Formal Meta-Analysis of Hypoxic Gene Expression Profiles Reveals a Universal Gene Signature.

Integrating transcriptional profiles results in identifying gene expression signatures that are more robust than those obtained for individual datasets. However, a direct comparison of datasets derived from heterogeneous experimental conditions is problematic, hence their integration requires applying of specific meta-analysis techniques. The transcriptional response to hypoxia has been the focus of intense research due to its central role in tissue homeostasis and prevalent diseases. Accordingly, many studies have determined the gene expression profile of hypoxic cells. Yet, despite this wealth of information, little effort has been made to integrate these datasets to produce a robust hypoxic signature. We applied a formal meta-analysis procedure to datasets comprising 430 RNA-seq samples from 43 individual studies including 34 different cell types, to derive a pooled estimate of the effect of hypoxia on gene expression in human cell lines grown ingin vitro. This approach revealed that a large proportion of the transcriptome is significantly regulated by hypoxia (8556 out of 20,888 genes identified across studies). However, only a small fraction of the differentially expressed genes (1265 genes, 15%) show an effect size that, according to comparisons to gene pathways known to be regulated by hypoxia, is likely to be biologically relevant. By focusing on genes ubiquitously expressed, we identified a signature of 291 genes robustly and consistently regulated by hypoxia. Overall, we have developed a robust gene signature that characterizes the transcriptomic response of human cell lines exposed to hypoxia in vitro by applying a formal meta-analysis to gene expression profiles.

Hypoxia classifier for transcriptome datasets.

Molecular gene signatures are useful tools to characterize the physiological state of cell populations, but most have developed under a narrow range of conditions and cell types and are often restricted to a set of gene identities. Focusing on the transcriptional response to hypoxia, we aimed to generate widely applicable classifiers sourced from the results of a meta-analysis of 69 differential expression datasets which included 425 individual RNA-seq experiments from 33 different human cell types exposed to different degrees of hypoxia (0.1-5%[Formula: see text]) for 2-48 h. The resulting decision trees include both gene identities and quantitative boundaries, allowing for easy classification of individual samples without control or normoxic reference. Each tree is composed of 3-5 genes mostly drawn from a small set of just 8 genes (EGLN1, MIR210HG, NDRG1, ANKRD37, TCAF2, PFKFB3, BHLHE40, and MAFF). In spite of their simplicity, these classifiers achieve over 95% accuracy in cross validation and over 80% accuracy when applied to additional challenging datasets. Our results indicate that the classifiers are able to identify hypoxic tumor samples from bulk RNAseq and hypoxic regions within tumor from spatially resolved transcriptomics datasets. Moreover, application of the classifiers to histological sections from normal tissues suggest the presence of a hypoxic gene expression pattern in the kidney cortex not observed in other normoxic organs. Finally, tree classifiers described herein outperform traditional hypoxic gene signatures when compared against a wide range of datasets. This work describes a set of hypoxic gene signatures, structured as simple decision tress, that identify hypoxic samples and regions with high accuracy and can be applied to a broad variety of gene expression datasets and formats.

Presión arterial por blanqueamiento. Medición en lactantes por personal de enfermería / Blood pressure measurement by the flush method for the nursing staff of some pediatric hospitals

Objetivo: determinar el conocimiento y aplicación por enfermeras que atienden lactantes, de la técnica de blanqueamiento para medir la presión arterial.Diseño: se realizó un estudio prospectivo observacional en dos fases: la primera, encuesta sobre las prácticas para medir presión arterial sistémica en lactantes, con énfasis en el método de blanqueamiento; la segunda, estudio de sombra para evaluar la realización de la técnica. Se aplicó el cuestionario en cinco centros hospitalarios con diferente nivel de atención, ubicados en distintos lugares del país. Se interrogó a enfermeras de base que atendían salas de recién nacidos o lactantes y que aceptaron participar en el estudio. Para la fase 2 se observó la aplicación de la técnica sólo en las enfermeras que admitieron conocerla. Resultados: se entrevistó a 210 enfermeras. Sólo en uno de los hospitales visitados se medía la presión arterial por blanqueamiento; más aún, menos de 20 por ciento de las enfermeras realizaba el procedimiento de forma rutinaria. En dos centros hubo personal que conocía la técnica por referencia o lectura, pero no la aplicaba. Del total, 24.2 por ciento (51/210) refirió conocer la técnica, pero sólo 12.9 por ciento (27/210) la describió; de éste, 96.3 por ciento (26/27) cometió errores por omisión o alteración. La evaluación de la técnica se realizó en 19 enfermeras. Sólo una la realizó correctamente, el resto tuvo deficiencias técnicas en el blanqueamiento (84 por ciento), posición (68 por ciento), retiro y apertura de válvula (68 por ciento), lectura (47 por ciento), insuflación (31 por ciento) y sitio de la toma (26 por ciento). Conclusiones: la medición de la presión arterial es un procedimiento que no se realiza en forma habitual en los lactantes, y todavía más infrecuente es utilizar la técnica de blanqueamiento; consecuentemente se identificó la necesidad de mayor adiestramiento téorico y práctico al respecto.