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- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 3. |
- Du, CW, et al.
(författare)
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Arsenic trioxide reduces the invasive and metastatic properties of nasopharyngeal carcinoma cells in vitro
- 2006
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Ingår i: Brazilian journal of medical and biological research. - 0100-879X .- 1414-431X. ; 39:5, s. 677-685
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Tidskriftsartikel (refereegranskat)abstract
- Nasopharyngeal carcinoma (NPC) is notorious for the metastases, which are in close association with Epstein-Barr virus-encoded latent membrane protein 1 (LMP1). Arsenic trioxide (As2O3) has been shown to induce apoptosis and differentiation in NPC xenografts. Then, can it repress the cancer cells' metastasis potential? To elucidate this issue, the present study was performed. LMP1-negative cell line HNE1 and LMP1-positive cell line HNE1-LMP1 were used as in vitro model. Cells (1 × 105/mL) were cultured with or without 3 μM As2O3 for 48 h. Then the survival cells were collected to investigate their potential of colony formation, attachment, invasion, and migration. Both confocal immunofluorescence staining and Western blot were used to detect the changes of LMP1 expression. The changes of MMP-9 were examined by RT-PCR assay and Western blot. The results were as follow: i) the colony formation inhibition rate (75.41 ± 3.9% in HNE1-LMP1 cells vs 37.89 ± 4.9% in HNE1 cells), the rate of attachment (HNE1-LMP1 vs HNE1: 56.40 ± 3.5 vs 65.87 ± 5.9%), the invasion inhibitory rate (HNE1-LMP1 vs HNE1: 56.50 ± 3.7 and 27.91 ± 2.1%), and the migration inhibitory rate (HNE1-LMP1 vs HNE1: 48.70 ± 3.9 vs 29.19 ± 6.27%) were all significantly different between the two cell lines (P < 0.01). ii) LMP1 was down-regulated in As2O3-treated HNE1-LMP1 cells. iii) The reduction of MMP-9 was found in As2O3-treated groups, more evident in HNE1-LMP1 cells. Thus, we conclude that As2O3 can reduce metastasis potential of NPC cells, involving inhibition of MMP-9 expression. LMP1 were also reduced in this process and seemed to enhance anti-metastasis activity of As2O3. © 2006 Brazilian Journal of Medical and Biological Research.
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| 8. |
- Buyanova, Irina A, et al.
(författare)
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Unusual effects of hydrogen on electronic and lattice properties of GaNP alloys
- 2006
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Ingår i: Physica. B, Condensed matter. - : Elsevier BV. - 0921-4526 .- 1873-2135. ; 376, s. 568-570
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Tidskriftsartikel (refereegranskat)abstract
- Hydrogen incorporation is shown to cause passivation of various N-related localized states and partial neutralization of N-induced changes in the electronic structure of the GaNxP1-x alloys with x < 0.008. According to the performed X-ray diffraction measurements, the hydrogenation is also found to cause strong expansion of the GaNP lattice which even changes from a tensile strain in the as-grown GaNP epilayers to a compressive strain in the post-hydrogenated structures with the highest H concentration. By comparing results obtained using two types of hydrogen treatments, i.e. by implantation from a Kaufman source and by using a remote dc H plasma, the observed changes are shown to be inherent to H due to its efficient complexing with N atoms, whereas possible effects of implantation damage are only marginal. (c) 2005 Elsevier B.V. All rights reserved.
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| 10. |
- Vorona, Igor, et al.
(författare)
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Signatures of grown-in defects in GaInNP alloys grown on a GaAs substrate from magnetic resonance studies
- 2006
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Ingår i: Physica. B, Condensed matter. - : Elsevier BV. - 0921-4526 .- 1873-2135. ; 376, s. 571-574
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Tidskriftsartikel (refereegranskat)abstract
- Three grown-in defects acting as centers of non-radiative recombination (NR) were detected in GaInNP alloys grown on a GaAs substrate using the optically detected magnetic resonance (ODMR) technique. Among them, one was proposed to be either a Ga-i-related defect or an AS(Ga)-related defect, from the resolved four-line hyperfine structure. The former model was concluded to be more favorable by weighing physical properties of the two defects, e.g. the likelihood for their presence in the studied structures, their spatial location, g-value and effect of rapid thermal annealing (RTA). RTA at 700 degrees C was shown to reduce concentrations of the studied defects but it introduced a new defect that likely directly participates in the monitored radiative recombination process in the RTA-treated samples. (c) 2005 Elsevier B.V. All rights reserved.
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