Experimental cancer genetics

The Experimental cancer genetics team aims to understand the fundamental genetic mechanisms by which cancers develop.

Their approach is to generate changes in the DNA sequence of mice (mutations) using a variety of techniques and to characterise the consequences of these sequence changes on cancer development. From this type of analysis, and in collaboration with several international research groups, the team is attempting to map cancer pathways, generating information that will be crucial for understanding the mechanisms of cancer formation in man. In addition, the team’s activities yield valuable genetic information on other important medical conditions such as infertility and fetal development.

The team is also involved in applying new-technology sequencing to decode the genomes of different mouse strains used widely in research laboratories throughout the world.

[Anne Weston, Wellcome Images]

Background

The genetic basis of cancer

Cancer occurs when there is an accumulation of genetic damage that confers a selective advantage on a cell, allowing it to evade normal growth control processes. Uncontrolled growth and reproduction of these damaged cells ultimately results in tumour formation. While some of the key events at the molecular level that are involved in cancer formation are known, there is still much work to be done to identify other genetic changes important in cancer formation that could represent new diagnostic markers or targets for new anti-cancer medicines.

Research

Our aims

The Experimental cancer genetics team's primary interest is in identifying and characterising the genes involved in the development of cancer in the mouse, with a view to extending this knowledge to the understanding of cancer development in man.

Figure 1. Stained sections of tumour tissue from the Rassf1a knockout mice.

Figure 1. Stained sections of tumour tissue from the Rassf1a knockout mice.

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Our approach

Our approach is to mimic in the mouse the successive accumulation of genetic alterations (mutations) that are known to occur in the progression of human cancer.

We introduce a series of changes into mouse DNA using a technique called 'insertional mutagenesis'. The word 'mutagenesis' means 'generating mutations', and the 'insertional' part means that we do this by inserting small segments of DNA into the mouse genome. This process is random. The DNA insertion may disrupt a gene and render it non-functional, or it may function to activate gene expression.

This research is known as a forward genetic screen because we do not know in advance which genes will be mutated by the insertional mutagen so essentially we randomly mutate the genome and assess how these mutations influence cancer formation later on as the animal ages. By performing these studies on a large scale we hope to be able to map cancer pathways.

There are several technologies that we use for insertional mutagenesis in the mouse. These are based on using either retroviruses or a mobile genetic element called a 'transposon'. Transposons and viruses target different parts of the genome and therefore mutate different sets of genes. Transposons can be used in a range of tissues, while the use of viruses for insertional mutagenesis is largely restricted to the blood system and mammary gland.

We are particularly interested in studying a tumour suppressor gene called Rassf1a that we have shown to play a role in many different types of cancer, an observation that supports the belief that this gene is an important tumour suppressor gene in humans. We are also interested in cancers of the pancreas, bowel and breast.

While our focus is on the identification and characterisation of genes involved in cancer formation, some of the mouse models we have developed show up problems in areas not related to cancer. At present members of the group are characterising knockout mice that have problems related to infertility, foetal overgrowth and developmental defects.

Internal collaborations

We utilise the Sanger Institute's strengths in DNA sequencing and bioinformatics as part of our work. We also collaborate with the Genome informatics group; the Cancer genome project; the Vertebrate development and genetics group; and with the Mouse genomics group.

External collaborations

Some of these experiments have been performed in collaboration with Anton Bern, Jos Jonkers and Maarten van Lohuizen from the Netherlands Cancer Institute (NKI) in The Netherlands, Lara Collier and David Largaespada from the University of Minnesota, USA, and David Tuveson, Nikki March and Doug Winton at the Cambridge Cancer Research Institute.

Resource development projects

We are currently sequencing the genomes of several key mouse strains as part of the Mouse Genomes Project.

Training and collaboration

The research environment of the group offers opportunities for training and collaboration for individuals with an interest in mouse genetics, bioinformatics and cancer genetics. PhD students and post doctoral research scientists are encouraged to develop independent projects in an active and supportive research environment. PhD training positions are organised by the Sanger Institute PhD programme and candidates interested in post-doctoral and research assistant positions can contact the laboratory directly. Our laboratory has interactions with other groups in the Sanger Institute, in particular Ensembl; Sequencing; Informatics; Mouse genomics; and the Cancer genome project.

Grant support

The work of this team is supported by grants from The Wellcome Trust and Cancer Research UK.

Selected publications

  • Deficiency for the ubiquitin ligase UBE3B in a blepharophimosis-ptosis-intellectual-disability syndrome.

