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 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.

Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets

Prostate cancer represents a substantial clinical challenge because it is difficult to predict outcome and advanced disease is often fatal. We sequenced the whole genomes of 112 primary and metastatic prostate cancer samples. From joint analysis of these cancers with those from previous studies (930 cancers in total), we found evidence for 22 previously unidentified putative driver genes harboring coding mutations, as well as evidence for NEAT1 and FOXA1 acting as drivers through noncoding mutations. Through the temporal dissection of aberrations, we identified driver mutations specifically associated with steps in the progression of prostate cancer, establishing, for example, loss of CHD1 and BRCA2 as early events in cancer development of ETS fusion-negative cancers. Computational chemogenomic (canSAR) analysis of prostate cancer mutations identified 11 targets of approved drugs, 7 targets of investigational drugs, and 62 targets of compounds that may be active and should be considered candidates for future clinical trials.

Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data

A variety of models have been proposed to explain regions of recurrent somatic copy number alteration (SCNA) in human cancer. Our study employs Whole Genome DNA Sequence (WGS) data from tumor samples (n = 103) to comprehensively assess the role of the Knudson two hit genetic model in SCNA generation in prostate cancer. 64 recurrent regions of loss and gain were detected, of which 28 were novel, including regions of loss with more than 15% frequency at Chr4p15.2-p15.1 (15.53%), Chr6q27 (16.50%) and Chr18q12.3 (17.48%). Comprehensive mutation screens of genes, lincRNA encoding sequences, control regions and conserved domains within SCNAs demonstrated that a two-hit genetic model was supported in only a minor proportion of recurrent SCNA losses examined (15/40). We found that recurrent breakpoints and regions of inversion often occur within Knudson model SCNAs, leading to the identification of ZNF292 as a target gene for the deletion at 6q14.3-q15 and NKX3.1 as a two-hit target at 8p21.3-p21.2. The importance of alterations of lincRNA sequences was illustrated by the identification of a novel mutational hotspot at the KCCAT42, FENDRR, CAT1886 and STCAT2 loci at the 16q23.1-q24.3 loss. Our data confirm that the burden of SCNAs is predictive of biochemical recurrence, define nine individual regions that are associated with relapse, and highlight the possible importance of ion channel and G-protein coupled-receptor (GPCR) pathways in cancer development. We concluded that a two-hit genetic model accounts for about one third of SCNA indicating that mechanisms, such haploinsufficiency and epigenetic inactivation, account for the remaining SCNA losses.

Altered expression of epithelial-to-mesenchymal transition proteins in extraprostatic prostate cancer

Epithelial to mesenchymal transition (EMT) of cancer cells involves loss of epithelial polarity and adhesiveness, and gain of invasive and migratory mesenchymal behaviours. EMT occurs in prostate cancer (PCa) but it is unknown whether this is in specific areas of primary tumours. We examined whether any of eleven EMT-related proteins have altered expression or subcellular localisation within the extraprostatic extension component of locally advanced PCa compared with other localisations, and whether similar changes may occur in in vitro organotypic PCa cell cultures and in vivo PCa models. Expression profiles of three proteins (E-cadherin, Snail, and α-smooth muscle actin) were significantly different in extraprostatic extension PCa compared with intra-prostatic tumour, and 18/27 cases had an expression change of at least one of these three proteins. Of the three significantly altered EMT proteins in pT3 samples, one showed similar significantly altered expression patterns in in vitro organotypic culture models, and two in in vivo Pten-/- model samples. These results suggest that changes in EMT protein expression can be observed in the extraprostatic extension component of locally invasive PCa. The biology of some of these changes in protein expression may be studied in certain in vitro and in vivo PCa models.

Predicting high-grade cancer at ten-core prostate biopsy using four kallikrein markers measured in blood in the ProtecT study

Background:

Many men with elevated prostate-specific antigen (PSA) levels in serum do not have aggressive prostate cancer and undergo unnecessary biopsy. Retrospective studies using cryopreserved serum suggest that four kallikrein markers can predict biopsy outcome.

