Isogenic GAA-KO Murine Muscle Cell Lines Mimicking Severe Pompe Mutations as Preclinical Models for the Screening of Potential Gene Therapy Strategies.

Pompe disease (PD) is a rare disorder caused by mutations in the acid alpha-glucosidase (GAA) gene. Most gene therapies (GT) partially rely on the cross-correction of unmodified cells through the uptake of the GAA enzyme secreted by corrected cells. In the present study, we generated isogenic murine GAA-KO cell lines resembling severe mutations from Pompe patients. All of the generated GAA-KO cells lacked GAA activity and presented an increased autophagy and increased glycogen content by means of myotube differentiation as well as the downregulation of mannose 6-phosphate receptors (CI-MPRs), validating them as models for PD. Additionally, different chimeric murine GAA proteins (IFG, IFLG and 2G) were designed with the aim to improve their therapeutic activity. Phenotypic rescue analyses using lentiviral vectors point to IFG chimera as the best candidate in restoring GAA activity, normalising the autophagic marker p62 and surface levels of CI-MPRs. Interestingly, in vivo administration of liver-directed AAVs expressing the chimeras further confirmed the good behaviour of IFG, achieving cross-correction in heart tissue. In summary, we generated different isogenic murine muscle cell lines mimicking the severe PD phenotype, as well as validating their applicability as preclinical models in order to reduce animal experimentation.

Bayesian Augmented Clinical Trials in TB Therapeutic Vaccination.

We propose a Bayesian hierarchical method for combining in silico and in vivo data onto an augmented clinical trial with binary end points. The joint posterior distribution from the in silico experiment is treated as a prior, weighted by a measure of compatibility of the shared characteristics with the in vivo data. We also formalise the contribution and impact of in silico information in the augmented trial. We illustrate our approach to inference with in silico data from the UISS-TB simulator, a bespoke simulator of virtual patients with tuberculosis infection, and synthetic physical patients from a clinical trial.

Moving forward through the in silico modeling of tuberculosis: a further step with UISS-TB.

BACKGROUND: In 2018, about 10 million people were found infected by tuberculosis, with approximately 1.2 million deaths worldwide. Despite these numbers have been relatively stable in recent years, tuberculosis is still considered one of the top 10 deadliest diseases worldwide. Over the years, Mycobacterium tuberculosis has developed a form of resistance to first-line tuberculosis treatments, specifically to isoniazid, leading to multi-drug-resistant tuberculosis. In this context, the EU and Indian DBT funded project STriTuVaD-In Silico Trial for Tuberculosis Vaccine Development-is supporting the identification of new interventional strategies against tuberculosis thanks to the use of Universal Immune System Simulator (UISS), a computational framework capable of predicting the immunity induced by specific drugs such as therapeutic vaccines and antibiotics. RESULTS: Here, we present how UISS accurately simulates tuberculosis dynamics and its interaction within the immune system, and how it predicts the efficacy of the combined action of isoniazid and RUTI vaccine in a specific digital population cohort. Specifically, we simulated two groups of 100 digital patients. The first group was treated with isoniazid only, while the second one was treated with the combination of RUTI vaccine and isoniazid, according to the dosage strategy described in the clinical trial design. UISS-TB shows to be in good agreement with clinical trial results suggesting that RUTI vaccine may favor a partial recover of infected lung tissue. CONCLUSIONS: In silico trials innovations represent a powerful pipeline for the prediction of the effects of specific therapeutic strategies and related clinical outcomes. Here, we present a further step in UISS framework implementation. Specifically, we found that the simulated mechanism of action of RUTI and INH are in good alignment with the results coming from past clinical phase IIa trials.

Generation of digital patients for the simulation of tuberculosis with UISS-TB.

BACKGROUND: The STriTuVaD project, funded by Horizon 2020, aims to test through a Phase IIb clinical trial one of the most advanced therapeutic vaccines against tuberculosis. As part of this initiative, we have developed a strategy for generating in silico patients consistent with target population characteristics, which can then be used in combination with in vivo data on an augmented clinical trial. RESULTS: One of the most challenging tasks for using virtual patients is developing a methodology to reproduce biological diversity of the target population, ie, providing an appropriate strategy for generating libraries of digital patients. This has been achieved through the creation of the initial immune system repertoire in a stochastic way, and through the identification of a vector of features that combines both biological and pathophysiological parameters that personalise the digital patient to reproduce the physiology and the pathophysiology of the subject. CONCLUSIONS: We propose a sequential approach to sampling from the joint features population distribution in order to create a cohort of virtual patients with some specific characteristics, resembling the recruitment process for the target clinical trial, which then can be used for augmenting the information from the physical the trial to help reduce its size and duration.

