ± 3.4%), ammonium nitrogen (98.8 ± 0.5%), total nitrogen (87.9 ± 4.9%) and phosphate (92.8 ± 6.7). The sludge yield of the system was 0.1648 g TSS g^-1COD; 54% lower compared to a conventional activated sludge (CAS) system. Real time quantitative polymerase chain reaction (q-PCR) showed an abundance of hydrolyzing and fermentative bacteria. Comparison at class and genus level confirmed an abundance of anaerobic hydrolyzing and fermentative bacteria, denitrifying bacteria able to simultaneous perform nitrogen and phosphate removal and phosphate accumulating organisms.

Tbx1 represses Mef2c gene expression and is correlated with histone 3 deacetylation of the anterior heart field enhancer

The TBX1 gene is haploinsufficient in 22q11.2 deletion syndrome (22q11.2DS), and genetic evidence from human patients and mouse models points to a major role of this gene in the pathogenesis of this syndrome. Tbx1 can activate and repress transcription, and previous work has shown that one of its functions is to negatively modulate cardiomyocyte differentiation. Tbx1 occupies the anterior heart field (AHF) enhancer of the Mef2c gene, which encodes a key cardiac differentiation transcription factor. Here, we show that increased dosage of Tbx1 correlates with downregulation of Mef2c expression and reduced acetylation of its AHF enhancer in cultured mouse myoblasts. Consistently, 22q11.2DS-derived and in vitro-differentiated human induced pluripotent stem cells (hiPSCs) expressed higher levels of MEF2C and showed increased AHF acetylation, compared with hiPSCs from a healthy donor. Most importantly, we show that in mouse embryos, loss of Tbx1 enhances the expression of the Mef2c-AHF-Cre transgene in a specific region of the splanchnic mesoderm, and in a dosage-dependent manner, providing an in vivo correlate of our cell culture data. These results indicate that Tbx1 regulates the Mef2c AHF enhancer by inducing histone deacetylation.

Tbx1 regulates brain vascularization

The transcription factor TBX1 is the major gene involved in 22q11.2 deletion syndrome (22q11.2DS). Using mouse models of these diseases, we have previously shown that TBX1 activates VEGFR3 in endothelial cells (EC), and that this interaction is critical for the development of the lymphatic vasculature. In this study, we show that TBX1 regulates brain angiogenesis. Using loss-of-function genetics and molecular approaches, we show that TBX1 regulates the VEGFR3 and DLL4 genes in brain ECs. In mice, loss of TBX1 causes global brain vascular defects, comprising brain vessel hyperplasia, enhanced angiogenic sprouting and vessel network disorganization. This phenotype is recapitulated in EC-specific Tbx1 conditional mutants and in an EC-only 3-dimensional cell culture system (matrigel), indicating that the brain vascular phenotype is cell autonomous. Furthermore, EC-specific conditional Tbx1 mutants have poorly perfused brain vessels and brain hypoxia, indicating that the expanded vascular network is functionally impaired. In EC-matrigel cultures, a Notch1 agonist is able to partially rescue microtubule hyperbranching induced by TBX1 knockdown. Thus, we have identified a novel transcriptional regulator of angiogenesis that exerts its effect in brain by negatively regulating angiogenesis through the DLL4/Notch1-VEGFR3 regulatory axis. Given the similarity of the phenotypic consequences of TBX1 mutation in humans and mice, this unexpected role of TBX1 in murine brain vascularization should stimulate clinicians to search for brain microvascular anomalies in 22q11.2DS patients and to evaluate whether some of the anatomical and functional brain anomalies in patients may have a microvascular origin.

