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

Parental and Grandparental Ages in the Autistic Spectrum Disorders: A Birth Cohort Study

Background: A number of studies have assessed ages of parents of children with autistic spectrum disorders (ASD), and reported both maternal and paternal age effects. Here we assess relationships with grandparental ages. Methods and Findings: We compared the parental and grandparental ages of children in the population-based Avon Longitudinal Study of Parents and Children (ALSPAC), according to their scores in regard to 4 autistic trait measures and whether they had been given a diagnosis of ASD. Mean maternal and paternal ages of ASD cases were raised, but this appears to be secondary to a maternal grandmother age effect (P = 0.006): OR = 1.66[95%CI 1.16, 2.37] for each 10-year increase in the grandmother’s age at the birth of the mother. Trait measures also revealed an association between the maternal grandmother’s age and the major autistic trait–the Coherence Scale (regression coefficient b = 0.142, [95%CI = 0.057, 0.228]P = 0.001). After allowing for confounders the effect size increased to b = 0.217[95%CI 0.125, 0.308](P,0.001) for each 10 year increase in age. Conclusions: Although the relationship between maternal grandmother’s age and ASD and a major autistic trait was unexpected, there is some biological plausibility, for the maternal side at least, given that the timing of female meiosis I permits direct effects on the grandchild’s genome during the grandmother’s pregnancy. An alternative explanation is the meiotic mismatch methylation (3 M) hypothesis, presented here for the first time. Nevertheless the findings should b

Molecular characterization of the thermally labile fraction of biochar by hydropyrolysis and pyrolysis-GC/MS

Agroenvironmental benefits and limitations of biochar in soil applications require a full understanding of the stability and fate of the various carbon fractions. Analytical hydropyrolysis (HyPy) enables the determination of the stable black carbon (BCHyPy) and thermally labile (semi-labile; non-BCHyPy) fractions in biochar and soil samples. The non-BCHyPy fraction can be analysed at a molecular level by gas chromatography-mass spectrometry (GC-MS). In the present study, HyPy was applied to the characterisation of biochars produced from pine wood, beech wood and corn digestate with the same pyrolysis unit at low (340–400 °C) and high (600 °C) temperatures. Results were compared with those from Py-GC-MS. HyPy provided consistent information concerning the thermal stability of biochar samples, with BCHyPy levels related with the relative abundance of the charred fraction estimated by Py-GC-MS and the hydrogen/carbon (H/C) ratios. The non-BCHyPy fractions were featured by the presence of polycyclic aromatic hydrocarbons (PAHs) from two to seven rings, including alkylated derivatives up to C4. Partially hydrogenated PAHs were also detected. The yields of non-BCHyPy were higher for those biochars produced at lower temperatures and always more abundant than the levels of solvent-extractable PAHs. The methylated/parent PAH ratios from HyPy and Py-GC-MS exhibited lower values for the most charred biochar. The observed differences in the abundance of the stable fraction and the molecular chemistry of the semi-labile fraction can be usefully utilised to drive the process conditions to the desired properties of the resulting biochars and to predict the impact of biochar amendment to soil organic pools. The concentrations of priority PAHs in the semi-labile fraction was evaluated in the mg g−1 level suggesting that it could be an important fraction of the polyaromatic carbon pool in soil

