AI powered quantification of nuclear morphology in cancers enables prediction of genome instability and prognosis.

While alterations in nucleus size, shape, and color are ubiquitous in cancer, comprehensive quantification of nuclear morphology across a whole-slide histologic image remains a challenge. Here, we describe the development of a pan-tissue, deep learning-based digital pathology pipeline for exhaustive nucleus detection, segmentation, and classification and the utility of this pipeline for nuclear morphologic biomarker discovery. Manually-collected nucleus annotations were used to train an object detection and segmentation model for identifying nuclei, which was deployed to segment nuclei in H&E-stained slides from the BRCA, LUAD, and PRAD TCGA cohorts. Interpretable features describing the shape, size, color, and texture of each nucleus were extracted from segmented nuclei and compared to measurements of genomic instability, gene expression, and prognosis. The nuclear segmentation and classification model trained herein performed comparably to previously reported models. Features extracted from the model revealed differences sufficient to distinguish between BRCA, LUAD, and PRAD. Furthermore, cancer cell nuclear area was associated with increased aneuploidy score and homologous recombination deficiency. In BRCA, increased fibroblast nuclear area was indicative of poor progression-free and overall survival and was associated with gene expression signatures related to extracellular matrix remodeling and anti-tumor immunity. Thus, we developed a powerful pan-tissue approach for nucleus segmentation and featurization, enabling the construction of predictive models and the identification of features linking nuclear morphology with clinically-relevant prognostic biomarkers across multiple cancer types.

Long-term exposure of Daphnia magna to polystyrene microplastic (PS-MP) leads to alterations of the proteome, morphology and life-history.

In the past years, the research focus on the effects of MP on aquatic organisms extended from marine systems towards freshwater systems. An important freshwater model organism in the MP field is the cladoceran Daphnia, which plays a central role in lacustrine ecosystems and has been established as a test organism in ecotoxicology. To investigate the effects of MP on Daphnia magna, we performed a chronic exposure experiment with polystyrene MP under strictly standardized conditions. Chronic exposure of D. magna to PS microparticles led to a significant reduction in body length and number of offspring. To shed light on underlying molecular mechanisms induced by microplastic ingestion in D. magna, we assessed the effects of PS-MP at the proteomic level, as proteins, e.g., enzymes, are especially relevant for an organism's physiology. Using a state-of-the-art mass spectrometry based approach, we were able to identify 28,696 different peptides, which could be assigned to 3784 different proteins. Using a customized bioinformatic workflow, we identified 41 proteins significantly altered in abundance (q-value <0.05) in the PS exposed D. magna. Among the proteins increased in the PS treated group were several sulfotransferases, involved in basic biochemical pathways, as well as GABA transaminase catalyzing the degradation of the neurotransmitter GABA. In the abundance decreased group, we found essential proteins such as the DNA-directed RNA polymerase subunit and other proteins connected to biotic and inorganic stress and reproduction. Strikingly, we further identified several digestive enzymes that are significantly downregulated in the PS treated animals, which could have interfered with the affected animal's nutrient supply. This may explain the altered morphological and life history traits of the PS exposed daphnids. Our results indicate that long-term exposure to PS microplastics, which are frequently detected in environmental samples, may affect the fitness of daphnids.

Projected Dose Optimization of Amino- and Hydroxypyrrolidine Purine PI3Kδ Immunomodulators.

The approvals of idelalisib and duvelisib have validated PI3Kδ inhibitors for the treatment for hematological malignancies driven by the PI3K/AKT pathway. Our program led to the identification of structurally distinct heterocycloalkyl purine inhibitors with excellent isoform and kinome selectivity; however, they had high projected human doses. Improved ligand contacts gave potency enhancements, while replacement of metabolic liabilities led to extended half-lives in preclinical species, affording PI3Kδ inhibitors with low once-daily predicted human doses. Treatment of C57BL/6-Foxp3-GDL reporter mice with 30 and 100 mg/kg/day of 3c (MSD-496486311) led to a 70% reduction in Foxp3-expressing regulatory T cells as observed through bioluminescence imaging with luciferin, consistent with the role of PI3K/AKT signaling in Treg cell proliferation. As a model for allergic rhinitis and asthma, treatment of ovalbumin-challenged Brown Norway rats with 0.3 to 30 mg/kg/day of 3c gave a dose-dependent reduction in pulmonary bronchoalveolar lavage inflammation eosinophil cell count.

