Compound heterozygosity for two variants in BMP5 in human skeletal dysostosis with atrioventricular septal defect.

The growth and development of the skeleton is regulated by bone morphogenetic proteins of which several are linked to genetic skeletal disorders. So far, no human skeletal malformations have been associated with variants in BMP5. Here, we report a patient with biallelic loss of function variants in BMP5 and a syndromic phenotype including skeletal dysostosis, dysmorphic features, hypermobility, laryngo-tracheo-bronchomalacia and atrioventricular septal defect. We discuss the phenotype in relation to the known tissue-specific expression of Bmp5 and similar morphological abnormalities previously reported in experimental animal models. Our findings suggest a new association between BMP5 variants and a range of developmental anomalies, involving ears, heart and skeleton, thereby increasing understanding of BMP5's role in human development.

Crosstalk between microbiome, regulatory T cells and HCA2 orchestrates the inflammatory response in a murine psoriasis model.

The organ-specific microbiome plays a crucial role in tissue homeostasis, among other things by inducing regulatory T cells (Treg). This applies also to the skin and in this setting short chain fatty acids (SCFA) are relevant. It was demonstrated that topical application of SCFA controls the inflammatory response in the psoriasis-like imiquimod (IMQ)-induced murine skin inflammation model. Since SCFA signal via HCA2, a G-protein coupled receptor, and HCA2 expression is reduced in human lesional psoriatic skin, we studied the effect of HCA2 in this model. HCA2 knock-out (HCA2-KO) mice reacted to IMQ with stronger inflammation, presumably due to an impaired function of Treg. Surprisingly, injection of Treg from HCA2-KO mice even enhanced the IMQ reaction, suggesting that in the absence of HCA2 Treg switch from a suppressive into a proinflammatory type. HCA2-KO mice differed in the composition of the skin microbiome from wild type mice. Co-housing reversed the exaggerated response to IMQ and prevented the alteration of Treg, implying that the microbiome dictates the outcome of the inflammatory reaction. The switch of Treg into a proinflammatory type in HCA2-KO mice could be a downstream phenomenon. This opens the opportunity to reduce the inflammatory tendency in psoriasis by altering the skin microbiome.

MCT1-dependent energetic failure and neuroinflammation underlie optic nerve degeneration in Wolfram syndrome mice.

Wolfram syndrome 1 (WS1) is a rare genetic disorder caused by mutations in the WFS1 gene leading to a wide spectrum of clinical dysfunctions, among which blindness, diabetes, and neurological deficits are the most prominent. WFS1 encodes for the endoplasmic reticulum (ER) resident transmembrane protein wolframin with multiple functions in ER processes. However, the WFS1-dependent etiopathology in retinal cells is unknown. Herein, we showed that Wfs1 mutant mice developed early retinal electrophysiological impairments followed by marked visual loss. Interestingly, axons and myelin disruption in the optic nerve preceded the degeneration of the retinal ganglion cell bodies in the retina. Transcriptomics at pre-degenerative stage revealed the STAT3-dependent activation of proinflammatory glial markers with reduction of the homeostatic and pro-survival factors glutamine synthetase and BDNF. Furthermore, label-free comparative proteomics identified a significant reduction of the monocarboxylate transport isoform 1 (MCT1) and its partner basigin that are highly enriched on retinal glia and myelin-forming oligodendrocytes in optic nerve together with wolframin. Loss of MCT1 caused a failure in lactate transfer from glial to neuronal cell bodies and axons leading to a chronic hypometabolic state. Thus, this bioenergetic impairment is occurring concurrently both within the axonal regions and cell bodies of the retinal ganglion cells, selectively endangering their survival while impacting less on other retinal cells. This metabolic dysfunction occurs months before the frank RGC degeneration suggesting an extended time-window for intervening with new therapeutic strategies focused on boosting retinal and optic nerve bioenergetics in WS1.

Electrophysiologically Determined Spectral Responses in Lobesia botrana (Lepidoptera: Tortricidae).

