Detailed molecular characterisation of acute myeloid leukaemia with a normal karyotype using targeted DNA capture

This work is licensed under a Creative Commons Attribution 3.0 Unported License.-- et al.Advances in sequencing technologies are giving unprecedented insights into the spectrum of somatic mutations underlying acute myeloid leukaemia with a normal karyotype (AML-NK). It is clear that the prognosis of individual patients is strongly influenced by the combination of mutations in their leukaemia and that many leukaemias are composed of multiple subclones, with differential susceptibilities to treatment. Here, we describe a method, employing targeted capture coupled with next-generation sequencing and tailored bioinformatic analysis, for the simultaneous study of 24 genes recurrently mutated in AML-NK. Mutational analysis was performed using open source software and an in-house script (Mutation Identification and Analysis Software), which identified dominant clone mutations with 100% specificity. In each of seven cases of AML-NK studied, we identified and verified mutations in 2-4 genes in the main leukaemic clone. Additionally, high sequencing depth enabled us to identify putative subclonal mutations and detect leukaemia-specific mutations in DNA from remission marrow. Finally, we used normalised read depths to detect copy number changes and identified and subsequently verified a tandem duplication of exons 2-9 of MLL and at least one deletion involving PTEN. This methodology reliably detects sequence and copy number mutations, and can thus greatly facilitate the classification, clinical research, diagnosis and management of AML-NK.We acknowledge the use of the National Institute of Health Research (NIHR) Biomedical Research Centre, University of Cambridge. We thank Drs J Craig and C Crawley of Cambridge University NHS Hospitals trust for allowing us to approach their patients for samples. GV is funded by a Wellcome Trust Senior Fellowship in Clinical Science. Work in GV’s laboratory is also funded by Leukaemia Lymphoma Research and the Kay Kendal Leukaemia Fund.Peer Reviewe

Correlation of Matrix Metalloproteinases and Tissue Inhibitors of Matrix Metalloproteinase Expression in Ileal Carcinoids, Lymph Nodes and Liver Metastasis with Prognosis and Survival

Purpose: Ileal carcinoids are gut epithelial tumors originating from serotonin-containing enterochromaffin (EC) cells. Therapeutic options for effectively inhibiting the growth and spread of metastatic carcinoids are still limited. We aimed to identify the role of matrix metalloproteinases (MMPs) and their endogenous tissue inhibitors (TIMPs) during tumor development and metastasis. Patients and Methods: Tissue samples were obtained from surgically treated patients. Expression of the EC-cell marker, vesicular monoamine transporter-1 (VMAT-1), was used to verify ileal carcinoids. We investigated the differential expression of MMP-2, 7, 9, 11, and 13 and their endogenous inhibitors (TIMP-1, 2, and 3) by quantitative real-time RT-PCR in 25 primary tumors, their corresponding lymph node metastases and/or liver metastases and matched normal mucosa. Results: Significantly increased expression of VMAT-1, MMP-2, MMP-11, TIMP-1 and TIMP-3 was determined by quantitative RT-PCR in EC-cell carcinoids compared to normal intestinal mucosa (p < 0.05). In contrast, MMP-2 and MMP-9 as well as TIMP-1, TIMP-2, and TIMP-3 expression in primary tumors of patients with liver metastases (M1) was significantly lower than in patients lacking liver metastases (M0). EC-cell tumors were significantly larger in the M1 group of tumors, while VMAT-1 expression was significantly decreased. We found an inverse correlation between tumor size and prognosis. Univariate analysis further revealed that decreased expression of VMAT-1, MMP-2 and TIMP-3 in primary tumors was significantly associated with a reduced survival time of the patients. Conclusion: Our data reveal that MMP-2 and TIMP-3 expression together with VMAT-1 expression are of potential prognostic and clinical value in ileal carcinoids. Copyright (C) 2008 S. Karger AG, Base

A genetic progression model of BrafV600E-induced intestinal tumorigenesis reveals targets for therapeutic intervention

Rad, R., Cadiñanos, J., Rad, L., Varela, I., Strong, A., Kriegl, L., Constantino-Casas, F., Eser, S., Hieber, M., Seidler, B., Price, S., Fraga, M., Calvanese, V., Hoffman, G., Ponstingl, H., Schneider, G., Yusa, K., Grove, C., Schmid, R.M., Wang, W., Vassiliou, G., Kirchner, T., McDermott, U., Liu, P., Saur, D., Bradley, A

Bacterial virulence factors and human genetic factors contributing to the development of severe histological alterations of the gastric mucosa during Helicobacter pylori infection

Die Infektion mit H. pylori ist die Hauptursache für die Entstehung des Magenkarzinoms. Da jedoch nur ein kleiner Teil der infizierten Patienten ein Karzinom entwickelt, ist es von außerordentlicher Bedeutung, bakterielle Faktoren und genetische Risikofaktoren des Menschen zu identifizieren, die mit der Krebsentstehung assoziiert sind. In der vorliegenden Studie wurde gezeigt, daß die bakteriellen Virulenzfaktoren CagA und VacA und humane Interleukin-1 Polymorphismen synergistisch auf die Entstehung präkanzeröser Läsionen des Magens wirken. Das Vorhandensein dieser Faktoren ist mit einem bis zu 25fach erhöhten Risiko zur Entwicklung von schweren histologischen Veränderungen der Magenmukosa assoziiert. Desweiteren wurde der Einfluß des bakteriellen Adhäsins BabA auf die Kolonisation, Inflammation und Karzinogenese untersucht. Es wurde sowohl die Assoziation des Adhärenzfaktors mit der gastralen Pathologie gezeigt, wie auch der Mechanismus der BabA vermittelten Pathogenese aufgedeckt.Helicobacter pylori Infection is the main cause for the development of gastric cancer. As only a small proportion of infected patients develops cancer, it is important to identify bacterial factors and host genetic factors associated with cancer develpment. In the current study we show that the bacterial virulence factors CagA and VacA and human Interleukin-1 Polymorphisms act synergistically on the development of precancerous stomach lesions. Presence of these factors is associated with an up to 25 fold increased risk to develop severe histological changes of the gastric mucosa. Furthermore, we investigated the influence of the bacterial adhesin BabA on colonisation, inflammation and carcinogenesis. We show here the associattion of the adherence factor with gastric pathology and describe the mechanisms of BabA mediated pathogenesis

Disentangling PTEN-cooperating tumor suppressor gene networks in cancer.

We have recently performed a whole-body, genome-wide screen in mice using a single-copy inactivating transposon for the identification of Pten (phosphatase and tensin homolog)-cooperating tumor suppressor genes (TSGs). We identified known and putative TSGs in multiple cancer types and validated the functional and clinical relevance of several promising candidates for human prostate cancer