Transcriptional control in cardiac progenitors: Tbx1 interacts with the BAF chromatin remodeling complex and regulates Wnt5a

Mutations of the Wnt5a gene, encoding a ligand of the non-canonical Wnt pathway, and the Ror2 gene, encoding its receptor, have been found in patients with cardiac outflow tract defects. We found that Wnt5a is expressed in the second heart field (SHF), a population of cardiac progenitor cells destined to populate the cardiac outflow tract and the right ventricle. Because of cardiac phenotype similarities between Wnt5a and Tbx1 mutant mice, we tested potential interactions between the two genes. We found a strong genetic interaction in vivo and determined that the loss of both genes caused severe hypoplasia of SHF–dependent segments of the heart. We demonstrated that Wnt5a is a transcriptional target of Tbx1 and explored the mechanisms of gene regulation. Tbx1 occupies T-box binding elements within the Wnt5a gene and interacts with the Baf60a/Smarcd1 subunit of a chromatin remodeling complex. It also interacts with the Setd7 histone H3K4 monomethyltransferase. Tbx1 enhances Baf60a occupation at the Wnt5a gene and enhances its H3K4 monomethylation status. Finally, we show that Baf60a is required for Tbx1–driven regulation of target genes. These data suggest a model in which Tbx1 interacts with, and probably recruits a specific subunit of, the BAF complex as well as histone methylases to activate or enhance transcription. We speculate that this may be a general mechanism of T-box function and that Baf60a is a key component of the transcriptional control in cardiac progenitors.

We have demonstrated a novel interaction between the Tbx1 gene, the mutation of which causes DiGeorge syndrome, and Wnt5a, another human disease gene, which is important for oriented cell migration and cell polarity. We found that, in mice, reduced dosage of each of the two genes enhances the phenotype caused by the mutation of the other. Loss of the two genes in mice has very severe consequences for heart development. Our genetic and biochemical data determined that Tbx1, a transcription factor of the T-box family, regulates Wnt5a expression. We found that Tbx1 targets the BAF chromatin remodeling complex to the Wnt5a gene and interacts with a histone monomethyltransferase. Tbx1 expression increases Baf60a occupation of the Wnt5a gene and enhances its H3K4 monomethylation status, while Baf60a knockdown abolishes the ability of Tbx1 to regulate Wnt5a and other target genes. Overall, our data identify Wnt5a as an important effector of Tbx1 function in heart development and demonstrate that Tbx1 regulates the gene by interacting with the chromatin remodeling and histone methylation machinery.

Tbx1 is a negative modulator of Mef2c

The developmental role of the T-box transcription factor Tbx1 is exquisitely dosage-sensitive. In this study, we performed a microarray-based transcriptome analysis of E9.5 embryo tissues across a previously generated Tbx1 mouse allelic series. This analysis identified several genes whose expression was affected by Tbx1 dosage. Interestingly, we found that the expression of the gene encoding the cardiogenic transcription factor Mef2c was negatively correlated to Tbx1 dosage. In vivo data revealed Mef2c up-regulation in the second heart field (SHF) of Tbx1 null mutant embryos compared with wild-type littermates at E9.5. Conversely, Mef2c expression was decreased in the SHF and in somites of Tbx1 gain-of-function mutants. These results are consistent with the described role of Tbx1 in suppressing cardiac progenitor cell differentiation and indicate also a negative effect of Tbx1 on Mef2c during skeletal muscle differentiation. We show that Tbx1 occupies conserved regulatory regions of the Mef2c locus, suggesting a direct effect on Mef2c transcription. However, we also show that Tbx1 interferes with the Gata4→ Mef2c regulatory pathway. Overall, our study uncovered a target of Tbx1 with critical developmental roles, so highlighting the power of the dosage gradient approach that we used.