Microplastics in Freshwater Biota: A Critical Review of Isolation, Characterization, and Assessment Methods.

Freshwater systems provide key pathways for microplastic (MP) pollution, and although existing studies have demonstrated the susceptibility of freshwater biota to ingestion, translocation, and trophic transfer, specific challenges pertaining to methodological standardization remain largely unresolved, particularly with respect to isolating, characterizing, and assessing MPs. Here, a critical review is performed outlining the challenges and limitations currently faced by freshwater MP researchers, which may well apply across the MP research spectrum. Recommendations are provided for methodological standardization, particularly in MP characterization, quality assurance, and quality control (QA/QC) procedures as well as reporting. Considerations for the assessment of MPs in freshwater biota as a means of improving comparisons between studies are discussed. Technological advancements, including the improvement of laboratory infrastructure for identifying MPs within the smaller size range as well as methodological standardization are essential in providing policy makers with tools and measures necessary to determine the distribution of MPs within freshwater ecosystems, while also allowing for comparability and providing compliance for future monitoring requirements.

Effects of microplastic particles and leaching additive on the life history and morphology of Daphnia magna.

Plastic waste is continuously introduced not only into marine, but also freshwater environments, where it fragments into microplastics. Organisms may be affected by the particles themselves due to ingestion and indirectly via incorporated additives such as plasticizers, since these substances have the ability to leach out of the polymer matrix. Although it has been indicated that the likelihood of additives leaching out into the gut lumen of organisms exposed to microplastics is low, studies distinguishing between the effects of the synthetic polymer itself and incorporated additives of the same polymer are scarce. Since this is obligatory for risk assessment, we analyzed the chronic effects of flexible polyvinylchloride (PVC), a widely used polymer, containing the plasticizer diisononylphthalate (DiNP) on morphology and life history of the freshwater crustacean Daphnia magna and compared these effects with the effects of rigid PVC, lacking DiNP, as well as a glass bead control. After up to 31 days of exposure, rigid PVC and glass beads did not affect body length and relative tail spine length of D. magna, whereas flexible PVC led to an increased body length and a reduced number of offspring. None of the treatments increased the mortality significantly. We were able to show that 2.67µg/L DiNP leached out of the flexible PVC into the surrounding medium using GC-MS. Yet, we were not able to measure leachate inside the gut lumen of D. magna. The effects emerged towards the end of the experiment, due to the time dependent process of leaching. Therefore, the results highlight the relevance of long-term chronic exposure experiments, especially as leaching of additives takes time. Further, our study shows the importance to distinguish between microplastics containing leachable additives and the raw polymer in ecotoxicological testing.

Structure Overhaul Affords a Potent Purine PI3Kδ Inhibitor with Improved Tolerability.

PI3Kδ catalytic activity is required for immune cell activation, and has been implicated in inflammatory diseases as well as hematological malignancies in which the AKT pathway is overactive. A purine PI3Kδ inhibitor bearing a benzimidazolone-piperidine motif was found to be poorly tolerated in dog, which was attributed to diffuse vascular injury. Several strategies were implemented to mitigate this finding, including reconstruction of the benzimidazolone-piperidine selectivity motif. Structure-based design led to the identification of O- and N-linked heterocycloalkyls, with pyrrolidines being particularly ligand efficient and kinome selective, and having an improved safety pharmacology profile. A representative was advanced into a dog tolerability study where it was found to be well tolerated, with no histopathological evidence of vascular injury.

Spatial and temporal variation of macro-, meso- and microplastic abundance on a remote coral island of the Maldives, Indian Ocean.

