Genome-scale analysis identifies paralog lethality as a vulnerability of chromosome 1p loss in cancer.

Functional redundancy shared by paralog genes may afford protection against genetic perturbations, but it can also result in genetic vulnerabilities due to mutual interdependency1-5. Here, we surveyed genome-scale short hairpin RNA and CRISPR screening data on hundreds of cancer cell lines and identified MAGOH and MAGOHB, core members of the splicing-dependent exon junction complex, as top-ranked paralog dependencies6-8. MAGOHB is the top gene dependency in cells with hemizygous MAGOH deletion, a pervasive genetic event that frequently occurs due to chromosome 1p loss. Inhibition of MAGOHB in a MAGOH-deleted context compromises viability by globally perturbing alternative splicing and RNA surveillance. Dependency on IPO13, an importin-β receptor that mediates nuclear import of the MAGOH/B-Y14 heterodimer9, is highly correlated with dependency on both MAGOH and MAGOHB. Both MAGOHB and IPO13 represent dependencies in murine xenografts with hemizygous MAGOH deletion. Our results identify MAGOH and MAGOHB as reciprocal paralog dependencies across cancer types and suggest a rationale for targeting the MAGOHB-IPO13 axis in cancers with chromosome 1p deletion

Characterization of defect structures in nanocrystalline materials by X-ray line profile analysis

X-ray line profile analysis is a powerful alternative tool for determining dislocation densities, dislocation type, crystallite and subgrain size and size-distributions, and planar defects, especially the frequency of twin boundaries and stacking faults. The method is especially useful in the case of submicron grain size or nanocrystalline materials, where X-ray line broadening is a well pronounced effect, and the observation of defects with very large density is often not easy by transmission electron microscopy. The fundamentals of X-ray line broadening are summarized in terms of the different qualitative breadth methods, and the more sophisticated and more quantitative whole pattern fitting procedures. The efficiency and practical use of X-ray line profile analysis is shown by discussing its applications to metallic, ceramic, diamond-like and polymer nanomaterials

Magnetic enhancement of Co0.2_{0.2}Zn0.8_{0.8}Fe2_2O4_4 spinel oxide by mechanical milling

We report the magnetic properties of mechanically milled Co$_{0.2}$Zn$_{0.8}$Fe$_2$O$_4$ spinel oxide. After 24 hours milling of the bulk sample, the XRD spectra show nanostructure with average particle size $\approx$ 20 nm. The as milled sample shows an enhancement in magnetization and ordering temperature compared to the bulk sample. If the as milled sample is annealed at different temperatures for the same duration, recrystallization process occurs and approaches to the bulk structure on increasing the annealing temperatures. The magnetization of the annealed samples first increases and then decreases. At higher annealing temperature ($\sim$ 1000$^{0}$C) the system shows two coexisting magnetic phases {\it i.e.}, spin glass state and ferrimagnetic state, similar to the as prepared bulk sample. The room temperature M\"{o}ssbauer spectra of the as milled sample, annealed at 300$^{0}$C for different durations (upto 575 hours), suggest that the observed change in magnetic behaviour is strongly related with cations redistribution between tetrahedral (A) and octahedral (O) sites in the spinel structure. Apart from the cation redistribution, we suggest that the enhancement of magnetization and ordering temperature is related with the reduction of B site spin canting and increase of strain induced anisotropic energy during mechanical milling.Comment: 14 pages LaTeX, 10 ps figure

Nanocrystalline materials studied by powder diffraction line profile analysis

X-ray powder diffraction is a powerful tool for characterising the microstructure of crystalline materials in terms of size and strain. It is widely applied for nanocrystalline materials, especially since other methods, in particular electron microscopy is, on the one hand tedious and time consuming, on the other hand, due to the often metastable states of nanomaterials it might change their microstructures. It is attempted to overview the applications of microstructure characterization by powder diffraction on nanocrystalline metals, alloys, ceramics and carbon base materials. Whenever opportunity is given, the data provided by the X-ray method are compared and discussed together with results of electron microscopy. Since the topic is vast we do not try to cover the entire field

Prospects for Improving Alfalfa Yield Using Genomic- and Phenomic-Based Breeding

Alfalfa (Medicago sativa L.) is a perennial outcrossing legume that is cultivated as an important forage crop in many parts of the world. Yield is the most important trait for profitable alfalfa production, yet over the last 30 years yield improvement in California has stagnated. Current breeding methods focus on recurrent phenotypic selection; however, alternatives incorporating genomic- and phenomic-based information may enhance genetic gain and help to address the lack of yield improvement. Here we attempt to increase the yield potential of alfalfa using genomic selection (GS) in combination with high throughput phenotyping (HTP). A total of 193 families from two closely related elite populations were sown in the greenhouse and transplanted into mini sward plots at two locations near Davis, CA in May 2020. The trial was managed as a high-input system under full irrigation. Families were genotyped and phenotyped for biomass yield by mechanical harvest and a combination of drone and tower-based remote sensors across 12 harvests, 3 in the establishment year (2020), 7 in the first full year of production (2021) and 2 in 2022. Alfalfa yields ranged from 13-27 tonnes DM/hectare/year with a number of half-sib families outperforming popular cultivars in the first 2 years of production. Biomass volume predicted from the drone-based cameras had a moderate prediction accuracy with an overall R2 of 0.55. Some individual harvests reached accuracies as high as 0.85. Genotyping resulted in a dataset with 6,838 SNPs. Allele frequencies were used to generate a relationship matrix for GS. Narrow-sense heritability for dry matter yield was 0.31 and the predictive ability of the GS model was 0.15

