Center for Molecular Pathology

London, United Kingdom

Center for Molecular Pathology

London, United Kingdom
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Frampton M.,Center for Molecular Pathology | Houlston R.S.,Institute of Cancer Research
Genetics in Medicine | Year: 2017

Purpose:This study investigated the utility of modeling modifiable lifestyle risk factors in addition to genetic variation in colorectal cancer (CRC) screening/prevention.Methods:We derived a polygenic risk score for CRC susceptibility variants in combination with the established nongenetic risk factors of inflammatory bowel disease (IBD), adiposity, alcohol, red meat, fruit, vegetables, smoking, physical activity, and aspirin. We used the 37 known risk variants and 50 and 100% of all risk variants as calculated from a heritability estimate. We derived absolute risk from UK population age structure, incidence, and mortality rate data.Results:Taking into account all risk factors (known variants), 42.2% of 55-to 59-year-old men with CRC have a risk at least as high as that of an average 60-year-old, the minimum eligible age for the UK NHS National Bowel Cancer Screening Program. If the male population is stratified by known variants and IBD status, then risk-difference estimates imply that for 10,000 50-year-old men in the 99th percentile, 760 cases could be prevented over a 25-year period through the modifiable risk factors, but in the lowest percentile, only 90 could be prevented.Conclusion:CRC screening and prevention centered on modifiable risk factors could be optimized if targeted at individuals at higher polygenic risk. © American College of Medical Genetics and Genomics.

Janols H.,Center for Molecular Pathology | Bergenfelz C.,Center for Molecular Pathology | Allaoui R.,Center for Molecular Pathology | Larsson A.-M.,Lund University | And 3 more authors.
Journal of Leukocyte Biology | Year: 2014

The causative microorganisms dictate the type of MDSC generated in sepsis patients, and a large proportion of PMN-MDSCs in gram-positive sepsis includes immunosuppressive myeloid blasts. MDSCs constitute a heterogeneous population of immature myeloid cells that potently suppress immune responses. They were identified originally in cancer patients and have since been reported to occur also in chronic inflammation, autoimmunity, and even bacterial infections. Human MDSCs are commonly divided into Mo- MDSCs and granulocytic (PMN-MDSCs) subtypes. To what extent the bona fide cancer MDSCs are representative of the proposed MDSCs found in other diseases is not well known. PMN-MDSCs have been found previously to be enriched among LDGs in density gradientcentrifuged blood. In this study, we analyzed potential MDSCs in sepsis patients with different causative microorganisms, using total peripheral blood compared with density gradient-centrifuged blood. We found a high frequency of typical CD14+HLA-DRlow Mo-MDSCs in all sepsis patients, whereas the typical PMN-MDSCs, as well as a prominent CD14low PMN-MDSC-like population, appeared preferentially in gram-positive cases. The CD14low PMN-MDSC variant was demonstrated to suppress T cell proliferation in vitro via a ROS-dependent mechanism, to display an increased IL-10:TNF-α ratio, and to present with signs of immaturity: blast morphology and low cytokine levels. We conclude that a spectrum of cells with MDSC features is enriched in sepsis and that the microbial origin of sepsis contributes to the substantial interindividual patient variation in the MDSC pattern. © Society for Leukocyte Biology.

Wong N.A.C.S.,Royal Infirmary | Gonzalez D.,Center for Molecular Pathology | Salto-Tellez M.,Queen's University of Belfast | Butler R.,University of Wales | And 6 more authors.
Journal of Clinical Pathology | Year: 2014

Analysis of colorectal carcinoma (CRC) tissue for KRAS codon 12 or 13 mutations to guide use of anti-epidermal growth factor receptor (EGFR) therapy is now considered mandatory in the UK. The scope of this practice has been recently extended because of data indicating that NRAS mutations and additional KRAS mutations also predict for poor response to anti-EGFR therapy. The following document provides guidance on RAS (i.e., KRAS and NRAS) testing of CRC tissue in the setting of personalised medicine within the UK and particularly within the NHS. This guidance covers issues related to case selection, preanalytical aspects, analysis and interpretation of such RAS testing.