Electrophysiological methods were used to test the visual sensitivity of European grapevine moth, Lobesia botrana (Lepidoptera: Tortricidae) to wavelengths ranging from 300 to 700 nm. For male and females tested, a main, peak response occurred in the 460-540 nm range (blue-green wavelengths) with females having a generally lower response to wavelengths in that range. A second smaller peak was observed for both sexes at the 340-420 nm range. A general linear model indicated that males, virgin females, and mated females did not react differently to changes in wavelength. No moths showed any obvious sensitivity to wavelengths between 580 and 700 nm. Based on our retinal recording data we suggest that UV light traps (≤480 nm) could be utilized alongside pheromone traps when monitoring L. botrana in high risk areas.

Discovery of Novel BRD4 Ligand Scaffolds by Automated Navigation of the Fragment Chemical Space.

Fragment-based drug discovery (FBDD) is a very effective hit identification method. However, the evolution of fragment hits into suitable leads remains challenging and largely artisanal. Fragment evolution is often scaffold-centric, meaning that its outcome depends crucially on the chemical structure of the starting fragment. Considering that fragment screening libraries cover only a small proportion of the corresponding chemical space, hits should be seen as probes highlighting privileged areas of the chemical space rather than actual starting points. We have developed an automated computational pipeline to mine the chemical space around any specific fragment hit, rapidly finding analogues that share a common interaction motif but are structurally novel and diverse. On a prospective application on the bromodomain-containing protein 4 (BRD4), starting from a known fragment, the platform yields active molecules with nonobvious scaffold changes. The procedure is fast and inexpensive and has the potential to uncover many hidden opportunities in FBDD.

Predictive Models of Genetic Redundancy in Arabidopsis thaliana.

Genetic redundancy refers to a situation where an individual with a loss-of-function mutation in one gene (single mutant) does not show an apparent phenotype until one or more paralogs are also knocked out (double/higher-order mutant). Previous studies have identified some characteristics common among redundant gene pairs, but a predictive model of genetic redundancy incorporating a wide variety of features derived from accumulating omics and mutant phenotype data is yet to be established. In addition, the relative importance of these features for genetic redundancy remains largely unclear. Here, we establish machine learning models for predicting whether a gene pair is likely redundant or not in the model plant Arabidopsis thaliana based on six feature categories: functional annotations, evolutionary conservation including duplication patterns and mechanisms, epigenetic marks, protein properties including posttranslational modifications, gene expression, and gene network properties. The definition of redundancy, data transformations, feature subsets, and machine learning algorithms used significantly affected model performance based on holdout, testing phenotype data. Among the most important features in predicting gene pairs as redundant were having a paralog(s) from recent duplication events, annotation as a transcription factor, downregulation during stress conditions, and having similar expression patterns under stress conditions. We also explored the potential reasons underlying mispredictions and limitations of our studies. This genetic redundancy model sheds light on characteristics that may contribute to long-term maintenance of paralogs, and will ultimately allow for more targeted generation of functionally informative double mutants, advancing functional genomic studies.

Composite modeling of leaf shape along shoots discriminates Vitis species better than individual leaves.

PREMISE: Leaf morphology is dynamic, continuously deforming during leaf expansion and among leaves within a shoot. Here, we measured the leaf morphology of more than 200 grapevines (Vitis spp.) over four years and modeled changes in leaf shape along the shoot to determine whether a composite leaf shape comprising all the leaves from a single shoot can better capture the variation and predict species identity compared with individual leaves. METHODS: Using homologous universal landmarks found in grapevine leaves, we modeled various morphological features as polynomial functions of leaf nodes. The resulting functions were used to reconstruct modeled leaf shapes across the shoots, generating composite leaves that comprehensively capture the spectrum of leaf morphologies present. RESULTS: We found that composite leaves are better predictors of species identity than individual leaves from the same plant. We were able to use composite leaves to predict the species identity of previously unassigned grapevines, which were verified with genotyping. DISCUSSION: Observations of individual leaf shape fail to capture the true diversity between species. Composite leaf shape-an assemblage of modeled leaf snapshots across the shoot-is a better representation of the dynamic and essential shapes of leaves, in addition to serving as a better predictor of species identity than individual leaves.