Methods:

Free, intact and total PSA, and kallikrein-related peptidase 2 were measured in cryopreserved blood from 6129 men with elevated PSA (≥3.0ng/mL) participating in the prospective, randomized trial Prostate Testing for Cancer and Treatment. Marker levels from 4765 men providing anticoagulated plasma were incorporated into statistical models to predict any-grade and high-grade (Gleason score ≥7) prostate cancer at 10-core biopsy. The models were corrected for optimism by 10-fold cross validation and independently validated using markers measured in serum from 1364 men. All statistical tests were two-sided.

Results:

The four kallikreins enhanced prostate cancer detection compared with PSA and age alone. Area under the curve (AUC) for the four kallikreins was 0.719 (95% confidence interval [CI] = 0.704 to 0.734) vs 0.634 (95% CI = 0.617 to 0.651, P < .001) for PSA and age alone for any-grade cancer, and 0.820 (95% CI = 0.802 to 0.838) vs 0.738 (95% CI = 0.716 to 0.761) for high-grade cancer. Using a 6% risk of high-grade cancer as an illustrative cutoff, for 1000 biopsied men with PSA levels of 3.0ng/mL or higher, the model would reduce the need for biopsy in 428 men, detect 119 high-grade cancers, and delay diagnosis of 14 of 133 high-grade cancers. Models exhibited excellent discrimination on independent validation among men with only serum samples available for analysis.

Conclusions:

A statistical model based on kallikrein markers was validated in a large prospective study and reduces unnecessary biopsies while delaying diagnosis of high-grade cancers in few men.

Whole-genome sequencing of bladder cancers reveals somatic CDKN1A mutations and clinicopathological associations with mutation burden

Bladder cancers are a leading cause of death from malignancy. Molecular markers might predict disease progression and behaviour more accurately than the available prognostic factors. Here we use whole-genome sequencing to identify somatic mutations and chromosomal changes in 14 bladder cancers of different grades and stages. As well as detecting the known bladder cancer driver mutations, we report the identification of recurrent protein-inactivating mutations in CDKN1A and FAT1. The former are not mutually exclusive with TP53 mutations or MDM2 amplification, showing that CDKN1A dysfunction is not simply an alternative mechanism for p53 pathway inactivation. We find strong positive associations between higher tumour stage/grade and greater clonal diversity, the number of somatic mutations and the burden of copy number changes. In principle, the identification of sub-clones with greater diversity and/or mutation burden within early-stage or low-grade tumours could identify lesions with a high risk of invasive progression.

A central role for monocytes in Toll-like receptor-mediated activation of the vasculature

There is increasing evidence that activation of inflammatory responses in a variety of tissues is mediated co-operatively by the actions of more than one cell type. In particular, the monocyte has been implicated as a potentially important cell in the initiation of inflammatory responses to Toll-like receptor (TLR)-activating signals. To determine the potential for monocyte-regulated activation of tissue cells to underpin inflammatory responses in the vasculature, we established cocultures of primary human endothelial cells and monocytes and dissected the inflammatory responses of these systems following activation with TLR agonists. We observed that effective activation of inflammatory responses required bidirectional signalling between the monocyte and the tissue cell. Activation of cocultures was dependent on interleukin-1 (IL-1). Although monocyte-mediated IL-1beta production was crucial to the activation of cocultures, TLR specificity to these responses was also provided by the endothelial cells, which served to regulate the signalling of the monocytes. TLR4-induced IL-1beta production by monocytes was increased by TLR4-dependent endothelial activation in coculture, and was associated with increased monocyte CD14 expression. Activation of this inflammatory network also supported the potential for downstream monocyte-dependent T helper type 17 activation. These data define co-operative networks regulating inflammatory responses to TLR agonists, identify points amenable to targeting for the amelioration of vascular inflammation, and offer the potential to modify atherosclerotic plaque instability after a severe infection.

Characterisation of user-defined health status in older adults with intellectual disabilities

BACKGROUND

Older adults with Intellectual Disabilities (ID) have an excess disease burden that standard health assessments are designed to detect. Older adults with ID have a broader concept of health with dimensions of well being in addition to absence of disease in line with the World Health Organization's health definition. We sought to characterise user-defined health status in a sample of older adults with ID.

METHODS

We administered a user-led health assessment to 57 adults with ID aged 40 years and over. Cluster analysis on user-defined health themes of participation, nutrition and hygiene/self-care identified clear separation of participants into a healthier and a less healthy group.