The extreme HBL behaviour of Markarian 501 during 2012

A multiwavelength campaign was organized to take place between March and July of 2012. Excellent temporal coverage was obtained with more than 25 instruments, including the MAGIC, FACT and VERITAS Cherenkov telescopes, the instruments on board the Swift and Fermi spacecraft, and the telescopes operated by the GASP-WEBT collaboration. Mrk 501 showed a very high energy (VHE) gamma-ray flux above 0.2 TeV of $\sim$0.5 times the Crab Nebula flux (CU) for most of the campaign. The highest activity occurred on 2012 June 9, when the VHE flux was $\sim$3 CU, and the peak of the high-energy spectral component was found to be at $\sim$2 TeV. This study reports very hard X-ray spectra, and the hardest VHE spectra measured to date for Mrk 501. The fractional variability was found to increase with energy, with the highest variability occurring at VHE, and a significant correlation between the X-ray and VHE bands. The unprecedentedly hard X-ray and VHE spectra measured imply that their low- and high-energy components peaked above 5 keV and 0.5 TeV, respectively, during a large fraction of the observing campaign, and hence that Mrk 501 behaved like an extreme high-frequency- peaked blazar (EHBL) throughout the 2012 observing season. This suggests that being an EHBL may not be a permanent characteristic of a blazar, but rather a state which may change over time. The one-zone synchrotron self-Compton (SSC) scenario can successfully describe the segments of the SED where most energy is emitted, with a significant correlation between the electron energy density and the VHE gamma-ray activity, suggesting that most of the variability may be explained by the injection of high-energy electrons. The one-zone SSC scenario used reproduces the behaviour seen between the measured X-ray and VHE gamma-ray fluxes, and predicts that the correlation becomes stronger with increasing energy of the X-rays

An intermittent extreme BL Lac: MWL study of 1ES 2344+514 in an enhanced state

Extreme high-frequency BL Lacs (EHBL) feature their synchrotron peak of the broad-band spectral energy distribution (SED) at nu(s) >= 10(17) Hz. The BL Lac object 1ES 2344+514 was included in the EHBL family because of its impressive shift of the synchrotron peak in 1996. During the following years, the source appeared to be in a low state without showing any extreme behaviours. In 2016 August, 1ES 2344+514 was detected with the groundbased gamma-ray telescope FACT during a high gamma-ray state, triggering multiwavelength (MWL) observations. We studied the MWL light curves of 1ES 2344+514 during the 2016 flaring state, using data from radio to very-high-energy (VHE) gamma-rays taken with OVRO, KAIT, KVA, NOT, some telescopes of the GASP-WEBT collaboration at the Teide, Crimean, and St. Petersburg observatories, Swift-UVOT, Swift-XRT, Fermi-LAT, FACT, and MAGIC. With simultaneous observations of the flare, we built the broad-band SED and studied it in the framework of a leptonic and a hadronic model. The VHE gamma-ray observations show a flux level of 55 per cent of the Crab Nebula flux above 300 GeV, similar to the historical maximum of 1995. The combination of MAGIC and Fermi-LAT spectra provides an unprecedented characterization of the inverse-Compton peak for this object during a flaring episode. The Gamma index of the intrinsic spectrum in the VHE gamma-ray band is 2.04 +/- 0.12(stat) +/- 0.15(sys). We find the source in an extreme state with a shift of the position of the synchrotron peak to frequencies above or equal to 1018 Hz

Nanoparticle delivery of immunostimulatory oligonucleotides enhances response to checkpoint inhibitor therapeutics

© 2020 National Academy of Sciences. All rights reserved. The recent advent of immune checkpoint inhibitor (CPI) antibodies has revolutionized many aspects of cancer therapy, but the efficacy of these breakthrough therapeutics remains limited, as many patients fail to respond for reasons that still largely evade understanding. An array of studies in human patients and animal models has demonstrated that local signaling can generate strongly immunosuppressive microenvironments within tumors, and emerging evidence suggests that delivery of immunostimulatory molecules into tumors can have therapeutic effects. Nanoparticle formulations of these cargoes offer a promising way to maximize their delivery and to enhance the efficacy of checkpoint inhibitors. We developed a modular nanoparticle system capable of encapsulating an array of immunostimulatory oligonucleotides that, in some cases, greatly increase their potency to activate inflammatory signaling within immune cells in vitro. We hypothesized that these immunostimulatory nanoparticles could suppress tumor growth by activating similar signaling in vivo, and thereby also improve responsiveness to immune checkpoint inhibitor antibody therapies. We found that our engineered nanoparticles carrying a CpG DNA ligand of TLR9 can suppress tumor growth in several animal models of various cancers, resulting in an abscopal effect on distant tumors, and improving responsiveness to anti- CTLA4 treatment with combinatorial effects after intratumoral administration. Moreover, by incorporating tumor-homing peptides, immunostimulatory nucleotide-bearing nanoparticles facilitate antitumor efficacy after systemic intravenous (i.v.) administration