MID1 mutation screening in a large cohort of Opitz G/BBB syndrome patients: twenty-nine novel mutations identified

Opitz G/BBB Syndrome (OS) is a multiple congenital anomaly disorder characterized by defects along the body midline. The disease is characterized by variable expressivity of signs that include hypertelorism, cleft lip and/or palate, laryngo-tracheo-esophageal abnormalities, cardiac defects, and hypospadias. OS patients also present with mental retardation and brain anatomical abnormalities. An autosomal dominant form mapping to chromosome 22 and an X-linked form of OS are known. The gene responsible for the X-linked form of OS, MID1, codes for a member of the Tripartite Motif family of E3 ubiquitin ligases. Here we report 29 novel mutations in 29 unrelated patients of a cohort of 140 male OS cases. These mutations are found in both familial and sporadic cases. They are scattered along the entire length of the gene and are represented by missense and nonsense mutations, insertions and deletions causing frame shift mutations, and deletion of either single exons or the entire gene. The variety of the mutations found confirms that loss-of-function is the mechanism underlying the OS phenotype. Moreover, the low percentage of MID1-mutated OS patients, 47% of the familial and 13% of the sporadic cases, suggests a wider genetic heterogeneity underlying the OS phenotype.

Mig12, a novel Opitz syndrome gene product partner, is expressed in the embryonic ventral midline and co-operates with Mid1 to bundle and stabilize microtubules

BACKGROUND

Opitz G/BBB syndrome is a genetic disorder characterized by developmental midline abnormalities, such as hypertelorism, cleft palate, and hypospadias. The gene responsible for the X-linked form of this disease, MID1, encodes a TRIM/RBCC protein that is anchored to the microtubules. The association of Mid1 with the cytoskeleton is regulated by dynamic phosphorylation, through the interaction with the alpha4 subunit of phosphatase 2A (PP2A). Mid1 acts as an E3 ubiquitin ligase, regulating PP2A degradation on microtubules.

RESULTS

In spite of these findings, the biological role exerted by the Opitz syndrome gene product is still unclear and the presence of other potential interacting moieties in the Mid1 structure prompted us to search for additional cellular partners. Through a yeast two-hybrid screening approach, we identified a novel gene, MIG12, whose protein product interacts with Mid1. We confirmed by immunoprecipitation that this interaction occurs in vivo and that it is mediated by the Mid1 coiled-coil domain. We found that Mig12 is mainly expressed in the neuroepithelial midline, urogenital apparatus, and digits during embryonic development. Transiently expressed Mig12 is found diffusely in both nucleus and cytoplasm, although it is enriched in the microtubule-organizing center region. Consistently with this, endogenous Mig12 protein is partially detected in the polymerized tubulin fraction after microtubule stabilization. When co-transfected with Mid1, Mig12 is massively recruited to thick filamentous structures composed of tubulin. These microtubule bundles are resistant to high doses of depolymerizing agents and are composed of acetylated tubulin, thus representing stabilized microtubule arrays.

CONCLUSIONS

Our findings suggest that Mig12 co-operates with Mid1 to stabilize microtubules. Mid1-Mig12 complexes might be implicated in cellular processes that require microtubule stabilization, such as cell division and migration. Impairment in Mig12/Mid1-mediated microtubule dynamic regulation, during the development of embryonic midline, may cause the pathological signs observed in Opitz syndrome patients.

X-linked Opitz syndrome: novel mutations in the MID1 gene and redefinition of the clinical spectrum

Opitz (or G/BBB) syndrome is a pleiotropic genetic disorder characterized by hypertelorism, hypospadias, and additional midline defects. This syndrome is heterogeneous with an X-linked (XLOS) and an autosomal dominant (ADOS) form. The gene implicated in the XLOS form, MID1, encodes a protein containing a RING-Bbox-Coiled-coil motif belonging to the tripartite motif (TRIM) family. To further clarify the molecular basis of XLOS, we have undertaken mutation analysis of the MID1 gene in patients with Opitz syndrome (OS). We found novel mutations in 11 of 63 male individuals referred to us as sporadic or familial X-linked OS cases. The mutations are scattered throughout the gene, although more are represented in the 3' region. By reviewing all the MID1-mutated OS patients so far described, we confirmed that hypertelorism and hypospadias are the most frequent manifestations, being present in almost every XLOS individual. However, it is clear that laryngo-tracheo-esophageal (LTE) defects are also common anomalies, being manifested by all MID1-mutated male patients. Congenital heart and anal abnormalities are less frequent than reported in literature. In addition, we can include limb defects in the OS clinical synopsis as we found a MID1-mutated patient showing syndactyly. The low frequency of mutations in MID1 and the high variability of the phenotype suggest the involvement of other genes in the OS phenotype.