Plastic debris is ubiquitous in the marine environment and the world's shores represent a major sink. However, knowledge about plastic abundance in remote areas is scarce. Therefore, plastic abundance was investigated on a small island of the Maldives. Plastic debris (>1mm) was sampled once in natural long-term accumulation zones at the north shore and at the high tide drift line of the south shore on seven consecutive days to quantify daily plastic accumulation. Reliable identification of plastic debris was ensured by FTIR spectroscopy. Despite the remoteness of the island a considerable amount of plastic debris was present. At both sites a high variability in plastic abundance on a spatial and temporal scale was observed, which may be best explained by environmental factors. In addition, our results show that snapshot sampling may deliver biased results and indicate that future monitoring programs should consider spatial and temporal variation of plastic deposition.

Military blast exposure, ageing and white matter integrity.

Mild traumatic brain injury, or concussion, is associated with a range of neural changes including altered white matter structure. There is emerging evidence that blast exposure-one of the most pervasive causes of casualties in the recent overseas conflicts in Iraq and Afghanistan-is accompanied by a range of neurobiological events that may result in pathological changes to brain structure and function that occur independently of overt concussion symptoms. The potential effects of brain injury due to blast exposure are of great concern as a history of mild traumatic brain injury has been identified as a risk factor for age-associated neurodegenerative disease. The present study used diffusion tensor imaging to investigate whether military-associated blast exposure influences the association between age and white matter tissue structure integrity in a large sample of veterans of the recent conflicts (n = 190 blast-exposed; 59 without exposure) between the ages of 19 and 62 years. Tract-based spatial statistics revealed a significant blast exposure × age interaction on diffusion parameters with blast-exposed individuals exhibiting a more rapid cross-sectional age trajectory towards reduced tissue integrity. Both distinct and overlapping voxel clusters demonstrating the interaction were observed among the examined diffusion contrast measures (e.g. fractional anisotropy and radial diffusivity). The regions showing the effect on fractional anisotropy included voxels both within and beyond the boundaries of the regions exhibiting a significant negative association between fractional anisotropy and age in the entire cohort. The regional effect was sensitive to the degree of blast exposure, suggesting a 'dose-response' relationship between the number of blast exposures and white matter integrity. Additionally, there was an age-independent negative association between fractional anisotropy and years since most severe blast exposure in a subset of the blast-exposed group, suggesting a specific influence of time since exposure on tissue structure, and this effect was also independent of post-traumatic stress symptoms. Overall, these data suggest that blast exposure may negatively affect brain-ageing trajectories at the microstructural tissue level. Additional work examining longitudinal changes in brain tissue integrity in individuals exposed to military blast forces will be an important future direction to the initial findings presented here.

The influence of simulated microgravity on the proteome of Daphnia magna.

BACKGROUND: The waterflea Daphnia is an interesting candidate for bioregenerative life support systems (BLSS). These animals are particularly promising because of their central role in the limnic food web and its mode of reproduction. However, the response of Daphnia to altered gravity conditions has to be investigated, especially on the molecular level, to evaluate the suitability of Daphnia for BLSS in space. METHODS: In this study, we applied a proteomic approach to identify key proteins and pathways involved in the response of Daphnia to simulated microgravity generated by a two-dimensional (2D) clinostat. We analyzed five biological replicates using 2D-difference gel electrophoresis proteomic analysis. RESULTS: We identified 109 protein spots differing in intensity (P<0.05). Substantial fractions of these proteins are involved in actin microfilament organization, indicating the disruption of cytoskeletal structures during clinorotation. Furthermore, proteins involved in protein folding were identified, suggesting altered gravity induced breakdown of protein structures in general. In addition, simulated microgravity increased the abundance of energy metabolism-related proteins, indicating an enhanced energy demand of Daphnia. CONCLUSIONS: The affected biological processes were also described in other studies using different organisms and systems either aiming to simulate microgravity conditions or providing real microgravity conditions. Moreover, most of the Daphnia protein sequences are well-conserved throughout taxa, indicating that the response to altered gravity conditions in Daphnia follows a general concept. Data are available via ProteomeXchange with identifier PXD002096.