Deans Z.C.,Royal Infirmary | Wallace A.,Saint Marys Hospital | O'Sullivan B.,Queen Elizabeth Hospital | Purvis A.,Royal Infirmary | And 3 more authors.
Journal of Clinical Pathology | Year: 2014

The availability of BRAF inhibitors has given metastatic melanoma patients an effective new treatment choice and molecular testing to determine the presence or absence of a BRAF codon 600 mutation is pivotal in the clinical management of these patients. This molecular test must be performed accurately and appropriately to ensure that the patient receives the most suitable treatment in a timely manner. Laboratories have introduced such testing; however, some experience low sample throughput making it critical that an external quality assurance programme is available to help promote a high standard of testing, reporting and provide an educational aspect for BRAF molecular testing. Laboratories took part in three rounds of external quality assessment (EQA) during a 12-month period giving participants a measure of the accuracy of genotyping, clinical interpretation of the result and experience in testing a range of different samples. Formalin fixed paraffin embedded tissue sections from malignant melanoma patients were distributed to participants for BRAF molecular testing. The standard of testing was generally high but distribution of a mutation other than the most common, p.(Val600Glu), highlighted concerns with detection or reporting of the presence of rarer mutations. The main issues raised in the interpretation of the results were the importance of clear unambiguous interpretation of the result tailored to the patient and the understanding that the treatment is different from that given to other stratified medicine programmes. The variability in reporting and wide range of methodologies used indicate a continuing need for EQA in this field.

PubMed | Sloan Kettering Cancer Center, Caen University Hospital Center, Munich Leukemia Laboratory, Royal Marsden Hospital and 7 more.
Type: Journal Article | Journal: Blood | Year: 2015

Hairy cell leukemia (HCL) is marked by near 100% mutational frequency of BRAFV600E mutations. Recurrent cooperating genetic events that may contribute to HCL pathogenesis or affect the clinical course of HCL are currently not described. Therefore, we performed whole exome sequencing to explore the mutational landscape of purine analog refractory HCL. In addition to the disease-defining BRAFV600E mutations, we identified mutations in EZH2, ARID1A, and recurrent inactivating mutations of the cell cycle inhibitor CDKN1B (p27). Targeted deep sequencing of CDKN1B in a larger cohort of HCL patients identify deleterious CDKN1B mutations in 16% of patients with HCL (n = 13 of 81). In 11 of 13 patients the CDKN1B mutation was clonal, implying an early role of CDKN1B mutations in the pathogenesis of HCL. CDKN1B mutations were not found to impact clinical characteristics or outcome in this cohort. These data identify HCL as having the highest frequency of CDKN1B mutations among cancers and identify CDNK1B as the second most common mutated gene in HCL. Moreover, given the known function of CDNK1B, these data suggest a novel role for alterations in regulation of cell cycle and senescence in HCL with CDKN1B mutations.

Bunting M.D.,Center for Molecular Pathology | Bunting M.D.,QIMR Berghofer Medical Research Institute | Comerford I.,Center for Molecular Pathology | Kara E.E.,Center for Molecular Pathology | And 2 more authors.
Immunology and Cell Biology | Year: 2014

T-cell selection and development occurs as precursor cells journey through the thymus and interact with stromal cells residing in distinct microenvironments. Although the chemokines CCL19, CCL21, CCL25 and CXCL12 are known to have major roles in intrathymic migration of thymocytes and thymocyte precursors, the significance of other chemokines such as CCL20, which is also expressed in the thymus, is unknown. This is of particular interest given that the thymus is the location of development of the natural regulatory T-cell (nTreg) population and that the CCL20 receptor CCR6 has an important role in peripheral tolerance via control of Treg cell migration. However, whether the CCL20/CCR6 axis has a role in the formation or migration of nTregs in the thymus is unknown. In this study, we addressed this by analyzing expression of CCR6/CCL20 within the thymus and assessing their role in thymocyte development using Ccr6-/- mice. CCL20 is predominately expressed in the thymic medulla and CCR6 expression is restricted to nTregs and a subset of early thymocyte progenitor double-negative 1 (DN1) cells (CD4-CD8 -CD25-CD44+CD117+). Ex vivo chemotaxis assays indicated that these two subsets were apparently the sole subsets of thymocytes responsive to CCL20. The data indicate that nTreg frequencies and localization are unperturbed by deletion of Ccr6. However, in Ccr6-/- thymi, reduced frequencies of DN2 and DN3 cells, the thymocyte progenitor subsets that follow the DN1 stage, were apparent. Together, these data indicate that CCR6 has a supplementary role in coordination of early thymocyte precursor migration events important for normal subsequent thymocyte precursor development, but is not required for normal nTreg development. © 2014 Australasian Society for Immunology Inc. All rights reserved.