    Basel-Vanagaite L, Dallapiccola B, Ramirez-Solis R, Segref A, Thiele H, Edwards A, Arends MJ, Miró X, White JK, Désir J, Abramowicz M, Dentici ML, Lepri F, Hofmann K, Har-Zahav A, Ryder E, Karp NA, Estabel J, Gerdin AK, Podrini C, Ingham NJ, Altmüller J, Nürnberg G, Frommolt P, Abdelhak S, Pasmanik-Chor M, Konen O, Kelley RI, Shohat M, Nürnberg P, Flint J, Steel KP, Hoppe T, Kubisch C, Adams DJ and Borck G

    American journal of human genetics 2012;91;6;998-1010

  • Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes.

    Biankin AV, Waddell N, Kassahn KS, Gingras MC, Muthuswamy LB, Johns AL, Miller DK, Wilson PJ, Patch AM, Wu J, Chang DK, Cowley MJ, Gardiner BB, Song S, Harliwong I, Idrisoglu S, Nourse C, Nourbakhsh E, Manning S, Wani S, Gongora M, Pajic M, Scarlett CJ, Gill AJ, Pinho AV, Rooman I, Anderson M, Holmes O, Leonard C, Taylor D, Wood S, Xu Q, Nones K, Fink JL, Christ A, Bruxner T, Cloonan N, Kolle G, Newell F, Pinese M, Mead RS, Humphris JL, Kaplan W, Jones MD, Colvin EK, Nagrial AM, Humphrey ES, Chou A, Chin VT, Chantrill LA, Mawson A, Samra JS, Kench JG, Lovell JA, Daly RJ, Merrett ND, Toon C, Epari K, Nguyen NQ, Barbour A, Zeps N, Australian Pancreatic Cancer Genome Initiative, Kakkar N, Zhao F, Wu YQ, Wang M, Muzny DM, Fisher WE, Brunicardi FC, Hodges SE, Reid JG, Drummond J, Chang K, Han Y, Lewis LR, Dinh H, Buhay CJ, Beck T, Timms L, Sam M, Begley K, Brown A, Pai D, Panchal A, Buchner N, De Borja R, Denroche RE, Yung CK, Serra S, Onetto N, Mukhopadhyay D, Tsao MS, Shaw PA, Petersen GM, Gallinger S, Hruban RH, Maitra A, Iacobuzio-Donahue CA, Schulick RD, Wolfgang CL, Morgan RA, Lawlor RT, Capelli P, Corbo V, Scardoni M, Tortora G, Tempero MA, Mann KM, Jenkins NA, Perez-Mancera PA, Adams DJ, Largaespada DA, Wessels LF, Rust AG, Stein LD, Tuveson DA, Copeland NG, Musgrove EA, Scarpa A, Eshleman JR, Hudson TJ, Sutherland RL, Wheeler DA, Pearson JV, McPherson JD, Gibbs RA and Grimmond SM

    Nature 2012;491;7424;399-405

  • The deubiquitinase USP9X suppresses pancreatic ductal adenocarcinoma.

    Pérez-Mancera PA, Rust AG, van der Weyden L, Kristiansen G, Li A, Sarver AL, Silverstein KA, Grützmann R, Aust D, Rümmele P, Knösel T, Herd C, Stemple DL, Kettleborough R, Brosnan JA, Li A, Morgan R, Knight S, Yu J, Stegeman S, Collier LS, ten Hoeve JJ, de Ridder J, Klein AP, Goggins M, Hruban RH, Chang DK, Biankin AV, Grimmond SM, Australian Pancreatic Cancer Genome Initiative, Wessels LF, Wood SA, Iacobuzio-Donahue CA, Pilarsky C, Largaespada DA, Adams DJ and Tuveson DA

    Nature 2012;486;7402;266-70

  • IFITM3 restricts the morbidity and mortality associated with influenza.

    Everitt AR, Clare S, Pertel T, John SP, Wash RS, Smith SE, Chin CR, Feeley EM, Sims JS, Adams DJ, Wise HM, Kane L, Goulding D, Digard P, Anttila V, Baillie JK, Walsh TS, Hume DA, Palotie A, Xue Y, Colonna V, Tyler-Smith C, Dunning J, Gordon SB, GenISIS Investigators, MOSAIC Investigators, Smyth RL, Openshaw PJ, Dougan G, Brass AL and Kellam P

    Nature 2012;484;7395;519-23

  • Disruption of mouse Cenpj, a regulator of centriole biogenesis, phenocopies Seckel syndrome.

