Machine learning combining multi-omics data and network algorithms identifies adrenocortical carcinoma prognostic biomarkers.

Background: Rare endocrine cancers such as Adrenocortical Carcinoma (ACC) present a serious diagnostic and prognostication challenge. The knowledge about ACC pathogenesis is incomplete, and patients have limited therapeutic options. Identification of molecular drivers and effective biomarkers is required for timely diagnosis of the disease and stratify patients to offer the most beneficial treatments. In this study we demonstrate how machine learning methods integrating multi-omics data, in combination with system biology tools, can contribute to the identification of new prognostic biomarkers for ACC. Methods: ACC gene expression and DNA methylation datasets were downloaded from the Xena Browser (GDC TCGA Adrenocortical Carcinoma cohort). A highly correlated multi-omics signature discriminating groups of samples was identified with the data integration analysis for biomarker discovery using latent components (DIABLO) method. Additional regulators of the identified signature were discovered using Clarivate CBDD (Computational Biology for Drug Discovery) network propagation and hidden nodes algorithms on a curated network of molecular interactions (MetaBase™). The discriminative power of the multi-omics signature and their regulators was delineated by training a random forest classifier using 55 samples, by employing a 10-fold cross validation with five iterations. The prognostic value of the identified biomarkers was further assessed on an external ACC dataset obtained from GEO (GSE49280) using the Kaplan-Meier estimator method. An optimal prognostic signature was finally derived using the stepwise Akaike Information Criterion (AIC) that allowed categorization of samples into high and low-risk groups. Results: A multi-omics signature including genes, micro RNA's and methylation sites was generated. Systems biology tools identified additional genes regulating the features included in the multi-omics signature. RNA-seq, miRNA-seq and DNA methylation sets of features revealed a high power to classify patients from stages I-II and stages III-IV, outperforming previously identified prognostic biomarkers. Using an independent dataset, associations of the genes included in the signature with Overall Survival (OS) data demonstrated that patients with differential expression levels of 8 genes and 4 micro RNA's showed a statistically significant decrease in OS. We also found an independent prognostic signature for ACC with potential use in clinical practice, combining 9-gene/micro RNA features, that successfully predicted high-risk ACC cancer patients. Conclusion: Machine learning and integrative analysis of multi-omics data, in combination with Clarivate CBDD systems biology tools, identified a set of biomarkers with high prognostic value for ACC disease. Multi-omics data is a promising resource for the identification of drivers and new prognostic biomarkers in rare diseases that could be used in clinical practice.

Systematic Characterization of Electronic Metal-Support Interactions in Ceria-Supported Pt Particles.

Electronic metal-support interactions affect the chemical and catalytic properties of metal particles supported on reducible metal oxides, but their characterization is challenging due to the complexity of the electronic structure of these systems. These interactions often involve different states with varying numbers and positions of strongly correlated d or f electrons and the corresponding polarons. In this work, we present an approach to characterize electronic metal-support interactions by means of computationally efficient density functional calculations within the projector augmented wave method. We describe Ce3+ cations with potentials that include a Ce4f electron in the frozen core, overcoming prevalent convergence and 4f electron localization issues. We systematically explore the stability and chemical properties of different electronic states for a Pt8/CeO2(111) model system, revealing the predominant effect of electronic metal-support interactions on Pt atoms located directly at the metal-oxide interface. Adsorption energies and the reactivity of these interface Pt atoms vary significantly upon donation of electrons to the oxide support, pointing to a strategy to selectively activate interfacial sites of metal particles supported on reducible metal oxides.

Structural disruption of BAF chromatin remodeller impairs neuroblastoma metastasis by reverting an invasiveness epigenomic program.