Salto-Tellez M.,Queen's University of Belfast | Gonzalez De Castro D.,Center for Molecular Pathology
Journal of Pathology | Year: 2014

Next-generation sequencing (NGS) is beginning to show its full potential for diagnostic and therapeutic applications. In particular, it is enunciating its capacity to contribute to a molecular taxonomy of cancer, to be used as a standard approach for diagnostic mutation detection, and to open new treatment options that are not exclusively organ-specific. If this is the case, how much validation is necessary and what should be the validation strategy, when bringing NGS into the diagnostic/clinical practice? This validation strategy should address key issues such as: what is the overall extent of the validation? Should essential indicators of test performance such as sensitivity of specificity be calculated for every target or sample type? Should bioinformatic interpretation approaches be validated with the same rigour? What is a competitive clinical turnaround time for a NGS-based test, and when does it become a cost-effective testing proposition? While we address these and other related topics in this commentary, we also suggest that a single set of international guidelines for the validation and use of NGS technology in routine diagnostics may allow us all to make a much more effective use of resources. Copyright © 2014 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. Copyright © 2014 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Piccirillo S.G.M.,University of Cambridge | Colman S.,Institute of Cancer Research | Potter N.E.,Institute of Cancer Research | Van Delft F.W.,Institute of Cancer Research | And 6 more authors.
Stem Cell Reports | Year: 2015

Glioblastoma (GBM) is a lethal malignancy whose clinical intransigence has been linked to extensive intraclonal genetic and phenotypic diversity and the common emergence of therapeutic resistance. This interpretation embodies the implicit assumption that cancer stem cells or tumor-propagating cells are themselves genetically and functionally diverse. To test this, we screened primary GBM tumors by SNP array to identify copy number alterations (a minimum of three) that could be visualized in single cells by multicolor fluorescence in situ hybridization. Interrogation of neurosphere-derived cells (from four patients) and cells derived from secondary transplants of these same cells in NOD-SCID mice allowed us to infer the clonal and phylogenetic architectures. Whole-exome sequencing and single-cell genetic analysis in one case revealed a more complex clonal structure. This proof-of-principle experiment revealed that subclones in each GBM had variable regenerative or stem cell activity, and highlighted genetic alterations associated with more competitive propagating activity in vivo. © 2015 The Authors.

PubMed | Center for Molecular Pathology
Type: Journal Article | Journal: Journal of clinical oncology : official journal of the American Society of Clinical Oncology | Year: 2016

22081 Background: We investigated the relationship between the two hypoxia-inducible-factor- (HIF-) subunits in invasive breast cancer in vivo and their specific correlations to clinicopathological parameters, survival, and VEGF expression.We first conducted immunohistochemical analyses of HIF-1, HIF-2, and VEGF expression in tissue microarrays with tumours from 512 consecutive breast cancer patients with long-term follow-up. HIF-1 and HIF-2 and their impact on survival were then verified in another cohort of 179 patients. HIF- protein andHIF-and VEGFmRNA levels after hypoxic induction and knock-down experiments in cultured breast cancer cell lines were studied by Western blot and Q-PCR techniques.We found no correlation between HIF-1 and HIF-2 expression and HIF- subtype specific correlations to clinicopathological parameters and VEGF. HIF-2 was an independent prognostic factor whereas HIF-1 exhibited variable, non-significant correlation to survival. Culture for 4 or 24 hours at 21%, 5%, and 1% oxygen levels resulted in varying HIF- protein levels, thereby verifying hypoxia level and time dependent induction of HIF-1 and HIF-2. Knock-down experiments showed a subtype specific, time dependent utilization of the two transcription factors in hypoxia induced VEGF expression.Our in vitro and in vivo results show evidence for differential regulation and utilization of the two HIF- subunits and that high protein expression associates to adverse outcome and distant metastasis in breast cancer. No significant financial relationships to disclose.

PubMed | Cancer Research UK Research Institute, University Utrecht, Center for Molecular Pathology and Leeds Institute of Cancer and Pathology
Type: | Journal: Nature communications | Year: 2016

Testicular germ cell tumour (TGCT) is the most common cancer in young men. Here we sought to identify risk factors for TGCT by performing whole-exome sequencing on 328 TGCT cases from 153 families, 634 sporadic TGCT cases and 1,644 controls. We search for genes that are recurrently affected by rare variants (minor allele frequency <0.01) with potentially damaging effects and evidence of segregation in families. A total of 8.7% of TGCT families carry rare disruptive mutations in the cilia-microtubule genes (CMG) as compared with 0.5% of controls (P=2.1 10

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