    McIntyre RE, Lakshminarasimhan Chavali P, Ismail O, Carragher DM, Sanchez-Andrade G, Forment JV, Fu B, Del Castillo Velasco-Herrera M, Edwards A, van der Weyden L, Yang F, Sanger Mouse Genetics Project, Ramirez-Solis R, Estabel J, Gallagher FA, Logan DW, Arends MJ, Tsang SH, Mahajan VB, Scudamore CL, White JK, Jackson SP, Gergely F and Adams DJ

    PLoS genetics 2012;8;11;e1003022

  • Insertional mutagenesis identifies multiple networks of cooperating genes driving intestinal tumorigenesis.

    March HN, Rust AG, Wright NA, ten Hoeve J, de Ridder J, Eldridge M, van der Weyden L, Berns A, Gadiot J, Uren A, Kemp R, Arends MJ, Wessels LF, Winton DJ and Adams DJ

    Nature genetics 2011;43;12;1202-9

  • In vivo identification of tumor- suppressive PTEN ceRNAs in an oncogenic BRAF-induced mouse model of melanoma.

    Karreth FA, Tay Y, Perna D, Ala U, Tan SM, Rust AG, DeNicola G, Webster KA, Weiss D, Perez-Mancera PA, Krauthammer M, Halaban R, Provero P, Adams DJ, Tuveson DA and Pandolfi PP

    Cell 2011;147;2;382-95

  • Mouse genomic variation and its effect on phenotypes and gene regulation.

    Keane TM, Goodstadt L, Danecek P, White MA, Wong K, Yalcin B, Heger A, Agam A, Slater G, Goodson M, Furlotte NA, Eskin E, Nellåker C, Whitley H, Cleak J, Janowitz D, Hernandez-Pliego P, Edwards A, Belgard TG, Oliver PL, McIntyre RE, Bhomra A, Nicod J, Gan X, Yuan W, van der Weyden L, Steward CA, Bala S, Stalker J, Mott R, Durbin R, Jackson IJ, Czechanski A, Guerra-Assunção JA, Donahue LR, Reinholdt LG, Payseur BA, Ponting CP, Birney E, Flint J and Adams DJ

    Nature 2011;477;7364;289-94

  • Sequence-based characterization of structural variation in the mouse genome.

    Yalcin B, Wong K, Agam A, Goodson M, Keane TM, Gan X, Nellåker C, Goodstadt L, Nicod J, Bhomra A, Hernandez-Pliego P, Whitley H, Cleak J, Dutton R, Janowitz D, Mott R, Adams DJ and Flint J

    Nature 2011;477;7364;326-9

  • A role for cohesin in T-cell-receptor rearrangement and thymocyte differentiation.

    Seitan VC, Hao B, Tachibana-Konwalski K, Lavagnolli T, Mira-Bontenbal H, Brown KE, Teng G, Carroll T, Terry A, Horan K, Marks H, Adams DJ, Schatz DG, Aragon L, Fisher AG, Krangel MS, Nasmyth K and Merkenschlager M

    Nature 2011;476;7361;467-71

  • Modeling the evolution of ETV6-RUNX1-induced B-cell precursor acute lymphoblastic leukemia in mice.

    van der Weyden L, Giotopoulos G, Rust AG, Matheson LS, van Delft FW, Kong J, Corcoran AE, Greaves MF, Mullighan CG, Huntly BJ and Adams DJ

    Blood 2011;118;4;1041-51

  • Disruption of mouse Slx4, a regulator of structure-specific nucleases, phenocopies Fanconi anemia.

    Crossan GP, van der Weyden L, Rosado IV, Langevin F, Gaillard PH, McIntyre RE, Sanger Mouse Genetics Project, Gallagher F, Kettunen MI, Lewis DY, Brindle K, Arends MJ, Adams DJ and Patel KJ

    Nature genetics 2011;43;2;147-52

  • Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma.

    Varela I, Tarpey P, Raine K, Huang D, Ong CK, Stephens P, Davies H, Jones D, Lin ML, Teague J, Bignell G, Butler A, Cho J, Dalgliesh GL, Galappaththige D, Greenman C, Hardy C, Jia M, Latimer C, Lau KW, Marshall J, McLaren S, Menzies A, Mudie L, Stebbings L, Largaespada DA, Wessels LF, Richard S, Kahnoski RJ, Anema J, Tuveson DA, Perez-Mancera PA, Mustonen V, Fischer A, Adams DJ, Rust A, Chan-on W, Subimerb C, Dykema K, Furge K, Campbell PJ, Teh BT, Stratton MR and Futreal PA

    Nature 2011;469;7331;539-42

  • Rec8-containing cohesin maintains bivalents without turnover during the growing phase of mouse oocytes.