BACKGROUND: Epigenetic programming during development is essential for determining cell lineages, and alterations in this programming contribute to the initiation of embryonal tumour development. In neuroblastoma, neural crest progenitors block their course of natural differentiation into sympathoadrenergic cells, leading to the development of aggressive and metastatic paediatric cancer. Research of the epigenetic regulators responsible for oncogenic epigenomic networks is crucial for developing new epigenetic-based therapies against these tumours. Mammalian switch/sucrose non-fermenting (mSWI/SNF) ATP-dependent chromatin remodelling complexes act genome-wide translating epigenetic signals into open chromatin states. The present study aimed to understand the contribution of mSWI/SNF to the oncogenic epigenomes of neuroblastoma and its potential as a therapeutic target. METHODS: Functional characterisation of the mSWI/SNF complexes was performed in neuroblastoma cells using proteomic approaches, loss-of-function experiments, transcriptome and chromatin accessibility analyses, and in vitro and in vivo assays. RESULTS: Neuroblastoma cells contain three main mSWI/SNF subtypes, but only BRG1-associated factor (BAF) complex disruption through silencing of its key structural subunits, ARID1A and ARID1B, impairs cell proliferation by promoting cell cycle blockade. Genome-wide chromatin remodelling and transcriptomic analyses revealed that BAF disruption results in the epigenetic repression of an extensive invasiveness-related expression program involving integrins, cadherins, and key mesenchymal regulators, thereby reducing adhesion to the extracellular matrix and the subsequent invasion in vitro and drastically inhibiting the initiation and growth of neuroblastoma metastasis in vivo. CONCLUSIONS: We report a novel ATPase-independent role for the BAF complex in maintaining an epigenomic program that allows neuroblastoma invasiveness and metastasis, urging for the development of new BAF pharmacological structural disruptors for therapeutic exploitation in metastatic neuroblastoma.

Data-driven identification of inherent features of eukaryotic stress-responsive genes.

Living organisms are continuously challenged by changes in their environment that can propagate to stresses at the cellular level, such as rapid changes in osmolarity or oxygen tension. To survive these sudden changes, cells have developed stress-responsive mechanisms that tune cellular processes. The response of Saccharomyces cerevisiae to osmostress includes a massive reprogramming of gene expression. Identifying the inherent features of stress-responsive genes is of significant interest for understanding the basic principles underlying the rewiring of gene expression upon stress. Here, we generated a comprehensive catalog of osmostress-responsive genes from 5 independent RNA-seq experiments. We explored 30 features of yeast genes and found that 25 (83%) were distinct in osmostress-responsive genes. We then identified 13 non-redundant minimal osmostress gene traits and used statistical modeling to rank the most stress-predictive features. Intriguingly, the most relevant features of osmostress-responsive genes are the number of transcription factors targeting them and gene conservation. Using data on HeLa samples, we showed that the same features that define yeast osmostress-responsive genes can predict osmostress-responsive genes in humans, but with changes in the rank-ordering of feature-importance. Our study provides a holistic understanding of the basic principles of the regulation of stress-responsive gene expression across eukaryotes.

LRRC8A-containing chloride channel is crucial for cell volume recovery and survival under hypertonic conditions.

Regulation of cell volume is essential for tissue homeostasis and cell viability. In response to hypertonic stress, cells need rapid electrolyte influx to compensate water loss and to prevent cell death in a process known as regulatory volume increase (RVI). However, the molecular component able to trigger such a process was unknown to date. Using a genome-wide CRISPR/Cas9 screen, we identified LRRC8A, which encodes a chloride channel subunit, as the gene most associated with cell survival under hypertonic conditions. Hypertonicity activates the p38 stress-activated protein kinase pathway and its downstream MSK1 kinase, which phosphorylates and activates LRRC8A. LRRC8A-mediated Cl- efflux facilitates activation of the with-no-lysine (WNK) kinase pathway, which in turn, promotes electrolyte influx via Na+/K+/2Cl- cotransporter (NKCC) and RVI under hypertonic stress. LRRC8A-S217A mutation impairs channel activation by MSK1, resulting in reduced RVI and cell survival. In summary, LRRC8A is key to bidirectional osmotic stress responses and cell survival under hypertonic conditions.

Differences between young and older adults in physiological and subjective responses to emotion induction using films.