Renal transplantation using vascular conduit reconstruction in deceased kidneys with multiple renal arteries and short renal veins / Trasplante renal mediante reconstrucción de conducto vascular en riñones de donantes fallecidos con arterias renales múltiples y venas renales cortas

ANTECEDENTES: El trasplante renal con variantes anatómicas vasculares sigue siendo un desafío. Debido a su éxito variable en lo que respecta a la función del injerto después del trasplante, estos órganos se descartan frecuentemente, asumiendo de antemano una tasa inasequible de complicaciones vasculares. PACIENTES Y MÉTODOS: Realizamos 3 trasplantes de riñón utilizando órganos de donantes fallecidos que presentaban variantes vasculares (arterias múltiples y venas cortas), incluyendo un riñón en herradura indivisible. Se utilizaron diferentes injertos extraídos de la aorta, la arteria ilíaca común y la vena cava inferior del mismo donante para reconstruir la configuración vascular inicial mediante la creación de conductos arteriales y venosos individuales, con el fin de simplificar la anastomosis vascular en el receptor. RESULTADOS: No se registraron complicaciones postoperatorias. Los tiempos de isquemia caliente fueron comparables con los de aloinjertos renales de una sola arteria. En ningún caso se observó un retraso en la función del injerto y todos los pacientes recuperaron la función renal normal después del trasplante. CONCLUSIONES: La reconstrucción vascular mediante injertos arteriales y venosos del mismo donante fallecido puede ser un recurso útil para simplificar la anastomosis vascular durante la cirugía de trasplante, evitando así su descarte de antemano, reduciendo al mínimo las complicaciones perioperatorias y permitiendo tasas normales de función de los injertos en el seguimiento a largo plazo. El resultado satisfactorio obtenido mediante la utilización de este enfoque ayudaría a ampliar los criterios de donantes para incluir órganos que presentan variantes anatómicas vasculares

BACKGROUND: Transplantation of kidneys with vascular anatomical variants remains a challenge. Due to its varying success in regard to graft function after transplantation, these organs have been frequently discarded assuming in advance an unaffordable rate of vascular complications. PATIENTS AND METHODS: We performed three kidney transplants using organs from deceased donors harboring vascular variants (multiple arteries and short veins), including an unsplittable horseshoe kidney. Different grafts harvested from the same donor aorta, common iliac artery, and inferior vena cava, were used to reconstruct the initial vascular configuration by creating single arterial and venous conduits aimed to simplify the vascular anastomoses in the recipient. RESULTS: No post-operative complications were recorded. Warm ischemia times remained comparable to single artery renal allografts. No delayed graft function was noted in any case, and every patient regained normal renal function after transplantation. CONCLUSIONS: Vascular reconstruction using arterial and venous grafts harvested from the same deceased donor may result a helpful tool to simplify vascular anastomoses during transplantation surgery, thus avoiding their discard in advance, minimizing perioperative complications, and enabling normal graft function rates in the long-term follow-up. The successful outcome obtained by using this approach would help to expand the donor criteria for the inclusion of organs containing vascular anatomical variants

Renal transplantation using vascular conduit reconstruction in deceased kidneys with multiple renal arteries and short renal veins. / Trasplante renal mediante reconstrucción de conducto vascular en riñones de donantes fallecidos con arterias renales múltiples y venas renales cortas.

BACKGROUND: Transplantation of kidneys with vascular anatomical variants remains a challenge. Due to its varying success in regard to graft function after transplantation, these organs have been frequently discarded assuming in advance an unaffordable rate of vascular complications. PATIENTS AND METHODS: We performed three kidney transplants using organs from deceased donors harboring vascular variants (multiple arteries and short veins), including an unsplittable horseshoe kidney. Different grafts harvested from the same donor aorta, common iliac artery, and inferior vena cava, were used to reconstruct the initial vascular configuration by creating single arterial and venous conduits aimed to simplify the vascular anastomoses in the recipient. RESULTS: No post-operative complications were recorded. Warm ischemia times remained comparable to single artery renal allografts. No delayed graft function was noted in any case, and every patient regained normal renal function after transplantation. CONCLUSIONS: Vascular reconstruction using arterial and venous grafts harvested from the same deceased donor may result a helpful tool to simplify vascular anastomoses during transplantation surgery, thus avoiding their discard in advance, minimizing perioperative complications, and enabling normal graft function rates in the long-term follow-up. The successful outcome obtained by using this approach would help to expand the donor criteria for the inclusion of organs containing vascular anatomical variants.

