Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Aspectos importantes de prevención del personal sanitario en los hospitales durante la epidemia del nuevo Coronavirus 2019

Today, the novel coronavirus has spread widely throughout the world and poses new challenges to ensure the health and safety of health personnel. Because health personnel are at the frontlines in the fight against the novel coronavirus, which is one of the groups most affected and vulnerable during the pandemic, it is necessary to remind that the preventive measures adopted by health personnel are essential. Especially in emergency situations, essential measures must be taken to prevent occupational exposure during the novel coronavirus pandemic. Health professionals are working with great intensity and enormous social responsibility. In addition to the applause, they deserve more attention.Al día de hoy, el nuevo coronavirus SARSCoV- 2 se ha extendido ampliamente por el mundo y plantea nuevos desafíos para garantizar la salud y seguridad del personal sanitario. Debido a que dicho personal está en primera línea de la lucha contra el nuevo coronavirus, siendo uno de los grupos más afectados y vulnerables durante la pandemia, es necesario tener en cuenta que las medidas preventivas adoptadas por ellos son fundamentales. Especialmente en situaciones de emergencia, hay que tomar las medidas imprescindibles para la prevención de la exposición ocupacional durante esta nueva pandemia. Los profesionales sanitarios están trabajando con una gran intensidad y una enorme responsabilidad social pero, además de los aplausos, merecen más atención

Islet ChREBP-β is increased in diabetes and controls ChREBP-α and glucose-induced gene expression via a negative feedback loop

Objective: Carbohydrate-response element-binding protein (ChREBP) is the major transcription factor conferring glucose-induced gene expression in pancreatic islets, liver and adipose tissue. Recently, a novel ChREBP isoform, ChREBP-β, was identified in adipose tissue and found to be also expressed in islets and involved in glucose-induced beta cell proliferation. However, the physiological function of this less abundant β-isoform in the islet, and in diabetes, is largely unknown. The aims of the present study, therefore, were to determine how diabetes affects ChREBP-β and elucidate its physiological role in pancreatic beta cells. Methods: Non-obese diabetic and obese, diabetic ob/ob mice were used as models of T1D and T2D and human islets and the rat INS-1 beta cell line were exposed to low/high glucose and used for ChREBP isoform-specific gain-and-loss-of-function experiments. Changes in ChREBP-β and ChREBP-α were assessed by qRT-PCR, immunoblotting, promoter luciferase, and chromatin immunoprecipitation studies. Results: Expression of the ChREBP-β isoform was highly induced in diabetes and by glucose, whereas ChREBP-α was downregulated. Interestingly, ChREBP-β gain-of-function experiments further revealed that it was ChREBP-β that downregulated ChREBP-α through a negative feedback loop. On the other hand, ChREBP-β knockdown led to unabated ChREBP-α activity and glucose-induced expression of target genes, suggesting that one of the physiological roles of this novel β-isoform is to help keep glucose-induced and ChREBP-α-mediated gene expression under control. Conclusions: We have identified a previously unappreciated negative feedback loop by which glucose-induced ChREBP-β downregulates ChREBP-α-signaling providing new insight into the physiological role of islet ChREBP-β and into the regulation of glucose-induced gene expression. Keywords: Carbohydrate response element binding protein, Pancreatic islet, Glucose-induced gene expression, Transcription, Diabete

Deletion of Gdf15 Reduces ER Stress-induced Beta-cell Apoptosis and Diabetes.

Endoplasmic reticulum (ER) stress contributes to pancreatic beta-cell apoptosis in diabetes, but the factors involved are still not fully elucidated. Growth differentiation factor 15 (GDF15) is a stress response gene and has been reported to be increased and play an important role in various diseases. However, the role of GDF15 in beta cells in the context of ER stress and diabetes is still unclear. In this study, we have discovered that GDF15 promotes ER stress-induced beta-cell apoptosis and that downregulation of GDF15 has beneficial effects on beta-cell survival in diabetes. Specifically, we found that GDF15 is induced by ER stress in beta cells and human islets, and that the transcription factor C/EBPβ is involved in this process. Interestingly, ER stress-induced apoptosis was significantly reduced in INS-1 cells with Gdf15 knockdown and in isolated Gdf15 knockout mouse islets. In vivo, we found that Gdf15 deletion attenuates streptozotocin-induced diabetes by preserving beta cells and insulin levels. Moreover, deletion of Gdf15 significantly delayed diabetes development in spontaneous ER stress-prone Akita mice. Thus, our findings suggest that GDF15 contributes to ER stress-induced beta-cell apoptosis and that inhibition of GDF15 may represent a novel strategy to promote beta-cell survival and treat diabetes

Supplemental Material - Characteristics of parent-child separation related to bullying involvement among left-behind children in China

Supplemental Material for Characteristics of parent-child separation related to bullying involvement among left-behind children in China by Jiayao Xu, Shi Guo, Jingjing Lu, Guanlan Zhao, Hailati Akezhuoli, Menmen Wang, Feng Wang and Xudong Zhou in Journal of Social and Personal Relationships.</p

Serum miR-204 is an early biomarker of type 1 diabetes-associated pancreatic beta-cell loss

Pancreatic beta-cell death is a major factor in the pathogenesis of type 1 diabetes (T1D), but straightforward methods to measure beta-cell loss in humans are lacking, underlining the need for novel biomarkers. Using studies in INS-1 cells, human islets, diabetic mice, and serum samples of subjects with T1D at different stages, we have identified serum miR-204 as an early biomarker of T1D-associated beta-cell loss in humans. MiR-204 is a highly enriched microRNA in human beta-cells, and we found that it is released from dying beta-cells and detectable in human serum. We further discovered that serum miR-204 was elevated in children and adults with T1D and in autoantibody-positive at-risk subjects but not in type 2 diabetes or other autoimmune diseases and was inversely correlated with remaining beta-cell function in recent-onset T1D. Thus, serum miR-204 may provide a much needed novel approach to assess early T1D-associated human beta-cell loss even before onset of overt disease