Emotional response in aging is typically studied using the dimensional or the discrete models of emotion. Moreover, it is typically studied using subjective or physiological variables but not using both perspectives simultaneously. Additionally, tenderness is neglected in emotion induction procedures with older adults, with the present work being the first to include the study of physiological tenderness using film clips. This study integrated two separate approaches to emotion research, comparing 68 younger and 39 older adults and using a popular set of film clips to induce tenderness, amusement, anger, fear, sadness and disgust emotions. The direction of subjective emotional patterns was evaluated with self-reports and that of physiological emotional patterns was evaluated with a wearable emotion detection system. The findings suggest a dual-process framework between subjective and physiological responses, manifested differently in young and older adults. In terms of arousal, the older adults exhibited higher levels of subjective arousal in negative emotions and tenderness while young adults showed higher levels of physiological arousal in these emotions. These findings yield information on the multidirectionality of positive and negative emotions, corroborating that emotional changes in the adult lifespan appear to be subject to the relevance of the emotion elicitor to each age group.

Theoretical exploration of the forces governing the interaction between gold-phthalocyanine and gold surface clusters.

Here we aim to explore the nature of the forces governing the adsorption of gold-phthalocyanine on gold substrates. For this, we designed computational models of metal-free phthalocyanine and gold-phthalocyanine deposited over a gold metallic surface represented by cluster models of different sizes and geometries. Thereby, we were able to determine the role of the metal center and of the size of the substrate in the interaction process. For this purpose, we worked within the framework provided by density functional theory, were the inclusion of the semi-empirical correction of the dispersion forces of Grimme's group was indispensable. It has been shown that the interaction between molecules and surfaces is ruled by van der Waals attractive forces, which determine the stabilization of the studied systems and their geometric properties. Their contribution was characterized by energy decomposition analysis and through the visualization of the dispersion interactions by means of the NCI methodology. Moreover, calculations of Density of States (DOS) showed that the molecule-surface system displays a metal-organic interface evidenced by changes in their electronic structure, in agreement with a charge transfer process found to take place between the interacting parts.

Sensitive high-throughput single-cell RNA-seq reveals within-clonal transcript correlations in yeast populations.

Single-cell RNA sequencing has revealed extensive cellular heterogeneity within many organisms, but few methods have been developed for microbial clonal populations. The yeast genome displays unusually dense transcript spacing, with interleaved and overlapping transcription from both strands, resulting in a minuscule but complex pool of RNA that is protected by a resilient cell wall. Here, we have developed a sensitive, scalable and inexpensive yeast single-cell RNA-seq (yscRNA-seq) method that digitally counts transcript start sites in a strand- and isoform-specific manner. YscRNA-seq detects the expression of low-abundance, noncoding RNAs and at least half of the protein-coding genome in each cell. In clonal cells, we observed a negative correlation for the expression of sense-antisense pairs, whereas paralogs and divergent transcripts co-expressed. By combining yscRNA-seq with index sorting, we uncovered a linear relationship between cell size and RNA content. Although we detected an average of ~3.5 molecules per gene, the number of expressed isoforms is restricted at the single-cell level. Remarkably, the expression of metabolic genes is highly variable, whereas their stochastic expression primes cells for increased fitness towards the corresponding environmental challenge. These findings suggest that functional transcript diversity acts as a mechanism that provides a selective advantage to individual cells within otherwise transcriptionally heterogeneous populations.

Yeast Single-cell RNA-seq, Cell by Cell and Step by Step.

Single-cell RNA-seq (scRNA-seq) has become an established method for uncovering the intrinsic complexity within populations. Even within seemingly homogenous populations of isogenic yeast cells, there is a high degree of heterogeneity that originates from a compact and pervasively transcribed genome. Research with microorganisms such as yeast represents a major challenge for single-cell transcriptomics, due to their small size, rigid cell wall, and low RNA content per cell. Because of these technical challenges, yeast-specific scRNA-seq methodologies have recently started to appear, each one of them relying on different cell-isolation and library-preparation methods. Consequently, each approach harbors unique strengths and weaknesses that need to be considered. We have recently developed a yeast single-cell RNA-seq protocol (yscRNA-seq), which is inexpensive, high-throughput and easy-to-implement, tailored to the unique needs of yeast. yscRNA-seq provides a unique platform that combines single-cell phenotyping via index sorting with the incorporation of unique molecule identifiers on transcripts that allows to digitally count the number of molecules in a strand- and isoform-specific manner. Here, we provide a detailed, step-by-step description of the experimental and computational steps of yscRNA-seq protocol. This protocol will ease the implementation of yscRNA-seq in other laboratories and provide guidelines for the development of novel technologies.