Long-Term Health-Related Quality of Life After Venovenous Extracorporeal Membrane Oxygenation.

This study examined the long-term health-related quality of life in adult patients treated with venovenous extracorporeal membrane oxygenation (V-V ECMO) for severe acute respiratory failure in Ireland. A retrospective, cross-sectional survey was conducted to elicit self-reported quality of life in V-V ECMO survivors who were discharged from the intensive care unit for ≥6 months. Twenty-nine patients with respiratory failure were treated with V-V ECMO from 2009 to 2013. Of the 19 (66%) patients who survived to hospital discharge, 13 participated in the study. The mean age was 44 ± 11 years, and seven were male. At a median follow-up of 36 (14-39) months, study participants reported decreased indices of physical health compared with age- and sex-matched general population in Ireland while their mental health was similar to age- and sex-matched general population in Ireland. Fifty-four percent of participants had symptoms of anxiety, 15 percent had symptoms of depression, while 23 percent of participants were at risk of posttraumatic stress disorder. Sixty-seven percent of previously employed participants had returned to work. This study highlights the protracted nature of physical and psychologic recovery in patients surviving up to three years after V-V ECMO for severe acute respiratory failure.

Parche vascular del donante para reconstrucción de aorta y vena cava inferior en trasplante de riñón pediátrico en bloque / Donor vascular patch for reconstruction of the aorta and inferior vena cava in pediatric en bloc kidney transplantation

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RNASeqDesign: A framework for RNA-Seq genome-wide power calculation and study design issues.

Massively parallel sequencing (a.k.a. next-generation sequencing, NGS) technology has emerged as a powerful tool in characterizing genomic profiles. Among many NGS applications, RNA sequencing (RNA-Seq) has gradually become a standard tool for global transcriptomic monitoring. Although the cost of NGS experiments has dropped constantly, the high sequencing cost and bioinformatic complexity are still obstacles for many biomedical projects. Unlike earlier fluorescence-based technologies such as microarray, modelling of NGS data should consider discrete count data. In addition to sample size, sequencing depth also directly relates to the experimental cost. Consequently, given total budget and pre-specified unit experimental cost, the study design issue in RNA-Seq is conceptually a more complex multi-dimensional constrained optimization problem rather than one-dimensional sample size calculation in traditional hypothesis setting. In this paper, we propose a statistical framework, namely "RNASeqDesign", to utilize pilot data for power calculation and study design of RNA-Seq experiments. The approach is based on mixture model fitting of p-value distribution from pilot data and a parametric bootstrap procedure based on approximated Wald test statistics to infer genome-wide power for optimal sample size and sequencing depth. We further illustrate five practical study design tasks for practitioners. We perform simulations and three real applications to evaluate the performance and compare to existing methods.

Fluid Balance and Recovery of Native Lung Function in Adult Patients Supported by Venovenous Extracorporeal Membrane Oxygenation and Continuous Renal Replacement Therapy.

Fluid overload is associated with increased mortality in adult patients with acute respiratory distress syndrome. In patients requiring venovenous extracorporeal membrane oxygenation (VV-ECMO), the effects of fluid removal on survival and lung recovery remain undefined. We assessed the impact of early fluid removal in adult patients supported by VV-ECMO and concomitant continuous renal replacement therapy, in an 18-bed tertiary intensive care unit between 2010 and 2015. Twenty-four patients met inclusion criteria, of these 15 (63%) survived to hospital discharge. In our patient group, a more negative cumulative daily fluid balance was strongly associated with improved pulmonary compliance (2.72 ml/cmH2O per 1 L negative fluid balance; 95% confidence interval [CI]: 1.61-3.83; P < 0.001). In addition, a more negative mean daily fluid balance was associated with improved pulmonary compliance (4.37 ml/cmH2O per 1 L negative fluid balance; 95% CI: 2.62-6.13; P < 0.001). Survivors were younger and had lower mean daily fluid balance (-0.33 L [95% CI: -1.22 to -0.06] vs. -0.07 L [95% CI: -0.76 to 0.06]; P = 0.438) and lower cumulative fluid balance up to day 14 (-4.60 L [95% CI: -8.40 to -1.45] vs. -1.00 L [95% CI: -4.60 to 0.90]; P = 0.325), although the fluid balance effect alone did not reach statistical significance.

