A Pathogenic Mosaic TP53 Mutation in Two Germ Layers Detected by Next Generation Sequencing

Background

Li-Fraumeni syndrome is caused by germline TP53 mutations and is clinically characterized by a predisposition to a range of cancers, most commonly sarcoma, brain tumours and leukemia. Pathogenic mosaic TP53 mutations have only rarely been described.

Methods and Findings

We describe a 2 years old child presenting with three separate cancers over a 6 month period; two soft tissue mesenchymal tumors and an aggressive metastatic neuroblastoma. As conventional testing of blood DNA by Sanger sequencing for mutations in TP53, ALK, and SDH was negative, whole exome sequencing of the blood DNA of the patient and both parents was performed to screen more widely for cancer predisposing mutations. In the patient''s but not the parents'' DNA we found a c.743 G>A, p.Arg248Gln (CCDS11118.1) TP53 mutation in 3–20% of sequencing reads, a level that would not generally be detectable by Sanger sequencing. Homozygosity for this mutation was detected in all tumor samples analyzed, and germline mosaicism was demonstrated by analysis of the child''s newborn blood spot DNA. The occurrence of separate tumors derived from different germ layers suggests that this de novo mutation occurred early in embryogenesis, prior to gastrulation.

Conclusion

The case demonstrates pathogenic mosaicim, detected by next generation deep sequencing, that arose in the early stages of embryogenesis.     

FEV1 Is a Better Predictor of Mortality than FVC: The PLATINO Cohort Study

Objective

To determine whether the presence of chronic obstructive lung disease (COPD) and reduction of lung function parameters were predictors of mortality in a cohort.

Materials/Patients and Methods

Population based cohorts were followed in Montevideo, Santiago and Sao Paulo during 5, 6 and 9 years, respectively. Outcomes included all-cause, cardiovascular, respiratory and cancer mortality; exposures were COPD, forced expiratory volume in one second (FEV₁) and forced vital capacity (FVC). Cox regression was used for analyses. Sensitivity, specificity, positive and negative predictive values, receiver operator characteristics curves and Youden''s index were calculated.

Results

Main causes of death were cardiovascular, respiratory and cancer. Baseline COPD was associated with overall mortality (HR = 1.43 for FEV₁/FVC<LLN; 2.01 for GOLD 2-4; 1.46 for GOLD 1-4; 1.50 for FEV₁/FEV₆ <LLN). For cardiovascular mortality, significant associations were found with GOLD 2-4 (HR = 2.68) and with GOLD 1-4 (HR = 1.78) for both genders together (not among women). Low FEV₁ was risk for overall and respiratory mortality (both genders combined). FVC was not associated with overall mortality. For most COPD criteria sensitivity was low and specificity high. The area under the curve for FEV₁ was greater than for FVC for overall and cardiovascular mortality.

Answer to the Question

COPD and low FEV₁ are important predictors for overall and cardiovascular mortality in Latin America.     

New insights into the functional roles of reactive oxygen species during embryo sac development and fertilization in Arabidopsis thaliana

Previously considered as toxic by-products of aerobic metabolism, reactive oxygen species (ROS) are emerging as essential signaling molecules in eukaryotes. Recent evidence showed that maintenance of ROS homeostasis during female gametophyte development is crucial for embryo sac patterning and fertilization. Although ROS are exclusively detected in the central cell of mature embryo sacs, the study of mutants deficient in ROS homeostasis suggests that controlled oxidative bursts might take place earlier during gametophyte development. Also, a ROS burst that depends on pollination takes place inside the embryo sac. This oxidative response might be required for pollen tube growth arrest and for sperm cell release. In this mini-review, we will focus on new insights into the role of ROS during female gametophyte development and fertilization. Special focus will be made on the mitochondrial Mn-Superoxide dismutase (MSD1), which has been recently reported to be essential for maintaining ROS homeostasis during embryo sac formation.     

All together now

Maintenance of genomic stability during eukaryotic cell division relies on the Spindle Assembly Checkpoint (SAC), which has evolved as a surveillance mechanism that monitors kinetochore-microtubule attachment and prevents APC/C-mediated mitotic exit until all chromosomes are properly attached to the mitotic spindle. Reversible protein phosphorylation has long been accredited as a regulatory mechanism of the SAC. Nevertheless, knowledge of how several mitotic kinases act in concert within the signaling pathway to orchestrate SAC function is still emerging. In a recent study, we undertook a comprehensive dissection of the hierarchical framework controlling SAC function in Drosophila cells. We found that Polo lies at the top of the SAC pathway promoting the efficient recruitment of Mps1 to unattached kinetochores. This renders Mps1 fully active to control BubR1 phosphorylation that generates the 3F3/2 phosphoepitope at tensionless kinetochores. We have proposed that Polo is required for SAC function and that the molecular outcome of Mps1-dependent 3F3/2 formation is to promote the association of Cdc20 with BubR1 allowing proper kinetochore recruitment of Cdc20 and efficient assembly of the Mitotic Checkpoint Complex (MCC) required for a sustained SAC response.     

