Breast cancer brain metastases show increased levels of genomic aberration-based homologous recombination deficiency scores relative to their corresponding primary tumors.

Background: Based on its mechanism of action, PARP inhibitor therapy is expected to benefit mainly tumor cases with homologous recombination deficiency (HRD). Therefore, identification of tumor types with increased HRD is important for the optimal use of this class of therapeutic agents. HRD levels can be estimated using various mutational signatures from next generation sequencing data and we used this approach to determine whether breast cancer brain metastases show altered levels of HRD scores relative to their corresponding primary tumor. Patients and methods: We used a previously published next generation sequencing dataset of 21 matched primary breast cancer/brain metastasis pairs to derive the various mutational signatures/HRD scores strongly associated with HRD. We also carried out the myChoice HRD analysis on an independent cohort of 17 breast cancer patients with matched primary/brain metastasis pairs. Results: All of the mutational signatures indicative of HRD showed a significant increase in the brain metastases relative to their matched primary tumor in the previously published whole exome sequencing dataset. In the independent validation cohort, the myChoice HRD assay showed an increased level in 87.5% of the brain metastases relative to the primary tumor, with 56% of brain metastases being HRD positive according to the myChoice criteria. Conclusions: The consistent observation that brain metastases of breast cancer tend to have higher HRD measures may raise the possibility that brain metastases may be more sensitive to PARP inhibitor treatment. This observation warrants further investigation to assess whether this increase is common to other metastatic sites as well, and whether clinical trials should adjust their strategy in the application of HRD measures for the prioritization of patients for PARP inhibitor therapy.

Loss of BRCA1 or BRCA2 markedly increases the rate of base substitution mutagenesis and has distinct effects on genomic deletions.

This corrects the article DOI: 10.1038/onc.2016.243.

Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut.

BACKGROUND: Detection of somatic mutations is one of the main goals of next generation DNA sequencing. A wide range of experimental systems are available for the study of spontaneous or environmentally induced mutagenic processes. However, most of the routinely used mutation calling algorithms are not optimised for the simultaneous analysis of multiple samples, or for non-human experimental model systems with no reliable databases of common genetic variations. Most standard tools either require numerous in-house post filtering steps with scarce documentation or take an unpractically long time to run. To overcome these problems, we designed the streamlined IsoMut tool which can be readily adapted to experimental scenarios where the goal is the identification of experimentally induced mutations in multiple isogenic samples. METHODS: Using 30 isogenic samples, reliable cohorts of validated mutations were created for testing purposes. Optimal values of the filtering parameters of IsoMut were determined in a thorough and strict optimization procedure based on these test sets. RESULTS: We show that IsoMut, when tuned correctly, decreases the false positive rate compared to conventional tools in a 30 sample experimental setup; and detects not only single nucleotide variations, but short insertions and deletions as well. IsoMut can also be run more than a hundred times faster than the most precise state of art tool, due its straightforward and easily understandable filtering algorithm. CONCLUSIONS: IsoMut has already been successfully applied in multiple recent studies to find unique, treatment induced mutations in sets of isogenic samples with very low false positive rates. These types of studies provide an important contribution to determining the mutagenic effect of environmental agents or genetic defects, and IsoMut turned out to be an invaluable tool in the analysis of such data.

Loss of BRCA1 or BRCA2 markedly increases the rate of base substitution mutagenesis and has distinct effects on genomic deletions.

Loss-of-function mutations in the BRCA1 and BRCA2 genes increase the risk of cancer. Owing to their function in homologous recombination repair, much research has focused on the unstable genomic phenotype of BRCA1/2 mutant cells manifest mainly as large-scale rearrangements. We used whole-genome sequencing of multiple isogenic chicken DT40 cell clones to precisely determine the consequences of BRCA1/2 loss on all types of genomic mutagenesis. Spontaneous base substitution mutation rates increased sevenfold upon the disruption of either BRCA1 or BRCA2, and the arising mutation spectra showed strong and specific correlation with a mutation signature associated with BRCA1/2 mutant tumours. To model endogenous alkylating damage, we determined the mutation spectrum caused by methyl methanesulfonate (MMS), and showed that MMS also induces more base substitution mutations in BRCA1/2-deficient cells. Spontaneously arising and MMS-induced insertion/deletion mutations and large rearrangements were also more common in BRCA1/2 mutant cells compared with the wild-type control. A difference in the short deletion phenotypes of BRCA1 and BRCA2 suggested distinct roles for the two proteins in the processing of DNA lesions, as BRCA2 mutants contained more short deletions, with a wider size distribution, which frequently showed microhomology near the breakpoints resembling repair by non-homologous end joining. An increased and prolonged gamma-H2AX signal in MMS-treated BRCA1/2 cells suggested an aberrant processing of stalled replication forks as the cause of increased mutagenesis. The high rate of base substitution mutagenesis demonstrated by our experiments is likely to significantly contribute to the oncogenic effect of the inactivation of BRCA1 or BRCA2.