Cas9/sgRNA selective targeting of the P23H Rhodopsin mutant allele for treating retinitis pigmentosa by intravitreal AAV9.PHP.B-based delivery.

P23H is the most common mutation in the RHODOPSIN (RHO) gene leading to a dominant form of retinitis pigmentosa (RP), a rod photoreceptor degeneration that invariably causes vision loss. Specific disruption of the disease P23H RHO mutant while preserving the wild-type (WT) functional allele would be an invaluable therapy for this disease. However, various technologies tested in the past failed to achieve effective changes and consequently therapeutic benefits. We validated a CRISPR/Cas9 strategy to specifically inactivate the P23H RHO mutant, while preserving the WT allele in vitro. We, then, translated this approach in vivo by delivering the CRISPR/Cas9 components in murine Rho+/P23H mutant retinae. Targeted retinae presented a high rate of cleavage in the P23H but not WT Rho allele. This gene manipulation was sufficient to slow photoreceptor degeneration and improve retinal functions. To improve the translational potential of our approach, we tested intravitreal delivery of this system by means of adeno-associated viruses (AAVs). To this purpose, the employment of the AAV9-PHP.B resulted the most effective in disrupting the P23H Rho mutant. Finally, this approach was translated successfully in human cells engineered with the homozygous P23H RHO gene mutation. Overall, this is a significant proof-of-concept that gene allele specific targeting by CRISPR/Cas9 technology is specific and efficient and represents an unprecedented tool for treating RP and more broadly dominant genetic human disorders affecting the eye, as well as other tissues.

AAV-PHP.B-Mediated Global-Scale Expression in the Mouse Nervous System Enables GBA1 Gene Therapy for Wide Protection from Synucleinopathy.

The lack of technology for direct global-scale targeting of the adult mouse nervous system has hindered research on brain processing and dysfunctions. Currently, gene transfer is normally achieved by intraparenchymal viral injections, but these injections target a restricted brain area. Herein, we demonstrated that intravenous delivery of adeno-associated virus (AAV)-PHP.B viral particles permeated and diffused throughout the neural parenchyma, targeting both the central and the peripheral nervous system in a global pattern. We then established multiple procedures of viral transduction to control gene expression or inactivate gene function exclusively in the adult nervous system and assessed the underlying behavioral effects. Building on these results, we established an effective gene therapy strategy to counteract the widespread accumulation of α-synuclein deposits throughout the forebrain in a mouse model of synucleinopathy. Transduction of A53T-SCNA transgenic mice with AAV-PHP.B-GBA1 restored physiological levels of the enzyme, reduced α-synuclein pathology, and produced significant behavioral recovery. Finally, we provided evidence that AAV-PHP.B brain penetration does not lead to evident dysfunctions in blood-brain barrier integrity or permeability. Altogether, the AAV-PHP.B viral platform enables non-invasive, widespread, and long-lasting global neural expression of therapeutic genes, such as GBA1, providing an invaluable approach to treat neurodegenerative diseases with diffuse brain pathology such as synucleinopathies.

Proinflammatory cytokine interferon-γ and microbiome-derived metabolites dictate epigenetic switch between forkhead box protein 3 isoforms in coeliac disease.