Displasia ectodérmica hipohidrótica ligada al cromosoma X de novo por variante recurrente en un paciente mexicano / X-linked hypohidrotic ectodermal dysplasia by a de novo recurrent variant in a Mexican patient

Resumen Introducción: Las displasias ectodérmicas son un grupo de genodermatosis que se caracterizan por distrofia de las estructuras derivadas del ectodermo. De ellas, la variedad más común es la hipohidrótica, con una incidencia de 7/100,000 nacidos vivos observada en todos los grupos étnicos. La displasia ectodérmica hipohidrótica tiene distintas etiologías. La presentación más frecuente es la asociada a un patrón de herencia ligado al cromosoma X, causada por variantes patogénicas del gen EDA en Xq13.1. EDA codifica a la ectodisplasina A, una molécula de señalización que participa en la comunicación epitelio-mesénquima durante el desarrollo de la piel y los anexos. Caso clínico: Varón de 6 años con las características clínicas cardinales de la displasia ectodérmica hipohidrótica ligada al cromosoma X (DEHLX), que incluyen hipotricosis, oligodoncia e hipohidrosis. El análisis del gen EDA por secuenciación directa mostró la presencia de la variante patogénica c.466C>T, p.Arg156Cys, rs132630313 con presentación de novo en el paciente. Esta variante ya ha sido reportada en diferentes poblaciones, incluyendo familias mexicanas, y constituye un punto caliente para mutación en EDA. Se analizaron los hallazgos clínicos, la etiología y el manejo de la DEHLX, en la que de manera reciente se ha planteado la posibilidad de otorgar tratamiento prenatal para prevenir sus manifestaciones clínicas. Conclusiones: Se pone de relevancia que el análisis molecular en pacientes con DEHLX corrobora el diagnóstico clínico y permite brindar asesoramiento genético con bases moleculares.

Abstract Background: Ectodermal dysplasias are a group of genodermatoses characterized by dystrophy of ectodermal derived structures. The most frequent presentation of the ectodermal dysplasias is the hypohidrotic type, which has an incidence of 7/100,000 newborns and has been described in all ethnic groups. The hypohidrotic ectodermal dysplasia (HED) has different etiologies, and it is more frequently associated with an X-linked pattern of inheritance caused by pathogenic variants of the EDA gene in Xq13.1. EDA encodes the protein ectodisplasin A, a signal molecule which participates in epithelium and mesenchymal development of the skin. Case report: A 6 year-old male patient with the main clinical characteristics of the X-linked HED including hypotrichosis, hypodontia and hypohidrosis. The direct sequencing analysis of EDA in our patient detected a de novo pathogenic variant, c.466C>T, p.Arg156Cys, rs132630313. This variant has been previously described in different ethnic groups, including Mexican families, and is considered a mutational hotspot. The clinical characteristics, etiology and management of the X-linked HED, including the possibility of prenatal therapy in order to avoid the clinical manifestations are discussed. Conclusions: The molecular analysis in patients with X-linked HED is of relevance, as it enables to confirm the clinical diagnosis and also, it allows a genetic assessment with molecular bases.

X-linked hypohidrotic ectodermal dysplasia by a de novo recurrent variant in a Mexican patient.

Background: Ectodermal dysplasias are a group of genodermatoses characterized by dystrophy of ectodermal derived structures. The most frequent presentation of the ectodermal dysplasias is the hypohidrotic type, which has an incidence of 7/100,000 newborns and has been described in all ethnic groups. The hypohidrotic ectodermal dysplasia (HED) has different etiologies, and it is more frequently associated with an X-linked pattern of inheritance caused by pathogenic variants of the EDA gene in Xq13.1. EDA encodes the protein ectodisplasin A, a signal molecule which participates in epithelium and mesenchymal development of the skin. Case report: A 6 year-old male patient with the main clinical characteristics of the X-linked HED including hypotrichosis, hypodontia and hypohidrosis. The direct sequencing analysis of EDA in our patient detected a de novo pathogenic variant, c.466C>T, p.Arg156Cys, rs132630313. This variant has been previously described in different ethnic groups, including Mexican families, and is considered a mutational hotspot. The clinical characteristics, etiology and management of the X-linked HED, including the possibility of prenatal therapy in order to avoid the clinical manifestations are discussed. Conclusions: The molecular analysis in patients with X-linked HED is of relevance, as it enables to confirm the clinical diagnosis and also, it allows a genetic assessment with molecular bases.