    Tachibana-Konwalski K, Godwin J, van der Weyden L, Champion L, Kudo NR, Adams DJ and Nasmyth K

    Genes & development 2010;24;22;2505-16

  • PARK2 deletions occur frequently in sporadic colorectal cancer and accelerate adenoma development in Apc mutant mice.

    Poulogiannis G, McIntyre RE, Dimitriadi M, Apps JR, Wilson CH, Ichimura K, Luo F, Cantley LC, Wyllie AH, Adams DJ and Arends MJ

    Proceedings of the National Academy of Sciences of the United States of America 2010;107;34;15145-50

  • Novel candidate cancer genes identified by a large-scale cross-species comparative oncogenomics approach.

    Mattison J, Kool J, Uren AG, de Ridder J, Wessels L, Jonkers J, Bignell GR, Butler A, Rust AG, Brosch M, Wilson CH, van der Weyden L, Largaespada DA, Stratton MR, Futreal PA, van Lohuizen M, Berns A, Collier LS, Hubbard T and Adams DJ

    Cancer research 2010;70;3;883-95

  • Somatic structural rearrangements in genetically engineered mouse mammary tumors.

    Varela I, Klijn C, Stephens PJ, Mudie LJ, Stebbings L, Galappaththige D, van der Gulden H, Schut E, Klarenbeek S, Campbell PJ, Wessels LF, Stratton MR, Jonkers J, Futreal PA and Adams DJ

    Genome biology 2010;11;10;R100

  • The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus.

    Brass AL, Huang IC, Benita Y, John SP, Krishnan MN, Feeley EM, Ryan BJ, Weyer JL, van der Weyden L, Fikrig E, Adams DJ, Xavier RJ, Farzan M and Elledge SJ

    Cell 2009;139;7;1243-54

  • Discovery of candidate disease genes in ENU-induced mouse mutants by large-scale sequencing, including a splice-site mutation in nucleoredoxin.

    Boles MK, Wilkinson BM, Wilming LG, Liu B, Probst FJ, Harrow J, Grafham D, Hentges KE, Woodward LP, Maxwell A, Mitchell K, Risley MD, Johnson R, Hirschi K, Lupski JR, Funato Y, Miki H, Marin-Garcia P, Matthews L, Coffey AJ, Parker A, Hubbard TJ, Rogers J, Bradley A, Adams DJ and Justice MJ

    PLoS genetics 2009;5;12;e1000759

  • Normal germ line establishment in mice carrying a deletion of the Ifitm/Fragilis gene family cluster.

    Lange UC, Adams DJ, Lee C, Barton S, Schneider R, Bradley A and Surani MA

    Molecular and cellular biology 2008;28;15;4688-96

  • Loss of Rassf1a cooperates with Apc(Min) to accelerate intestinal tumourigenesis.

    van der Weyden L, Arends MJ, Dovey OM, Harrison HL, Lefebvre G, Conte N, Gergely FV, Bradley A and Adams DJ

    Oncogene 2008;27;32;4503-8

  • Large-scale mutagenesis in p19(ARF)- and p53-deficient mice identifies cancer genes and their collaborative networks.

    Uren AG, Kool J, Matentzoglu K, de Ridder J, Mattison J, van Uitert M, Lagcher W, Sie D, Tanger E, Cox T, Reinders M, Hubbard TJ, Rogers J, Jonkers J, Wessels L, Adams DJ, van Lohuizen M and Berns A

    Cell 2008;133;4;727-41

  • The Ras-association domain family (RASSF) members and their role in human tumourigenesis.

    van der Weyden L and Adams DJ

    Biochimica et biophysica acta 2007;1776;1;58-85

  • Renin enhancer is critical for control of renin gene expression and cardiovascular function.

    Adams DJ, Head GA, Markus MA, Lovicu FJ, van der Weyden L, Köntgen F, Arends MJ, Thiru S, Mayorov DN and Morris BJ

    The Journal of biological chemistry 2006;281;42;31753-61

  • Functional knockout of the matrilin-3 gene causes premature chondrocyte maturation to hypertrophy and increases bone mineral density and osteoarthritis.

    van der Weyden L, Wei L, Luo J, Yang X, Birk DE, Adams DJ, Bradley A and Chen Q

    The American journal of pathology 2006;169;2;515-27

  • TranscriptSNPView: a genome-wide catalog of mouse coding variation.

