Prof Ian Tomlinson
|Research Area:||Genetics and Genomics|
|Technology Exchange:||Chromosome mapping, Immunohistochemistry, SNP typing, Transcript profiling and Transgenesis|
|Scientific Themes:||Cancer Biology and Genetics & Genomics|
|Keywords:||Cancer genetics, Population genetics, Colorectal, Renal, Mouse models and Pseudo-hypoxia|
- The identification of genes that predispose to colorectal and other cancers
- Functional genetics of colorectal tumorigenesis, with emphasis on the relative importance of selection and genomic instability.
- Genetic changes and mechanisms of tumorigenesis in renal tumours.
|Prof Jenny Taylor||Wellcome Trust Centre for Human Genetics||University of Oxford||United Kingdom|
|Prof Chris Holmes||Wellcome Trust Centre for Human Genetics||University of Oxford||United Kingdom|
|Dr Jean-Baptiste Cazier||Wellcome Trust Centre for Human Genetics||University of Oxford||United Kingdom|
|Prof Simon Leedham||Wellcome Trust Centre for Human Genetics||University of Oxford||United Kingdom|
|Prof David Kerr CBE FMedSci FRCP (RDM)||Nuffield Division of Clinical Laboratory Sciences||University of Oxford||United Kingdom|
|Dr Rachel Midgley (RDM)||Oncology||University of Oxford||United Kingdom|
|Prof Jonathan M Grimes||Structural Biology||University of Oxford||United Kingdom|
Cancers with chromosomal instability (CIN) are held to be aneuploid/polyploid with multiple large-scale gains/deletions, but the processes underlying CIN are unclear and different types of CIN might exist. We investigated colorectal cancer cell lines using array-comparative genomic hybridization (CGH) for copy number changes and single-copy number polymorphism (SNP) microarrays for allelic loss (LOH). Many array-based CGH changes were not found by LOH because they did not cause true reduction-to-homozygosity. Conversely, many regions of SNP-LOH occurred in the absence of copy number change, comprising an average per cell line of 2 chromosomes with complete LOH; 1-2 terminal regions of LOH (mitotic recombination); and 1 interstitial region of LOH. SNP-LOH detected many novel changes, representing possible locations of uncharacterized tumor suppressor loci. Microsatellite unstable (MSI+) lines infrequently showed gains/deletions or whole-chromosome LOH, but their near-diploid karyotypes concealed mitotic recombination frequencies similar to those of MSI- lines. We analyzed p53 and chromosome 18q (SMAD4) in detail, including mutation screening. Almost all MSI- lines showed LOH and/or deletion of p53 and 18q; some near-triploid lines had acquired three independent changes at these loci. We found consistent results in primary colorectal cancers. Overall, the distributions of mitotic recombination and whole-chromosome LOH in the MSI- cell lines differed significantly from random, with some lines having much higher than expected levels of these changes. Moreover, lines with more LOH changes had significantly fewer copy number changes. These data suggest that CIN is not synonymous with copy number change and some cancers have a specific tendency to whole-chromosome deletion and regain or to mitotic recombination. Hide abstract
The nuclear-encoded Krebs cycle enzymes, fumarate hydratase (FH) and succinate dehydrogenase (SDHB, -C and -D), act as tumour suppressors. Germline mutations in FH predispose individuals to leiomyomas and renal cell cancer (HLRCC), whereas mutations in SDH cause paragangliomas and phaeochromocytomas (HPGL). In this study, we have shown that FH-deficient cells and tumours accumulate fumarate and, to a lesser extent, succinate. SDH-deficient tumours principally accumulate succinate. In situ analyses showed that these tumours also have over-expression of hypoxia-inducible factor 1alpha (HIF1alpha), activation of HIF1alphatargets (such as vascular endothelial growth factor) and high microvessel density. We found no evidence of increased reactive oxygen species in our cells. Our data provide in vivo evidence to support the hypothesis that increased succinate and/or fumarate causes stabilization of HIF1alpha a plausible mechanism, inhibition of HIF prolyl hydroxylases, has previously been suggested by in vitro studies. The basic mechanism of tumorigenesis in HPGL and HLRCC is likely to be pseudo-hypoxic drive, just as it is in von Hippel-Lindau syndrome. Hide abstract