RESULTS

Disease burden (P = 0.002) and medication use (P = 0.003) were greater in the less healthy group. The healthier group were taller (P = 0.005), stronger (P = 0.005) and had better vision (P < 0.001) than the less healthy group. Constipation (P = 0.014), urinary incontinence (P < 0.001) and faecal incontinence (P < 0.001) were commoner in the less healthy group. There were few significant differences between health groups on the majority of standard physical-examination items.

CONCLUSIONS

There is considerable overlap between user-defined health and that assessed by standard instruments. In addition, user-defined health encompasses aspects of physical fitness not captured by traditional disease-based health models.

Mutational analysis of the von Willebrand factor gene in type 1 von Willebrand disease using conformation sensitive gel electrophoresis: a comparison of fluorescent and manual techniques

Two versions of conformation sensitive gel electrophoresis, fluorescent (F-CSGE) and manual (M-CSGE) techniques, were compared for mutation analysis of the von Willebrand factor gene. 56 PCRs were used to amplify all 52 exons of the gene in seven type 1 von Willebrand disease cases, plus a healthy control. One hundred and ninety-two samples were analyzed on each F-CSGE gel, compared with 40 on M-CSGE. 125 amplicons revealed bandshifts using F-CSGE, but only 101 by M-CSGE. Five mutations were detected by both techniques. F-CSGE detected 45 different polymorphisms whereas M-CSGE detected only 39. F-CSGE is high-throughput and more sensitive than M-CSGE.

Functional mapping and identification of novel regulators for the Toll/Interleukin-1 signalling network by transcription expression cloning

Sustained inflammatory responses are central to the development and progression of chronic diseases, including atherosclerosis and rheumatoid arthritis. A large number of stimuli initiate inflammation by acting on Toll-Interleukin-1 related (TIR) domain containing receptors, producing multiple second messengers and thence large scale transcriptional changes. The mechanism by which this activation occurs is complex, and the continuing isolation of novel pathway components, mostly based on sequence similarities and protein-protein interaction studies, suggests that many elements of the TIR-initiated signalling network remain to be identified. Here we use a new technique, allowing identification of components based on function. We report the performance of the screen, our identification of human tribbles as a novel protein family regulating inflammatory signalling networks, and the detection of ten other components with poorly characterized roles in inflammatory signalling pathways. In total, we have identified 28 signalling molecules of diverse molecular mechanism by screening 11% of a cDNA library for the ability to modulation expression of human IL-8, and other molecules remain to be followed up. The results suggest that the number of human genes involved in IL-8 induction pathways exceed 100. The isolation of signalling components by the approach we describe allows detection of new classes of signalling components independent of existing techniques for doing so; it is simple and robust, and constitutes a general method for mapping signal transduction systems controlling gene expression.

Functional mapping of Toll/interleukin-1 signalling networks by expression cloning

Multiple cellular proteins have been identified as participating in Toll/interleukin-1 receptor-mediated inflammatory gene expression. The continuing isolation of novel components, based on sequence similarities, protein-protein interactions and protein purification, suggests that many elements of this signalling network remain to be identified. We report here the development of a high-throughput functional screening platform and its application for the identification of components of inflammatory signalling networks. Our results enable us to estimate that 100-150 gene products are involved in controlling the transcription of the human interleukin 8 gene. The approach, which is simple and robust, constitutes a general method for mapping signal transduction systems and for rapid isolation of a large number of signalling components based on the control of pathways leading to regulation of gene expression.