[Long-term development of chronic hepatitis caused by virus B in childhood]

Ten children with chronic hepatitis B have been followed for at least 3 years. All patients received 2 liver biopsies, the first after 1 year of continuous liver disfunction and HBsAg positivity, and the second 2 years after, that showed a mild improvement of the histologic lesions in 4 cases of chronic persistent hepatitis (CPH) and in 1 case of chronic lobular hepatitis (CLH). Three children out of 5 with chronic active hepatitis (CAN) changed to CPH and the other 2 remained unchanged without any evidence of cirrhosis. No patient received any drug for the treatment of hepatitis.

[Biliary atresia: pathogenetic considerations emerging from the histopathologic analysis of the liver parenchyma]

Nine patients had been surgically treated for extrahepatic biliary atresia from 1974 to 1982. The analysis of the hepatic specimens obtained during the surgical exploration revealed a wide spectrum of histopathologic lesions. In 3 patients we found severe Giant-cell transformation, while in the other 6 it was not possible to ascribe the histopathologic picture to a univocal pathogenesis. Comparing our results to the reports of other Authors we believe biliary atresia can not be explained by a single pathologic mechanism. The obstruction of the extrahepatic bile ducts might be the common morphologic denominator of different pathologic entities, from each of them it depends a different evolution of the hepatic lesions and a different survival after Kasai's operation.

[Intra-familial transmission of HBV infection]

We investigated 63 household contacts of 29 children positive for serologic markers of hepatitis B virus, in order to assess the intrafamiliar spread of HBV infection. 40 relatives of 15 children affected by chronic hepatitis B (Group I) and 23 relatives of 14 patients affected by hemophilia (Group II) were studied. HBV markers (HBsAg, anti-HBs, anti-HBc, HBeAg, anti-HBe) were tested in all the subjects by RIA. Positive markers were found in 39 (62%) of the subjects; the combined prevalence for all HBV markers was 75% in the Group I, and 39% in the Group II. The higher prevalence rate in Group I can be explained by the possible previous infection of another member of the family, whereas in Group II the child is almost surely the first infected subject. Besides, subjects of Group I have probably been in contact with HBV infected children a longer time, compared to subjects in Group II. Our data suggest that household contacts of children with HBV infection are at high risk and should therefore be immunized against HBV.

[Evaluation of the nutritional status and growth of children with chronic HBsAg-positive hepatitis]

Chronic hepatitis in children seems to have a better prognosis than in adults, with a discrete trend to spontaneous remission. Actually biopsy and liver enzymes are mandatory for a correct follow up of the disease, while few authors are interested in the assessment of growth and nutritional status. We think that an auxological approach is one of the main points in every chronic disease of the pediatric age, chiefly when some anabolic step might be affected. Our first result in a cross sectional study of growth and nutritional status in a selected group of untreated HBsAg+ chronic hepatitis children are as follows. According to enzyme values in the range of 16-171 UI/1 SGOT all patients are growing very well with a good-discrete nutritional status. Though anthropometric proteic nutritional status (muscle circumference) was in the range of normal distribution, we were able to show a moderate correlation between SGOT and muscle circumference (r = -0,50). Our impression is that some patients with a worse hepatic damage can be exposed at risk of proteic malnutrition which is a negative element in the prognosis of every chronic disease. Anthropometric auxology can detect degrees of proteic malnutrition, and can follow its development. So we recommend routine auxological assessment in all pediatric patients with chronic hepatitis.