Dimensión de ecocardiografía modo M bidimensional y Doppler en la enfermedad pulmonar obstructiva crónica

La ecocardiografía de modo M y bidimensional proporciona información anatómica y funcional del corazón derecho. Asociada a Eco-Doppler permite cuantificar de manera muy aproximada la presión del ventriculo derecho, además de informar sobre los intervalos sistólicos. Resultados : Se hizo una investigación descriptiva, observacional, análitica de casos y controles. Se estudiaron 32 casos de nuestro trabajo de EPOC y leña. Dichos pacientes fueron manejados desde el punto de vista clínico, radiológico, electrocardiográfico, espirométrico y ecocardiográfico. El grupo control estuvo constituido, para los intervalos sistólicos, espesor y diámetro de las cavidades normales, por los estudios ecocardiográficos normales, realizados en el Servicio de Ecocardiografía de la Unidad de Cardiología del Hospital San Juan de Dios de Santafé de Bogotá, en número de 51, y para las presiones pulmonares, por los estudios de cateterismo derecho practicados en el Servicio de Hemodinamia de la Unidad de Cardiología, en número de 66, en pacientes con cardiopatías congénitas o adquiridas. En casos de EPOC, los signos electrocardiográficos más frecuentes fueron el crecimiento auricular derecho (64.51 por ciento) y el crecimiento ventricular derecho (58.06 por ciento). Los Rayos X de otra parte mostraron los siguientes signos de hipertensión pulmonar : prominencia del tronco de la arteria pulmonar (78.51 por ciento) crecimiento auricular y ventricular derechos (64.28 por ciento) y aumento de la rama inferior derecha de la arteria pulmonar (60.71 por ciento). En cambio la ecocardiografía muestra aumento del espesor del ventrículo derecho (93.75 por ciento), aumento de su diámetro diastólico final (62.50 por ciento) y valores superiores a 35 mm de Hg de presión del ventrículo derecho en 65.62 por ciento. Son igualmente significativos el tiempo de aceleración del ventrículo derecho que disminuye, el PPE.V.D. que aumenta, y la relación PPE.V.D/TE.V.D aumentado. Conclusión : La ecocardiografía de modo M y bidimensional y la Eco Doppler, proporcionan información valiosa no invasiva, confiable y fácilmente repetible en casos de EPOC.

El fenómeno de refuerzo en un encuesta tuberculínica. Análisis económico

Tratando de determinar la magnitud del fenómeno de refuerzo (booster) en una encuesta tuberculínica en nuevos trabajadores, instauramos un programa usando los dos pasos de la prueba en el Hospital San Juan de Dios de Bogotá. Entre Junio de 1988 y Agosto de 1990, 373 nuevos trabajadores fueron encuestados, 283 (63.9 por ciento) tuvieron una reacción menor de 10 mm de diámetro. Doscientos tres (85.3 por ciento) de ellos recibieron la doble prueba cutánea y solamente siete personas (3,4 por ciento) presentaron el "efecto booster". El promedio de edad fue de 28 años y 93.5 por ciento de toda la muestra estuvo comprendida entre 20 y 39 años de edad. El análisis económico de la segunda prueba indicó que el costo total ($642.098.oo) excedió abrumadoramente la efectividad de detectar 3 por ciento del fenómeno de refuerzo en nuestra población de empleados hospitalarios. Recomendamos que cada institución, dependiendo de su situación particular epidemiológica en tuberculosis, efectue sus estudios antes de decidir que tipo de seguimiento tuberculínico usara en su personal hospitalario.