Sonoluminescence and phase diagrams of single bubbles at low dissolved air concentrations.

We studied experimentally the dependence of light emission and phase space boundaries of air bubbles in water on the level of degassing down to low partial pressures of 15 mmHg. We found that the maximum obtainable light intensity increased monotonically by lowering the concentration of dissolved air in water. We also present a new technique to obtain the acoustic pressure (P(a)) and ambient radius (R0) parameters, based on the information provided by the timing of the flashes in the acoustic cycle. Using this technique we give phase diagrams of the bubble in the (R0,P(a)) and (P(a), gas concentration) space, and discuss the parametric dependence of the light intensity. The resulting power-law dependence of the relative intensity normalized by the ambient volume of the bubble on the expansion ratio indicates that more extreme conditions are attainable inside a bubble at dissolved air concentration of 15 mmHg than at 150 mmHg.

The Missing Link: Early Methane ("T") Dwarfs in the Sloan Digital Sky Survey.

We report the discovery of three cool brown dwarfs that fall in the effective temperature gap between the latest L dwarfs currently known, with no methane absorption bands in the 1-2.5 µm range, and the previously known methane (T) dwarfs, whose spectra are dominated by methane and water. The newly discovered objects were detected as very red objects in the Sloan Digital Sky Survey imaging data and have JHK colors between the red L dwarfs and the blue Gl 229B-like T dwarfs. They show both CO and CH(4) absorption in their near-infrared spectra in addition to H(2)O, with weaker CH(4) absorption features in the H and K bands than those in all other methane dwarfs reported to date. Due to the presence of CH(4) in these bands, we propose that these objects are early T dwarfs. The three form part of the brown dwarf spectral sequence and fill in the large gap in the overall spectral sequence from the hottest main-sequence stars to the coolest methane dwarfs currently known.

The Discovery of a Second Field Methane Brown Dwarf from Sloan Digital Sky Survey Commissioning Data.

We report the discovery of a second field methane brown dwarf from the commissioning data of the Sloan Digital Sky Survey (SDSS). The object, SDSS J134646.45-003150.4 (hereafter SDSS 1346-00), was selected because of its very red color and stellar appearance. Its spectrum between 0.8 and 2.5 µm is dominated by strong absorption bands of H2O and CH4 and closely mimics those of Gliese 229B and SDSS 162414.37+002915.6 (hereafter SDSS 1624+00), two other known methane brown dwarfs. SDSS 1346-00 is approximately 1.5 mag fainter than Gliese 229B, suggesting that it lies about 11 pc from the Sun. The ratio of flux at 2.1 µm to that at 1.27 µm is larger for SDSS 1346-00 than for Gliese 229B and SDSS 1624+00, which suggests that SDSS 1346-00 has a slightly higher effective temperature than the others. Based on a search area of 130 deg2 and a detection limit of z*=19.8, we estimate a space density of 0.05 pc-3 for methane brown dwarfs with Teff approximately 1000 K in the 40 pc3 volume of our search. This estimate is based on small-sample statistics and should be treated with appropriate caution.

The Discovery of a High-Redshift Quasar without Emission Lines from Sloan Digital Sky Survey Commissioning Data.

We report observations of a luminous unresolved object at redshift z=4.62, with a featureless optical spectrum redward of the Lyalpha forest region, discovered from Sloan Digital Sky Survey commissioning data. The redshift is determined by the onset of the Lyalpha forest at lambda approximately 6800 Å and a Lyman limit system at lambda=5120 Å. A strong Lyalpha absorption system with weak metal absorption lines at z=4.58 is also identified in the spectrum. The object has a continuum absolute magnitude of -26.6 at 1450 Å in the rest frame (h0=0.5, q0=0.5) and therefore cannot be an ordinary galaxy. It shows no radio emission (the 3 sigma upper limit of its flux at 6 cm is 60 µJy), indicating a radio-to-optical flux ratio at least as small as that of the radio-weakest BL Lacertae objects known. It is also not linearly polarized to a 3 sigma upper limit of 4% in the observed I band. Therefore, it is either the most distant BL Lac object known to date, with very weak radio emission, or a new type of unbeamed quasar, whose broad emission line region is very weak or absent.

Improving signal peptide prediction accuracy by simulated neural network.

The accuracy of distinguishing amino-terminal signal peptides from cytosolic proteins has been improved to 95% by combining a neural network classifier with von Heijne's statistical prediction, the latter is itself 85-90% reliable. The network processed not the cleavage site, but amino-terminal 20-residue segments by the 'tiling' algorithm. Concordant positive predictions of both methods led to the safe identification of 496 novel signal peptides from the Protein Identification Resources.