Expression of SCF splice variants in human melanocytes and melanoma cell lines: potential prognostic implications

Stem cell factor (SCF), the ligand for c-Kit, is known to regulate developmental and functional processes of haematopoietic stem cells, mast cells and melanocytes. Two different splice variants form predominantly soluble (sSCF or SCF-1) and in addition some membrane-bound SCF (mSCF or SCF-2). In order to explore the prognostic significance of these molecules in melanoma, total SCF, SCF splice variants and c-Kit expression were studied in normal skin melanocytes and in 11 different melanoma cell lines, using reverse transcription polymerase chain reaction, immunocytochemistry and enzyme-linked immunosorbent assay. Nine of the 11 melanoma cell lines expressed SCF-1 mRNA, only two of them SCF-2, and these two also SCF-1. Coexpression of both SCF-1 and c-Kit was noted in five cell lines, and only one cell line as well as normal melanocytes expressed both SCF-1 and SCF-2 as well as c-Kit. Corresponding results were obtained on immunocytochemical staining. Of three exemplary melanoma cell lines studied, two expressing SCF mRNA also released SCF spontaneously and on stimulation, whereas the line lacking SCF and c-kit mRNA (SK-Mel-23) failed to do so. These data demonstrate thus that melanoma cell lines, particularly those known to metastasize in vivo, lose the ability to express SCF-2 mRNA, suggesting that this molecule may serve, next to c-Kit, as a prognostic marker for malignant melanoma. © 2000 Cancer Research Campaig

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). 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 promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

Chromothripsis is a mutational phenomenon characterized by massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies in selected cancer types have suggested that chromothripsis may be more common than initially inferred from low-resolution copy-number data. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we analyze patterns of chromothripsis across 2,658 tumors from 38 cancer types using whole-genome sequencing data. We find that chromothripsis events are pervasive across cancers, with a frequency of more than 50% in several cancer types. Whereas canonical chromothripsis profiles display oscillations between two copy-number states, a considerable fraction of events involve multiple chromosomes and additional structural alterations. In addition to non-homologous end joining, we detect signatures of replication-associated processes and templated insertions. Chromothripsis contributes to oncogene amplification and to inactivation of genes such as mismatch-repair-related genes. These findings show that chromothripsis is a major process that drives genome evolution in human cancer

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

On the chemical state and distribution of Zr- and V-based additives in reactive hydride composites

Reactive hydride composites (RHCs) are very promising hydrogen storage materials for future applications due to their reduced reaction enthalpies and high gravimetric capacities. At present, the materials' functionality is limited by the reaction kinetics. A significant positive influence can be observed with addition of transition-metal-based additives. To understand the effect of these additives, the chemical state and changes during the reaction as well as the microstructural distribution were investigated using x-ray absorption near-edge structure (XANES) spectroscopy and anomalous small-angle x-ray scattering (ASAXS). In this work, zirconium- and vanadium-based additives were added to 2LiBH4-MgH2 composites and 2LiH-MgB2 composites and measured in the vicinity of the corresponding absorption edge. The measurements reveal the formation of finely distributed zirconium diboride and vanadium-based nanoparticles. The potential mechanisms for the observed influence on the reaction kinetics are discussed

Formation of Ca(BH4)(2) from hydrogenation of CaH2+MgB2 composite

The hydrogenation of the CaH2+MgB2 Composite and the dehydrogenation of the resulting products are investigated in detail by in situ time-resolved synchrotron radiation powder X-ray diffraction, high-pressure differential scanning calorimetry, infrared, and thermovolumetric measurements. It is demonstrated that a Ca(BH4)(2)+MgH2 composite is formed by hydrogenating a CaH2+MgB2 composite, at 350 degrees C and 140 bar of hydrogen. Two phases of Ca(BH4)(2) were characterized: alpha- and beta-Ca(BH4)(2). alpha-Ca(BH4)(2) transforms to beta-Ca(BH4)(2) at about 130 degrees C. Under the conditions used in the present study, beta-Ca(BH4)(2) decomposes first to CaH2, Ca3Mg4H14, Mg, B (or MgB2 depending on experimental conditions), and hydrogen at 360 degrees C, before complete decomposition to CaH2, Mg, B (or MgB2), and hydrogen at 400 degrees C. During hydrogenation under 140 bar of hydrogen, beta-Ca(BH4)(2) is formed at 250 degrees C, and alpha-Ca(BH4)(2) is formed when the sample is cooled to less than 130 degrees C. Ti isopropoxide improves the kinetics of the reactions, during both hydrogenation and dehydrogenation. The dehydrogenation temperature decreases to 250 degrees C, with 1 wt % of this additive, and hydrogenation starts already at 200 degrees C. We propose that the improved kinetics of the above reactions with MgB2 (compared to pure boron) can be explained by the different boron bonding within the crystal structure of MgB2 and pure boron