Structural variation and its potential impact on genome instability: Novel discoveries in the EGFR landscape by long-read sequencing.

Structural variation (SV) is typically defined as variation within the human genome that exceeds 50 base pairs (bp). SV may be copy number neutral or it may involve duplications, deletions, and complex rearrangements. Recent studies have shown SV to be associated with many human diseases. However, studies of SV have been challenging due to technological constraints. With the advent of third generation (long-read) sequencing technology, exploration of longer stretches of DNA not easily examined previously has been made possible. In the present study, we utilized third generation (long-read) sequencing techniques to examine SV in the EGFR landscape of four haplotypes derived from two human samples. We analyzed the EGFR gene and its landscape (+/- 500,000 base pairs) using this approach and were able to identify a region of non-coding DNA with over 90% similarity to the most common activating EGFR mutation in non-small cell lung cancer. Based on previously published Alu-element genome instability algorithms, we propose a molecular mechanism to explain how this non-coding region of DNA may be interacting with and impacting the stability of the EGFR gene and potentially generating this cancer-driver gene. By these techniques, we were also able to identify previously hidden structural variation in the four haplotypes and in the human reference genome (hg38). We applied previously published algorithms to compare the relative stabilities of these five different EGFR gene landscape haplotypes to estimate their relative potentials to generate the EGFR exon 19, 15 bp canonical deletion. To our knowledge, the present study is the first to use the differences in genomic architecture between targeted cancer-linked phased haplotypes to estimate their relative potentials to form a common cancer-linked driver mutation

A genomic screen for activators of the antioxidant response element

The antioxidant response element (ARE) is a cis-acting regulatory enhancer element found in the 5′ flanking region of many phase II detoxification enzymes. Up-regulation of ARE-dependent target genes is known to have neuroprotective effects; yet, the mechanism of activation is largely unknown. By screening an arrayed collection of ≈15,000 full-length expression cDNAs in the human neuroblastoma cell line IMR-32 with an ARE-luciferase reporter, we have identified several cDNAs not previously associated with ARE activation. A subset of cDNAs, encoding sequestosome 1 (SQSTM1) and dipeptidylpeptidase 3 (DPP3), activated the ARE in primary mouse-derived cortical neurons. Overexpression of SQSTM1 and DPP3 in IMR-32 cells stimulated NF-E2-related factor 2 (NRF2) nuclear translocation and led to increased levels of NAD(P)H:quinone oxidoreductase 1, a protein which is transcriptionally regulated by the ARE. When transfected into IMR-32 neuroblastoma cells that were depleted of transcription factor NRF2 by RNA interference, SQSTM1 and DPP3 were unable to activate the ARE or induce NAD(P)H:quinone oxidoreductase 1 expression, indicating that the ARE activation upon ectopic expression of these cDNAs is mediated by NRF2. Studies with pharmacological inhibitors indicated that 1-phosphatidylinositol 3-kinase and protein kinase C signaling are essential for activity. Overexpression of these cDNAs conferred partial resistance to hydrogen peroxide or rotenone-induced toxicity, consistent with the induction of antioxidant and phase II detoxification enzymes, which can protect from oxidative stress. This work and other such studies may provide mechanisms for activating the ARE in the absence of general oxidative stress and a yet-unexploited therapeutic approach to degenerative diseases and aging

Probing the nuclear liquid-gas phase transition

Fragment distributions resulting from Au+Au collisions at an incident energy of E/A=600 MeV are studied. From the measured fragment and neutron distributions the mass and the excitation energy of the decaying pre-fragments were determined. A temperature scale was derived from observed yield ratios of He and Li isotopes. The relation between this isotope temperature and the excitation energy of the system exhibits a behavior which is expected for a phase transition. The nuclear vapor regime takes over at an excitation energy of 10 MeV per nucleon, a temperature of 5 MeV and may be characterized by a density of 0.15-0.3 normal nuclear density. (orig.)55 refs.SIGLEAvailable from TIB Hannover: RO 801(95-13) / FIZ - Fachinformationszzentrum Karlsruhe / TIB - Technische InformationsbibliothekDEGerman

Total and nuclear fission cross sections of "2"3"8U at relativistic energies

Total fission cross sections of "2"3"8U projectiles were measured at bombarding energies of 0.6 and 1 GeV per nucleon for seven different targets (Be, C, Al, Cu, In, Au and U). It is found that all data points fall onto one curve, independent of bombarding energy, once the electromagnetic contribution to the total fission cross sections is subtracted. The abrasion-ablation model predicts a significantly weaker target dependence than observed, and underestimates the nuclear fission cross sections for the heavier targets. (orig.)SIGLEAvailable from TIB Hannover: RO 801(96-11) / FIZ - Fachinformationszzentrum Karlsruhe / TIB - Technische InformationsbibliothekDEGerman

Charge-pickup of "2"3"8U at relativistic energies

Cross sections for the charge-pickup of "2"3"8U projectiles were measured at E/A=600 and 1000 MeV for seven different targets (Be, C, Al, Cu, In, Au and U). Events with two fission fragments with a sum charge of 93 in the exit channel were selected. Due to the significant excitation energy, the dominant part of produced Np nuclei fission instead of decaying to the ground state by evaporation. The observed cross sections can be well reproduced by intranuclear-cascade-plus-evaporation calculations and, therefore, confirm recent results that no exotic processes are needed to explain charge-pickup processes. (orig.)24 refs.Available from TIB Hannover: RO 801(95-60) / FIZ - Fachinformationszzentrum Karlsruhe / TIB - Technische InformationsbibliothekSIGLEDEGerman