    Cunningham F, Rios D, Griffiths M, Smith J, Ning Z, Cox T, Flicek P, Marin-Garcin P, Herrero J, Rogers J, van der Weyden L, Bradley A, Birney E and Adams DJ

    Nature genetics 2006;38;8;853

  • Geminin is essential to prevent endoreduplication and to form pluripotent cells during mammalian development.

    Gonzalez MA, Tachibana KE, Adams DJ, van der Weyden L, Hemberger M, Coleman N, Bradley A and Laskey RA

    Genes & development 2006;20;14;1880-4

  • Loss of TSLC1 causes male infertility due to a defect at the spermatid stage of spermatogenesis.

    van der Weyden L, Arends MJ, Chausiaux OE, Ellis PJ, Lange UC, Surani MA, Affara N, Murakami Y, Adams DJ and Bradley A

    Molecular and cellular biology 2006;26;9;3595-609

  • DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage.

    Zody MC, Garber M, Adams DJ, Sharpe T, Harrow J, Lupski JR, Nicholson C, Searle SM, Wilming L, Young SK, Abouelleil A, Allen NR, Bi W, Bloom T, Borowsky ML, Bugalter BE, Butler J, Chang JL, Chen CK, Cook A, Corum B, Cuomo CA, de Jong PJ, DeCaprio D, Dewar K, FitzGerald M, Gilbert J, Gibson R, Gnerre S, Goldstein S, Grafham DV, Grocock R, Hafez N, Hagopian DS, Hart E, Norman CH, Humphray S, Jaffe DB, Jones M, Kamal M, Khodiyar VK, LaButti K, Laird G, Lehoczky J, Liu X, Lokyitsang T, Loveland J, Lui A, Macdonald P, Major JE, Matthews L, Mauceli E, McCarroll SA, Mihalev AH, Mudge J, Nguyen C, Nicol R, O'Leary SB, Osoegawa K, Schwartz DC, Shaw-Smith C, Stankiewicz P, Steward C, Swarbreck D, Venkataraman V, Whittaker CA, Yang X, Zimmer AR, Bradley A, Hubbard T, Birren BW, Rogers J, Lander ES and Nusbaum C

    Nature 2006;440;7087;1045-9

Team

Team members

David Adams
Senior Group Leader
Daniela Robles Espinoza
Postdoctoral Fellow

David Adams

- Senior Group Leader

BSc (Hons), University of Technology, Sydney, 1996. PhD, University of Sydney, 2001. Senior Group Leader (& CR-UK Senior Fellow), 2006-present.

Research

I'm interested in finding cancer genes through sequencing and genetic screens and using model systems (mainly mouse and cells in culture) to understand how these genes work.

References

  • The mutational landscapes of genetic and chemical models of Kras-driven lung cancer.

    Westcott PM, Halliwill KD, To MD, Rashid M, Rust AG, Keane TM, Delrosario R, Jen KY, Gurley KE, Kemp CJ, Fredlund E, Quigley DA, Adams DJ and Balmain A

    1] Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA [2] Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, USA.

    Next-generation sequencing of human tumours has refined our understanding of the mutational processes operative in cancer initiation and progression, yet major questions remain regarding the factors that induce driver mutations and the processes that shape mutation selection during tumorigenesis. Here we performed whole-exome sequencing on adenomas from three mouse models of non-small-cell lung cancer, which were induced either by exposure to carcinogens (methyl-nitrosourea (MNU) and urethane) or by genetic activation of Kras (Kras(LA2)). Although the MNU-induced tumours carried exactly the same initiating mutation in Kras as seen in the Kras(LA2) model (G12D), MNU tumours had an average of 192 non-synonymous, somatic single-nucleotide variants, compared with only six in tumours from the Kras(LA2) model. By contrast, the Kras(LA2) tumours exhibited a significantly higher level of aneuploidy and copy number alterations compared with the carcinogen-induced tumours, suggesting that carcinogen-induced and genetically engineered models lead to tumour development through different routes. The wild-type allele of Kras has been shown to act as a tumour suppressor in mouse models of non-small-cell lung cancer. We demonstrate that urethane-induced tumours from wild-type mice carry mostly (94%) Kras Q61R mutations, whereas those from Kras heterozygous animals carry mostly (92%) Kras Q61L mutations, indicating a major role for germline Kras status in mutation selection during initiation. The exome-wide mutation spectra in carcinogen-induced tumours overwhelmingly display signatures of the initiating carcinogen, while adenocarcinomas acquire additional C > T mutations at CpG sites. These data provide a basis for understanding results from human tumour genome sequencing, which has identified two broad categories of tumours based on the relative frequency of single-nucleotide variations and copy number alterations, and underline the importance of carcinogen models for understanding the complex mutation spectra seen in human cancers.