The degree of segmental aneuploidy measured by total copy number abnormalities predicts survival and recurrence in superficial gastroesophageal adenocarcinoma

Background: Prognostic biomarkers are needed for superficial gastroesophageal adenocarcinoma (EAC) to predict clinical outcomes and select therapy. Although recurrent mutations have been characterized in EAC, little is known about their clinical and prognostic significance. Aneuploidy is predictive of clinical outcome in many malignancies but has not been evaluated in superficial EAC. Methods: We quantified copy number changes in 41 superficial EAC using Affymetrix SNP 6.0 arrays. We identified recurrent chromosomal gains and losses and calculated the total copy number abnormality (CNA) count for each tumor as a measure of aneuploidy. We correlated CNA count with overall survival and time to first recurrence in univariate and multivariate analyses. Results: Recurrent segmental gains and losses involved multiple genes, including: HER2, EGFR, MET, CDK6, KRAS (recurrent gains); and FHIT, WWOX, CDKN2A/B, SMAD4, RUNX1 (recurrent losses). There was a 40-fold variation in CNA count across all cases. Tumors with the lowest and highest quartile CNA count had significantly better overall survival (p = 0.032) and time to first recurrence (p = 0.010) compared to those with intermediate CNA counts. These associations persisted when controlling for other prognostic variables. Significance: SNP arrays facilitate the assessment of recurrent chromosomal gain and loss and allow high resolution, quantitative assessment of segmental aneuploidy (total CNA count). The non-monotonic association of segmental aneuploidy with survival has been described in other tumors. The degree of aneuploidy is a promising prognostic biomarker in a potentially curable form of EAC. © 2014 Davison et al

Glucocorticoid-Induced TNFR-Related Protein Stimulation Reverses Cardiac Allograft Acceptance Induced by CD40-CD40L Blockade

CD40-CD40L blockade has potent immunosuppressive effects in cardiac allograft rejection but is less effective in the presence of inflammatory signals. To better understand the factors that mediate CD40-CD40L blockade-resistant rejection, we studied the effects of stimulation through glucocorticoid-induced TNFR-related protein (GITR), a costimulatory protein expressed by regulatory and effector T cells. Stimulation of CD40−/− or wild-type recipient mice treated with anti-CD40L mAb (WT+anti-CD40L) and with agonistic anti-GITR mAb resulted in cardiac allograft rejection. GITR stimulation did not induce rejection once long-term graft acceptance was established. In vitro, GITR stimulation increased proliferation of effector T cells and decreased regulatory T cell () differentiation in both treatment groups. GITR-stimulated CD40−/− recipients rejected their allografts more rapidly compared to GITR-stimulated WT+anti-CD40L recipients, and this rejection, characterized by a robust Th2 response and significant eosinophilic infiltrate, could be mediated by CD4+ T cells alone. In contrast, both CD4+ and CD8+ T cells were required to induce rejection in GITR-stimulated WT+anti-CD40L-treated recipients, and the pathology of rejection was less severe. Hence, early GITR stimulation could initiate graft rejection despite CD40 deficiency or anti-CD40L mAb treatment, though the recipient response was dependent on the mechanism of CD40-CD40L disruption

STAG2 loss rewires oncogenic and developmental programs to promote metastasis in Ewing sarcoma

The core cohesin subunit STAG2 is recurrently mutated in Ewing sarcoma but its biological role is less clear. Here, we demonstrate that cohesin complexes containing STAG2 occupy enhancer and polycomb repressive complex (PRC2)-marked regulatory regions. Genetic suppression of STAG2 leads to a compensatory increase in cohesin-STAG1 complexes, but not in enhancer-rich regions, and results in reprogramming of cis-chromatin interactions. Strikingly, in STAG2 knockout cells the oncogenic genetic program driven by the fusion transcription factor EWS/FLI1 was highly perturbed, in part due to altered enhancer-promoter contacts. Moreover, loss of STAG2 also disrupted PRC2-mediated regulation of gene expression. Combined, these transcriptional changes converged to modulate EWS/FLI1, migratory, and neurodevelopmental programs. Finally, consistent with clinical observations, functional studies revealed that loss of STAG2 enhances the metastatic potential of Ewing sarcoma xenografts. Our findings demonstrate that STAG2 mutations can alter chromatin architecture and transcriptional programs to promote an aggressive cancer phenotype