Introducción: Las displasias ectodérmicas son un grupo de genodermatosis que se caracterizan por distrofia de las estructuras derivadas del ectodermo. De ellas, la variedad más común es la hipohidrótica, con una incidencia de 7/100,000 nacidos vivos observada en todos los grupos étnicos. La displasia ectodérmica hipohidrótica tiene distintas etiologías. La presentación más frecuente es la asociada a un patrón de herencia ligado al cromosoma X, causada por variantes patogénicas del gen EDA en Xq13.1. EDA codifica a la ectodisplasina A, una molécula de señalización que participa en la comunicación epitelio-mesénquima durante el desarrollo de la piel y los anexos. Caso clínico: Varón de 6 años con las características clínicas cardinales de la displasia ectodérmica hipohidrótica ligada al cromosoma X (DEHLX), que incluyen hipotricosis, oligodoncia e hipohidrosis. El análisis del gen EDA por secuenciación directa mostró la presencia de la variante patogénica c.466C>T, p.Arg156Cys, rs132630313 con presentación de novo en el paciente. Esta variante ya ha sido reportada en diferentes poblaciones, incluyendo familias mexicanas, y constituye un punto caliente para mutación en EDA. Se analizaron los hallazgos clínicos, la etiología y el manejo de la DEHLX, en la que de manera reciente se ha planteado la posibilidad de otorgar tratamiento prenatal para prevenir sus manifestaciones clínicas. Conclusiones: Se pone de relevancia que el análisis molecular en pacientes con DEHLX corrobora el diagnóstico clínico y permite brindar asesoramiento genético con bases moleculares.

Credibility of In Silico Trial Technologies-A Theoretical Framing.

Different research communities have developed various approaches to assess the credibility of predictive models. Each approach usually works well for a specific type of model, and under some epistemic conditions that are normally satisfied within that specific research domain. Some regulatory agencies recently started to consider evidences of safety and efficacy on new medical products obtained using computer modelling and simulation (which is referred to as In Silico Trials); this has raised the attention in the computational medicine research community on the regulatory science aspects of this emerging discipline. But this poses a foundational problem: in the domain of biomedical research the use of computer modelling is relatively recent, without a widely accepted epistemic framing for model credibility. Also, because of the inherent complexity of living organisms, biomedical modellers tend to use a variety of modelling methods, sometimes mixing them in the solution of a single problem. In such context merely adopting credibility approaches developed within other research communities might not be appropriate. In this paper we propose a theoretical framing for assessing the credibility of a predictive models for In Silico Trials, which accounts for the epistemic specificity of this research field and is general enough to be used for different type of models.

[Programa de entrenamiento en reparacion vascular en modelo experimental para residentes de cirugía general]. / Vascular reparation training program in experimental model for general surgery residents.

INTRODUCCIÓN: Los programas de entrenamiento simulado permiten optimizar recursos, aumentar la práctica técnica y acortar curvas de aprendizaje, y constituyen un método seguro, estandarizado y validado de aprendizaje para todos los entrenados. OBJETIVO: Desarrollar un programa de entrenamiento vascular mediante la elaboración de una anastomosis término-terminal de un vaso en un modelo experimental para residentes de cirugía general. MÉTODO: Para el desarrollo de este modelo de entrenamiento se utilizó una extremidad amputada a nivel supracondíleo libre de proceso médico-legal. Se realizó la disección de la arteria femoral, se dividió en dos porciones y se realizó una anastomosis término-terminal. Se diseño un sistema que incluye la evaluación de las siguientes variables utlizando la escalas OSATS (Objetive Structured Assesment of Technical Skills) y Likert: 1) nudo manual y punto simple; 2) permeabilidad de la anastomosis; 3) simetría de los puntos; 4) fuga de anastomosis; y 5) tiempo total de anastomosis. DISCUSIÓN: Al reconocer las ventajas del entrenamiento experimental, se propone un modelo biológico experimental reproducible, estandarizado y de bajo costo. CONCLUSIONES: El desarrollo de modelos biológicos experimentales permite al cirujano general la adquisición de habilidades y destrezas quirúrgicas, mejorando el desempeño durante un procedimiento quirúrgico y reduciendo riesgos. INTRODUCTION: Simulated training programs allow to optimize resources, increase technical practice and shorten learning curves, constituting a safe, standardized and validated method of learning for all those trained. OBJECTIVE: Develop a vascular training program through the elaboration of an end to end anastomosis of a vessel in an experimental model for General Surgery residents. METHOD: For the development of this training model, an amputated limb was used at the supracondylar level free of medical-legal process. The dissection of the femoral artery was performed, it was divided into two portions and an end to end anastomosis was performed. A system was designed that included the evaluation of the following variables using the OSATS (Objective Structured Assessment of Technical Skills) and Likert scales: 1) manual knot and single stitch; 2) permeability of the anastomosis; 3) symmetry of the stitches; 4) Anastomosis leakage; and 5) total time of the anastomosis. DISCUSSION: Recognizing the advantages of experimental training, a reproducible, standardized, and low cost experimental biological model is proposed. CONCLUSIONS: The development of experimental biological models, allows the general surgeon the acquisition of surgical skills and abilities, improving performance during a surgical procedure and reducing risks.