    Funded by: NCI NIH HHS: R01 CA111834, U01 CA084244, U01 CA141455, U01 CA176287

    Nature 2014

  • POT1 loss-of-function variants predispose to familial melanoma.

    Robles-Espinoza CD, Harland M, Ramsay AJ, Aoude LG, Quesada V, Ding Z, Pooley KA, Pritchard AL, Tiffen JC, Petljak M, Palmer JM, Symmons J, Johansson P, Stark MS, Gartside MG, Snowden H, Montgomery GW, Martin NG, Liu JZ, Choi J, Makowski M, Brown KM, Dunning AM, Keane TM, López-Otín C, Gruis NA, Hayward NK, Bishop DT, Newton-Bishop JA and Adams DJ

    1] Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK. [2].

    Deleterious germline variants in CDKN2A account for around 40% of familial melanoma cases, and rare variants in CDK4, BRCA2, BAP1 and the promoter of TERT have also been linked to the disease. Here we set out to identify new high-penetrance susceptibility genes by sequencing 184 melanoma cases from 105 pedigrees recruited in the UK, The Netherlands and Australia that were negative for variants in known predisposition genes. We identified families where melanoma cosegregates with loss-of-function variants in the protection of telomeres 1 gene (POT1), with a proportion of family members presenting with an early age of onset and multiple primary tumors. We show that these variants either affect POT1 mRNA splicing or alter key residues in the highly conserved oligonucleotide/oligosaccharide-binding (OB) domains of POT1, disrupting protein-telomere binding and leading to increased telomere length. These findings suggest that POT1 variants predispose to melanoma formation via a direct effect on telomeres.

    Funded by: Cancer Research UK: 13031, C1287/A9540, C588/A10589, C588/A4994, C8197/A10123; Wellcome Trust: WT091310, WT098051

    Nature genetics 2014;46;5;478-81

  • Inactivating CUX1 mutations promote tumorigenesis.

    Wong CC, Martincorena I, Rust AG, Rashid M, Alifrangis C, Alexandrov LB, Tiffen JC, Kober C, Chronic Myeloid Disorders Working Group of the International Cancer Genome Consortium, Green AR, Massie CE, Nangalia J, Lempidaki S, Döhner H, Döhner K, Bray SJ, McDermott U, Papaemmanuil E, Campbell PJ and Adams DJ

    1] Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK. [2] Department of Haematology, University of Cambridge, Hills Road, Cambridge, UK.

    A major challenge in cancer genetics is to determine which low-frequency somatic mutations are drivers of tumorigenesis. Here we interrogate the genomes of 7,651 diverse human cancers and find inactivating mutations in the homeodomain transcription factor gene CUX1 (cut-like homeobox 1) in ~1-5% of various tumors. Meta-analysis of CUX1 mutational status in 2,519 cases of myeloid malignancies reveals disruptive mutations associated with poor survival, highlighting the clinical significance of CUX1 loss. In parallel, we validate CUX1 as a bona fide tumor suppressor using mouse transposon-mediated insertional mutagenesis and Drosophila cancer models. We demonstrate that CUX1 deficiency activates phosphoinositide 3-kinase (PI3K) signaling through direct transcriptional downregulation of the PI3K inhibitor PIK3IP1 (phosphoinositide-3-kinase interacting protein 1), leading to increased tumor growth and susceptibility to PI3K-AKT inhibition. Thus, our complementary approaches identify CUX1 as a pan-driver of tumorigenesis and uncover a potential strategy for treating CUX1-mutant tumors.

    Funded by: Cancer Research UK: 13031, 16629, A13031, A14356, A6542, A6997; Medical Research Council: G0800034; Wellcome Trust: 079249, 082356, 093867, 100140

    Nature genetics 2014;46;1;33-8

  • The deubiquitinase USP9X suppresses pancreatic ductal adenocarcinoma.