Metastasis-suppressor transcript destabilization through TARBP2 binding of mRNA hairpins

Aberrant regulation of RNA stability has an important role in many disease states. Deregulated post-transcriptional modulation, such as that governed by microRNAs targeting linear sequence elements in messenger RNAs, has been implicated in the progression of many cancer types. A defining feature of RNA is its ability to fold into structures. However, the roles of structural mRNA elements in cancer progression remain unexplored. Here we performed an unbiased search for post-transcriptional modulators of mRNA stability in breast cancer by conducting whole-genome transcript stability measurements in poorly and highly metastatic isogenic human breast cancer lines. Using a computational framework that searches RNA sequence and structure space, we discovered a family of GC-rich structural cis-regulatory RNA elements, termed sRSEs for structural RNA stability elements, which are significantly overrepresented in transcripts displaying reduced stability in highly metastatic cells. By integrating computational and biochemical approaches, we identified TARBP2, a double-stranded RNA-binding protein implicated in microRNA processing, as the trans factor that binds the sRSE family and similar structural elements--collectively termed TARBP2-binding structural elements (TBSEs)--in transcripts. TARBP2 is overexpressed in metastatic cells and metastatic human breast tumours and destabilizes transcripts containing TBSEs. Endogenous TARBP2 promotes metastatic cell invasion and colonization by destabilizing amyloid precursor protein (APP) and ZNF395 transcripts, two genes previously associated with Alzheimer's and Huntington's disease, respectively. We reveal these genes to be novel metastasis suppressor genes in breast cancer. The cleavage product of APP, extracellular amyloid-α peptide, directly suppresses invasion while ZNF395 transcriptionally represses a pro-metastatic gene expression program. The expression levels of TARBP2, APP and ZNF395 in human breast carcinomas support their experimentally uncovered roles in metastasis. Our findings establish a non-canonical and direct role for TARBP2 in mammalian gene expression regulation and reveal that regulated RNA destabilization through protein-mediated binding of mRNA structural elements can govern cancer progression

Protease activity sensors noninvasively classify bacterial infections and antibiotic responsesResearch in context

Background: Respiratory tract infections represent a significant public health risk, and timely and accurate detection of bacterial infections facilitates rapid therapeutic intervention. Furthermore, monitoring the progression of infections after intervention enables ‘course correction’ in cases where initial treatments are ineffective, avoiding unnecessary drug dosing that can contribute to antibiotic resistance. However, current diagnostic and monitoring techniques rely on non-specific or slow readouts, such as radiographic imaging and sputum cultures, which fail to specifically identify bacterial infections and take several days to identify optimal antibiotic treatments. Methods: Here we describe a nanoparticle system that detects P. aeruginosa lung infections by sensing host and bacterial protease activity in vivo, and that delivers a urinary detection readout. One protease sensor is comprised of a peptide substrate for the P. aeruginosa protease LasA. A second sensor designed to detect elastases is responsive to recombinant neutrophil elastase and secreted proteases from bacterial strains. Findings: In mice infected with P. aeruginosa, nanoparticle formulations of these protease sensors—termed activity-based nanosensors (ABNs)—detect infections and monitor bacterial clearance from the lungs over time. Additionally, ABNs differentiate between appropriate and ineffective antibiotic treatments acutely, within hours after the initiation of therapy. Interpretation: These findings demonstrate how activity measurements of disease-associated proteases can provide a noninvasive window into the dynamic process of bacterial infection and resolution, offering an opportunity for detecting, monitoring, and characterizing lung infections. Fund: National Cancer Institute, National Institute of Environmental Health Sciences, National Institutes of Health, National Science Foundation Graduate Research Fellowship Program, and Howard Hughes Medical Institute. Keywords: Protease, Nanoparticle, Diagnostic, Bacterial pneumoni