A Novel Application of Non-Destructive Readout Technology to Localisation Microscopy.

The fitting precision in localisation microscopy is highly dependent on the signal to noise ratio. To increase the quality of the image it is therefore important to increase the signal to noise ratio of the measurements. We present an imaging system for localisation microscopy based on non-destructive readout camera technology that can increase the signal to noise ratio of localisation based microscopy. This approach allows for much higher frame rates through subsampling a traditional camera frame. By matching the effective exposure to both the start time and duration of a single molecule we diminish the effects of read noise and temporal noise. We demonstrate the application of this novel method to localisation microscopy and show both an increase in the attainable signal to noise ratio of data collection and an increase in the number of detected events.

Detecting Genetic Mosaicism in Cultures of Human Pluripotent Stem Cells.

Genetic changes in human pluripotent stem cells (hPSCs) gained during culture can confound experimental results and potentially jeopardize the outcome of clinical therapies. Particularly common changes in hPSCs are trisomies of chromosomes 1, 12, 17, and 20. Thus, hPSCs should be regularly screened for such aberrations. Although a number of methods are used to assess hPSC genotypes, there has been no systematic evaluation of the sensitivity of the commonly used techniques in detecting low-level mosaicism in hPSC cultures. We have performed mixing experiments to mimic the naturally occurring mosaicism and have assessed the sensitivity of chromosome banding, qPCR, fluorescence in situ hybridization, and digital droplet PCR in detecting variants. Our analysis highlights the limits of mosaicism detection by the commonly employed methods, a pivotal requirement for interpreting the genetic status of hPSCs and for setting standards for safe applications of hPSCs in regenerative medicine.

Intraspecific variation in essential oil composition of the medicinal plant Lippia integrifolia (Verbenaceae). Evidence for five chemotypes.

The aerial parts of Lippia integrifolia (incayuyo) are widely used in northwestern and central Argentina for their medicinal and aromatic properties. The essential oil composition of thirty-one wild populations of L. integrifolia covering most of its natural range was analyzed by GC and GC-MS. A total of one hundred and fifty two terpenoids were identified in the essential oils. Sesquiterpenoids were the dominant components in all but one of the collections analyzed, the only exception being a sample collected in San Juan province where monoterpenoids amounted to 51%. Five clearly defined chemotypes were observed. One possessed an exquisite and delicate sweet aroma with trans-davanone as dominant component (usually above 80%). Another with an exotic floral odour was rich in oxygenated sesquiterpenoids based on the rare lippifoliane and africanane skeletons. The trans-davanone chemotype is the first report of an essential oil containing that sesquiterpene ketone as the main constituent. The absolute configuration of trans-davanone from L. integrifolia was established as 6S, 7S, 10S, the enantiomer of trans-davanone from 'davana oil' (Artemisia pallens). Wild plants belonging to trans-davanone and lippifolienone chemotypes were propagated and cultivated in the same parcel of land in Santa Maria, Catamarca. The essential oil compositions of the cultivated plants were essentially identical to the original plants in the wild, indicating that the essential oil composition is largely under genetic control. Specimens collected near the Bolivian border that initially were identified as L. boliviana Rusby yielded an essential oil practically identical to the trans-davanone chemotype of L. integrifolia supporting the recent view that L. integrifolia (Gris.) Hieron. and L. boliviana Rusby are synonymous.

Inferring the time-invariant topology of a nonlinear sparse gene regulatory network using fully Bayesian spline autoregression.

We propose a semiparametric Bayesian model, based on penalized splines, for the recovery of the time-invariant topology of a causal interaction network from longitudinal data. Our motivation is inference of gene regulatory networks from low-resolution microarray time series, where existence of nonlinear interactions is well known. Parenthood relations are mapped by augmenting the model with kinship indicators and providing these with either an overall or gene-wise hierarchical structure. Appropriate specification of the prior is crucial to control the flexibility of the splines, especially under circumstances of scarce data; thus, we provide an informative, proper prior. Substantive improvement in network inference over a linear model is demonstrated using synthetic data drawn from ordinary differential equation models and gene expression from an experimental data set of the Arabidopsis thaliana circadian rhythm.