    Pérez-Mancera PA, Rust AG, van der Weyden L, Kristiansen G, Li A, Sarver AL, Silverstein KA, Grützmann R, Aust D, Rümmele P, Knösel T, Herd C, Stemple DL, Kettleborough R, Brosnan JA, Li A, Morgan R, Knight S, Yu J, Stegeman S, Collier LS, ten Hoeve JJ, de Ridder J, Klein AP, Goggins M, Hruban RH, Chang DK, Biankin AV, Grimmond SM, Australian Pancreatic Cancer Genome Initiative, Wessels LF, Wood SA, Iacobuzio-Donahue CA, Pilarsky C, Largaespada DA, Adams DJ and Tuveson DA

    Li Ka Shing Centre, Cambridge Research Institute, Cancer Research UK, Cambridge CB2 0RE, UK.

    Pancreatic ductal adenocarcinoma (PDA) remains a lethal malignancy despite much progress concerning its molecular characterization. PDA tumours harbour four signature somatic mutations in addition to numerous lower frequency genetic events of uncertain significance. Here we use Sleeping Beauty (SB) transposon-mediated insertional mutagenesis in a mouse model of pancreatic ductal preneoplasia to identify genes that cooperate with oncogenic Kras(G12D) to accelerate tumorigenesis and promote progression. Our screen revealed new candidate genes for PDA and confirmed the importance of many genes and pathways previously implicated in human PDA. The most commonly mutated gene was the X-linked deubiquitinase Usp9x, which was inactivated in over 50% of the tumours. Although previous work had attributed a pro-survival role to USP9X in human neoplasia, we found instead that loss of Usp9x enhances transformation and protects pancreatic cancer cells from anoikis. Clinically, low USP9X protein and messenger RNA expression in PDA correlates with poor survival after surgery, and USP9X levels are inversely associated with metastatic burden in advanced disease. Furthermore, chromatin modulation with trichostatin A or 5-aza-2'-deoxycytidine elevates USP9X expression in human PDA cell lines, indicating a clinical approach for certain patients. The conditional deletion of Usp9x cooperated with Kras(G12D) to accelerate pancreatic tumorigenesis in mice, validating their genetic interaction. We propose that USP9X is a major tumour suppressor gene with prognostic and therapeutic relevance in PDA.

    Funded by: Cancer Research UK: 13031; NCI NIH HHS: 2P50CA101955, CA106610, CA122183, CA128920, CA62924, K01 CA122183, K01 CA122183-05, P50 CA062924, P50 CA101955, P50CA62924; Wellcome Trust

    Nature 2012;486;7402;266-70

  • Mouse genomic variation and its effect on phenotypes and gene regulation.

    Keane TM, Goodstadt L, Danecek P, White MA, Wong K, Yalcin B, Heger A, Agam A, Slater G, Goodson M, Furlotte NA, Eskin E, Nellåker C, Whitley H, Cleak J, Janowitz D, Hernandez-Pliego P, Edwards A, Belgard TG, Oliver PL, McIntyre RE, Bhomra A, Nicod J, Gan X, Yuan W, van der Weyden L, Steward CA, Bala S, Stalker J, Mott R, Durbin R, Jackson IJ, Czechanski A, Guerra-Assunção JA, Donahue LR, Reinholdt LG, Payseur BA, Ponting CP, Birney E, Flint J and Adams DJ

    The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK.

    We report genome sequences of 17 inbred strains of laboratory mice and identify almost ten times more variants than previously known. We use these genomes to explore the phylogenetic history of the laboratory mouse and to examine the functional consequences of allele-specific variation on transcript abundance, revealing that at least 12% of transcripts show a significant tissue-specific expression bias. By identifying candidate functional variants at 718 quantitative trait loci we show that the molecular nature of functional variants and their position relative to genes vary according to the effect size of the locus. These sequences provide a starting point for a new era in the functional analysis of a key model organism.

    Funded by: Biotechnology and Biological Sciences Research Council: BB/F022697/1; Cancer Research UK: A6997; Medical Research Council: G0800024, MC_U127561112, MC_U137761446; NHLBI NIH HHS: K25 HL080079; NLM NIH HHS: 2T15LM007359; Wellcome Trust: 077192, 079912, 082356, 083573, 083573/Z/07/Z, 085906, 085906/Z/08/Z, 090532

    Nature 2011;477;7364;289-94

Daniela Robles Espinoza

- Postdoctoral Fellow

I graduated with a Bachelor degree in Genome Sciences from the National Autonomous University of Mexico in 2009. I then worked for a year in two research groups focusing in cancer gene discovery and signaling networks, before joining the Sanger Institute as a PhD student.

Research

My PhD project and current work focus on the identification of novel melanoma susceptibility genes in predisposed families, and the mechanisms by which they might cause disease. We utilise whole- and targeted- exome sequencing and bioinformatic tools followed by the biological validation of targets in an effort to understand the genetics underlying this disease.