Coeliac disease (CD) is an autoimmune enteropathy triggered by gluten and characterized by a strong T helper type 1 (Th1)/Th17 immune response in the small intestine. Regulatory T cells (Treg ) are CD4+ CD25++ forkhead box protein 3 (FoxP3+ ) cells that regulate the immune response. Conversely to its counterpart, FoxP3 full length (FL), the alternatively spliced isoform FoxP3 Δ2, cannot properly down-regulate the Th17-driven immune response. As the active state of CD has been associated with impairments in Treg cell function, we aimed at determining whether imbalances between FoxP3 isoforms may be associated with the disease. Intestinal biopsies from patients with active CD showed increased expression of FOXP3 Δ2 isoform over FL, while both isoforms were expressed similarly in non-coeliac control subjects (HC). Conversely to what we saw in the intestine, peripheral blood mononuclear cells (PBMC) from HC subjects did not show the same balance between isoforms. We therefore hypothesized that the intestinal microenvironment may play a role in modulating alternative splicing. The proinflammatory intestinal microenvironment of active patients has been reported to be enriched in butyrate-producing bacteria, while high concentrations of lactate have been shown to characterize the preclinical stage of the disease. We show that the combination of interferon (IFN)-γ and butyrate triggers the balance between FoxP3 isoforms in HC subjects, while the same does not occur in CD patients. Furthermore, we report that lactate increases both isoforms in CD patients. Collectively, these findings highlight the importance of the ratio between FoxP3 isoforms in CD and, for the first time, associate the alternative splicing process mechanistically with microbial-derived metabolites.

Rapid and efficient CRISPR/Cas9 gene inactivation in human neurons during human pluripotent stem cell differentiation and direct reprogramming.

The CRISPR/Cas9 system is a rapid and customizable tool for gene editing in mammalian cells. In particular, this approach has widely opened new opportunities for genetic studies in neurological disease. Human neurons can be differentiated in vitro from hPSC (human Pluripotent Stem Cells), hNPCs (human Neural Precursor Cells) or even directly reprogrammed from fibroblasts. Here, we described a new platform which enables, rapid and efficient CRISPR/Cas9-mediated genome targeting simultaneously with three different paradigms for in vitro generation of neurons. This system was employed to inactivate two genes associated with neurological disorder (TSC2 and KCNQ2) and achieved up to 85% efficiency of gene targeting in the differentiated cells. In particular, we devised a protocol that, combining the expression of the CRISPR components with neurogenic factors, generated functional human neurons highly enriched for the desired genome modification in only 5 weeks. This new approach is easy, fast and that does not require the generation of stable isogenic clones, practice that is time consuming and for some genes not feasible.

Coenzyme A corrects pathological defects in human neurons of PANK2-associated neurodegeneration.

Pantothenate kinase-associated neurodegeneration (PKAN) is an early onset and severely disabling neurodegenerative disease for which no therapy is available. PKAN is caused by mutations in PANK2, which encodes for the mitochondrial enzyme pantothenate kinase 2. Its function is to catalyze the first limiting step of Coenzyme A (CoA) biosynthesis. We generated induced pluripotent stem cells from PKAN patients and showed that their derived neurons exhibited premature death, increased ROS production, mitochondrial dysfunctions-including impairment of mitochondrial iron-dependent biosynthesis-and major membrane excitability defects. CoA supplementation prevented neuronal death and ROS formation by restoring mitochondrial and neuronal functionality. Our findings provide direct evidence that PANK2 malfunctioning is responsible for abnormal phenotypes in human neuronal cells and indicate CoA treatment as a possible therapeutic intervention.

Rapid Conversion of Fibroblasts into Functional Forebrain GABAergic Interneurons by Direct Genetic Reprogramming.

Transplantation of GABAergic interneurons (INs) can provide long-term functional benefits in animal models of epilepsy and other neurological disorders. Whereas GABAergic INs can be differentiated from embryonic stem cells, alternative sources of GABAergic INs may be more tractable for disease modeling and transplantation. We identified five factors (Foxg1, Sox2, Ascl1, Dlx5, and Lhx6) that convert mouse fibroblasts into induced GABAergic INs (iGABA-INs) possessing molecular signatures of telencephalic INs. Factor overexpression activates transcriptional networks required for GABAergic fate specification. iGABA-INs display progressively maturing firing patterns comparable to cortical INs, form functional synapses, and release GABA. Importantly, iGABA-INs survive and mature upon being grafted into mouse hippocampus. Optogenetic stimulation demonstrated functional integration of grafted iGABA-INs into host circuitry, triggering inhibition of host granule neuron activity. These five factors also converted human cells into functional GABAergic INs. These properties suggest that iGABA-INs have potential for disease modeling and cell-based therapeutic approaches to neurological disorders.