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

Control of metal-organic framework crystallization by metastable intermediate pre-equilibrium species

There is an increasing amount of interest in metal–organic frameworks (MOFs) for a variety of applications, from gas sensing and separations to electronics and catalysis. However, the mechanisms by which they crystallize remain poorly understood. Herein, an important new insight into MOF formation is reported. It is shown that, prior to network assembly, crystallization intermediates in the canonical ZIF‐8 system exist in a dynamic pre‐equilibrium, which depends on the reactant concentrations and the progress of reaction. Concentration can, therefore, be used as a synthetic handle to directly control particle size, with potential implications for industrial scale‐up and gas sorption applications. These findings enable the rationalization of apparent contradictions between previous studies of ZIF‐8 and opens up new opportunities for the control of crystallization in network solids more generally

Control of metal-organic framework crystallization by metastable intermediate pre-equilibrium species

There is an increasing amount of interest in metal–organic frameworks (MOFs) for a variety of applications, from gas sensing and separations to electronics and catalysis. However, the mechanisms by which they crystallize remain poorly understood. Herein, an important new insight into MOF formation is reported. It is shown that, prior to network assembly, crystallization intermediates in the canonical ZIF‐8 system exist in a dynamic pre‐equilibrium, which depends on the reactant concentrations and the progress of reaction. Concentration can, therefore, be used as a synthetic handle to directly control particle size, with potential implications for industrial scale‐up and gas sorption applications. These findings enable the rationalization of apparent contradictions between previous studies of ZIF‐8 and opens up new opportunities for the control of crystallization in network solids more generally

hMRE11 deficiency leads to microsatellite instability and defective DNA mismatch repair

DNA mismatch repair (MMR) is essential in the surveillance of accurate transmission of genetic information, and defects in this pathway lead to microsatellite instability and hereditary nonpolyposis colorectal cancer (HNPCC). Our previous study raised the possibility that hMRE11 might be involved in MMR through physical interaction with hMLH1. Here, we show that hMRE11 deficiency leads to significant increase in MSI for both mono- and dinucleotide sequences. Furthermore, RNA-interference-mediated hMRE11-knockdown in HeLa cells results in MMR deficiency. Analysis of seven HNPCC-associated hMLH1 missense mutations located within the hMRE11-interacting domain shows that four mutations (L574P, K618T, R659P and A681T) cause near-complete disruption of the interaction between hMRE11 and hMLH1, and two mutations (Q542L and L582V) cause a 30% reduction of protein interaction. These findings indicate that hMRE11 represents a functional component of the MMR pathway and the disruption of hMLH1-hMRE11 interaction could be an alternative molecular explanation for hMLH1 mutations in a subset of HNPCC tumours