BACKGROUND: Germ-line mutations in the base-excision-repair gene MYH have been associated with recessive inheritance of multiple colorectal adenomas. Tumors from affected persons displayed excess somatic transversions of a guanine-cytosine pair to a thymine-adenine pair (G:C-->T:A) in the APC gene. METHODS: We screened for germ-line MYH mutations in 152 patients with multiple (3 to 100) colorectal adenomas and 107 APC-mutation-negative probands with classic familial adenomatous polyposis (>100 adenomas). Subgroups were analyzed for changes in the related genes MTH1 and OGG1. Adenomas were tested for somatic APC mutations. RESULTS: Six patients with multiple adenomas and eight patients with polyposis had biallelic germline MYH variants. Missense and protein-truncating mutations were found, and the spectrums of mutations were very similar in the two groups of patients. In the tumors of carriers of biallelic mutations, all somatic APC mutations were G:C-->T:A transversions. In the group with multiple adenomas, about one third of patients with more than 15 adenomas had biallelic MYH mutations. In the polyposis group, no patient with biallelic MYH mutations had severe disease (>1000 adenomas), but three had extracolonic disease. No clearly pathogenic MTH1 or OGG1 mutations were identified. CONCLUSIONS: Germ-line MYH mutations predispose persons to a recessive phenotype, multiple adenomas, or polyposis coli. For patients with about 15 or more colorectal adenomas--especially if no germ-line APC mutation has been identified and the family history is compatible with recessive inheritance--genetic testing of MYH is indicated for diagnosis and calculation of the level of risk in relatives. Clinical care of patients with biallelic MYH mutations should be similar to that of patients with classic or attenuated familial adenomatous polyposis. Hide abstract
A novel method to study the three dimensional organisation of the genome during DNA replication
Double strand breaks in DNA are the initiating lesion for the translocation events that underlie the genome instability that causes cancer. However, the three dimensional organisation of the genetic material within the nucleus also influences the outcome of translocations because proximity of DNA strands increases the risk of their inappropriate joining. DNA replication has a dramatic effect both on break formation and on 3D nuclear organisation, but its roles in oncogenic translocations are und ...
DNA double-strand break repair in tumour suppression and oncogenesis
DNA double-strand breaks (DSBs) are highly toxic and must usually be accurately repaired to counteract the threat of oncogenic mutations. However some specialist tissues actually rely on mutagenic DSB repair as a means by which genetic material can be transferred between loci to create genetic diversity. To cope with this intrinsic discrepancy in desired DNA repair outcome between different tissues and cellular contexts, a complex regulatory system has evolved to maintain the right equilibrium b ...
Integrative cancer genomics for a next generation sequencing enabled clinic
Next generation sequencing technologies provides a tool for cancer researchers and clinicians to gain insight into the molecular landscape of cancer and recently it has become common research practice to adopt dense, multi-sample strategies whereby tissue is acquired from multiple primary and metastatic sites alongside blood samples. These data can allow the measurement and quantification of the evolution of the disease and treatment monitoring. However, computational methods for analysing such ...
Microenvironmental influence on colorectal cancer development and tumour behaviour
Project proposal. Adult stem cells are present in, and form the foundation of every organ of the body. Stem cell division is critical to maintain homeostasis but is usually restricted to a stem cell niche within a tissue and occurs in a highly regulated fashion. Stringent control of stem cell division and function along with daughter cell differentiation and death (collectively known as cell-fate determination), is achieved by networks of endogenous epithelial and paracrine secreted signalling ...
Statistical Machine Learning for Single Cell Genomics
Single cell genomics has transformed our ability to analyse cellular biology at the molecular level in a high-throughput way. The Yau Group is developing bespoke statistical methodologies to model single cell data including methods to perform dimensionality reduction, unsupervised clustering and pseudo-time assignment. A major theme of our work in this area is the development of distributed representation models coupled with multi-label classification algorithms to characterise complex multi-sca ...