Development of a primary microglia screening assay and its use to characterize inhibition of system xc- by erastin and its analogs

The inflammatory response in the central nervous system involves activated microglia. Under normal conditions they remove damaged neurons by phagocytosis. On the other hand, neurodegenerative diseases are thought to involve chronic microglia activation resulting in release of excess glutamate, proinflammatory cytokines and reactive oxygen species, leading to neuronal death. System x_C^- cystine/glutamate antiporter (SXC), a sodium independent heterodimeric transporter found in microglia and astrocytes in the CNS, imports cystine into the cell and exports glutamate. SXC has been shown to be upregulated in neurodegenerative diseases including multiple sclerosis, ALS, neuroAIDS Parkinson's disease and Alzheimer's disease. Consequently, SXC inhibitors could be of use in the treatment of diseases characterized by neuroinflammation and glutamate excitotoxicity. We report on the optimization of a primary microglia-based assay to screen for SXC inhibitors. Rat primary microglia were activated using lipopolysaccharides (LPS) and glutamate release and cystine uptake were monitored by fluorescence and radioactivity respectively. LPS-induced glutamate release increased with increasing cell density, time of incubation and LPS concentration. Conditions to screen for SXC inhibitors were optimized in 96-well format and subsequently used to evaluate SXC inhibitors. Known SXC inhibitors sulfasalazine, S-4CPG and erastin blocked glutamate release and cystine uptake while R-4CPG, the inactive enantiomer of S-4CPG, failed to inhibit glutamate release or cystine transport. In addition, several erastin analogs were evaluated using primary microglia and found to have EC₅₀ values in agreement with previous studies using established cell lines.     

Evolved distal tail carbohydrate binding modules of Lactobacillus phage J‐1: a novel type of anti‐receptor widespread among lactic acid bacteria phages

Bacteriophage replication requires specific host‐recognition. Some siphophages harbour a large complex, the baseplate, at the tip of their non‐contractile tail. This baseplate holds receptor binding proteins (RBPs) that can recognize the host cell‐wall polysaccharide (CWPS) and specifically attach the phage to its host. While most phages possess a dedicated RBP, the phage J‐1 that infects Lactobacillus casei seemed to lack one. It has been shown that the phage J‐1 distal tail protein (Dit) plays a role in host recognition and that its sequence comprises two inserted modules compared with ‘classical’ Dits. The first insertion is similar to carbohydrate‐binding modules (CBMs), whereas the second insertion remains undocumented. Here, we determined the structure of the second insertion and found it also similar to several CBMs. Expressed insertion CBM2, but not CBM1, binds to L. casei cells and neutralize phage attachment to the bacterial cell wall and the isolated and purified CWPS of L. casei BL23 prevents CBM2 attachment to the host. Electron microscopy single particle reconstruction of the J‐1 virion baseplate revealed that CBM2 is projected at the periphery of Dit to optimally bind the CWPS receptor. Taken together, these results identify J‐1 evolved Dit as the phage RBP.     

Endogamy costs and reproductive biology of <Emphasis Type="Italic">Laelia autumnalis</Emphasis>, an endemic orchid of Mexico

It has been hypothesized that the fitness of selfed progeny must be lowered by inbreeding depression. Most research into the breeding systems of orchids shows a similar fruit set from outcrossing and self-pollination, but few studies have measured seed production and viability. In five populations of Laelia autumnalis, in central México, we studied the species reproductive system and the early costs of endogamy. We performed spontaneous self-pollination, apomixis, assisted self-pollination, cross-pollination, and exogamous pollination (using pollen from a different population) treatments of bagged flowers and measured fruit set, seed production, and germination. No fruits were produced in the apomixis and spontaneous self-pollination treatments. Reproductive success from self-pollination was lower than that from cross- and exogamous pollination and no difference was found between the latter two treatments. The ratio between self-pollination and cross-pollination success in different traits ranged from 0.80?±?0.18 (fruit set) to 0.22?±?0.13 (seeds with embryo). The latter value suggests a high endogamy costs in the production of viable seeds. The concatenated success of the different traits studied showed that the relative fitness of self-pollination was 63% lower than with cross-pollination. Laelia autumnalis is a self-compatible non-autogamous species in which the cost of endogamy occurs at seed production and cannot be compensated for at other early stages. This also occurs in other orchid species and is likely to be a general pattern.     

Spatial and temporal variation in breeding parameters of two south-temperate populations of House Wrens

Studies of variation in breeding parameters are often based on temporal analyses of a single population. However, to differentiate between the effects of regional and local factors, neighboring populations with limited interpopulational dispersal need to be compared. We studied two nearby (< 5 km apart) populations of House Wrens (Troglodytes aedon bonariae) at two ranches (Los Zorzales, 10 years; La Esperanza, 13 years) in south-temperate Argentina to assess the possible effects of regional and local factors on breeding phenology. For each breeding season, we recorded laying dates, clutch sizes, and length of the breeding season, and estimated the reproductive synchrony of first and second breeding attempts. We examined how these breeding parameters were affected by weather, population density, and rates of nest failure. With favorable temperatures during the pre-reproductive period (September–October), wrens in both populations initiated first breeding attempts earlier. However, ordinal laying dates were also affected by local factors, with wrens at Los Zorzales initiating breeding attempts earlier than those at La Esperanza. We found a spatial correlation in clutch sizes between populations for the 2007–2012 breeding seasons, but clutch sizes of first and second nesting attempts showed low variability. Reproductive synchrony of first nesting attempts varied among years, suggesting an effect of regional factors. However, we detected no synchronization between populations and were unable to identify environmental variables that explained the temporal variation. Ordinal laying dates of second clutches were strongly correlated with the ordinal laying dates of first clutches. We also found that the length of breeding seasons was longer when daily nest mortality rates were lower. Although environmental factors seemed to affect the decision of when to start breeding, pairs with successful first nesting attempts were more likely to initiate second nests, thus affecting the length of the breeding season. The spatial variation and temporal variation of the breeding parameters of House Wrens in our study provide evidence of marked plasticity in their breeding decisions and allowed us to identify local and regional environmental factors related to this variation.