Geotechnical techniques for the construction of reactive barriers

One of the newest and most promising remediation techniques for the treatment of contaminated groundwater and soil is the reactive barrier wall (commonly known as PRB for permeable reactive barrier or reactive barrier). Although a variety of treatment media and strategies are available, the most common technique is to bury granular iron in a trench so that contaminated groundwater passes through the reactive materials, the contaminants are removed and the water becomes 'clean'. The principal advantages of the technique are the elimination of pumping, mass excavation, off-site disposal, and a very significant reduction in costs. The use of this technology is now becoming better known and implemented. Special construction considerations need to be made when planning the installation of reactive barriers or PRBs to ensure the design life of the installation and to be cost-effective. Geotechnical techniques such as slurry trenching, deep soil mixing, and grouting can be used to simplify and improve the installation of reactive materials relative to conventional trench and fill methods. These techniques make it possible to reduce the hazards to workers during installation, reduce waste and reduce costs for most installations. To date, most PRBs have been installed to shallow depths using construction methods such as open trenching and/or shored excavations. While these methods are usable, they are limited to shallow depths and more disruptive to the site's normal use. Geotechnical techniques are more quickly installed and less disruptive to site activities and thus more effective. Recently, laboratory studies and pilot projects have demonstrated that geotechnical techniques can be used successfully to install reactive barriers. This paper describes the factors that are important in designing a reactive barrier or PRB installation and discusses some of the potential problems and pitfalls that can be avoided with careful planning and the use of geotechnical techniques. Copyright 1999 Elsevier Science B.V.

Validation of the Health of the Nation Outcome Scales

BACKGROUND

The Health of the Nation Outcome Scales (HoNOS) were developed to assess the outcome of severe mental disorders in relation to the Health of the Nation Strategy for England.

AIMS

To validate the HoNOS.

METHOD

One hundred and fifteen patients were assessed by keyworkers using HoNOS, and by research workers using SCAN, SBS, and SRPS, and completing HoNOS in the light of this additional material. These assessments were repeated after 6 weeks.

RESULTS

The performance of HoNOS in the hands of keyworkers was generally poor, in relation both to the research workers' rating of HoNOS and to the criterion instruments. Performance was particularly poor when the change in scores was used as a measure of outcome.

CONCLUSIONS

There are serious problems in using HoNOS as a routine measure of clinical status in busy psychiatric services. Its performance is probably related to the training and experience of keyworkers. Sequential ratings are not a good method for assessing outcome. Managers and planners should be cautious in adopting HoNOS, but it is worthy consideration in developing a suite of locally agreed outcome measures.

The need for psychiatric treatment in the general population: the Camberwell Needs for Care Survey

BACKGROUND

This paper presents the first results of a two-stage psychiatric population survey, which uses a new method of directly evaluating needs for specific psychiatric treatment and the extent to which they have been met.

METHOD

The sample was drawn at random from the population of an area of inner south London with high levels of deprivation. Seven hundred and sixty subjects aged 18-65 completed the GHQ-28. All those scoring > 5 and half of the rest were invited to take part in the second stage, comprising measures of mental state (SCAN), social role performance (SRPS), life events and difficulties (LEDS) and a Treatment Inventory. This information was used to rate the community version of the Needs for Care Assessment (NFCAS-C).

RESULTS

In all, 408 subjects were interviewed in the second stage. The weighted 1 month prevalence of hierarchically ordered ICD-10 psychiatric disorders was 9.8%, the 1 year prevalence 12.3%. The equivalent prevalences for depressive episode were 3.1% and 5.3% respectively, while those for anxiety states were both 2.8%. At interview nearly 10% of the population were identified as having a need for the treatment of a psychiatric condition. This rose to 10.4% if the whole of the preceding year was assessed. Less than half of all potentially meetable needs were met. There was only partial overlap between diagnosis and an adjudged need for treatment.

CONCLUSION

A majority of people with mental health problems do not have proper treatment; given more resources and greater public and medical awareness, most could be treated by family doctors.

Measuring the need for psychiatric treatment in the general population: the community version of the MRC Needs for Care Assessment

The community version of the MRC Needs for Care Assessment Schedule (NFCAS-C) is a new instrument designed for the psychiatric conditions seen in general populations. Its principles are based on the original Needs for Care Assessment, although that was developed for the very different population of those with long-standing mental illness (Brewin et al. 1987). The NFCAS-C is designed to reproduce, in an itemized and systematic manner, the functioning of well-organized primary care and psychiatric services. It is primarily intended for research purposes, in particular, the comparison of treatment needs and services in different populations. In this paper we describe the problems of assessing the need for psychiatric care in general populations and the rationale and development of the instrument, while in its companion we present the results of a reliability study (Lesage et al. 1995).

New Salmonella serotype: Salmonella enteritidis ser. Ordonez

The antigenic formula of a new serotype, Salmonella enteritidis serotype Ordonez, was characterized as (1),13,23,37:y:l,w.