References

  • Nonsense Mutations in the Shelterin Complex Genes ACD and TERF2IP in Familial Melanoma.

    Aoude LG, Pritchard AL, Robles-Espinoza CD, Wadt K, Harland M, Choi J, Gartside M, Quesada V, Johansson P, Palmer JM, Ramsay AJ, Zhang X, Jones K, Symmons J, Holland EA, Schmid H, Bonazzi V, Woods S, Dutton-Regester K, Stark MS, Snowden H, van Doorn R, Montgomery GW, Martin NG, Keane TM, López-Otín C, Gerdes AM, Olsson H, Ingvar C, Borg A, Gruis NA, Trent JM, Jönsson G, Bishop DT, Mann GJ, Newton-Bishop JA, Brown KM, Adams DJ and Hayward NK

    Affiliations of authors: QIMR Berghofer Medical Research Institute, Brisbane, Australia (LGA, ALP, MG, PJ, JMP, JS, VB, SW, KDR, MSS, GWM, NGM, NKH); Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK (CDRE, TMK, DJA); Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark (KW, AMG); Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK (MH, HSn, DTB, JANB); Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD (JC, KMB); Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología del Principado de Asturias (IUOPA) Universidad de Oviedo, Oviedo, Spain (VQ, AJR, CLO); Cancer Genomics Research Laboratory, NCI Frederick, SAIC-Frederick Inc., Frederick MD (XZ, KJ); Department of Dermatology, Leiden University Medical Centre, Leiden, the Netherlands (RvD, NAG); Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden (HO, CI, ÅB, GJ); Translational Genomics Institute, Phoenix, AZ (JMT); University of Sydney at Westmead Millennium Institute, Westmead, Sydney, NSW, Australia (EAH, HSc, GJM); Melanoma Institute Australia, North Sydney, NSW, Australia (EAH, HSc, GJM).

    Background: The shelterin complex protects chromosomal ends by regulating how the telomerase complex interacts with telomeres. Following the recent finding in familial melanoma of inactivating germline mutations in POT1, encoding a member of the shelterin complex, we searched for mutations in the other five components of the shelterin complex in melanoma families.

    Methods: Next-generation sequencing techniques were used to screen 510 melanoma families (with unknown genetic etiology) and control cohorts for mutations in shelterin complex encoding genes: ACD, TERF2IP, TERF1, TERF2, and TINF 2. Maximum likelihood and LOD [logarithm (base 10) of odds] analyses were used. Mutation clustering was assessed with χ(2) and Fisher's exact tests. P values under .05 were considered statistically significant (one-tailed with Yates' correction).

    Results: Six families had mutations in ACD and four families carried TERF2IP variants, which included nonsense mutations in both genes (p.Q320X and p.R364X, respectively) and point mutations that cosegregated with melanoma. Of five distinct mutations in ACD, four clustered in the POT1 binding domain, including p.Q320X. This clustering of novel mutations in the POT1 binding domain of ACD was statistically higher (P = .005) in melanoma probands compared with population control individuals (n = 6785), as were all novel and rare variants in both ACD (P = .040) and TERF2IP (P = .022). Families carrying ACD and TERF2IP mutations were also enriched with other cancer types, suggesting that these variants also predispose to a broader spectrum of cancers than just melanoma. Novel mutations were also observed in TERF1, TERF2, and TINF2, but these were not convincingly associated with melanoma.

    Conclusions: Our findings add to the growing support for telomere dysregulation as a key process associated with melanoma susceptibility.

    Journal of the National Cancer Institute 2015;107;2

  • Telomere-regulating Genes and the Telomere Interactome in Familial Cancers.

    Robles-Espinoza CD, Del Castillo Velasco-Herrera M, Hayward NK and Adams DJ

    Experimental Cancer Genetics, Wellcome Trust Sanger Institute cdre@sanger.ac.uk.

    Telomeres are repetitive sequence structures at the ends of linear chromosomes that consist of double-stranded DNA repeats followed by a short single-stranded DNA (ssDNA) protrusion. Telomeres need to be replicated each cell cycle and protected from DNA-processing enzymes, tasks that cells execute using specialized protein complexes such as telomerase (TERT), which aids in telomere maintenance and replication, and the shelterin complex, which protects chromosome ends. These complexes are also able to interact with a variety of other proteins, referred to as the telomere interactome, in order to fulfil their biological functions and control signaling cascades originating from telomeres. Given their essential role in genomic maintenance and cell cycle control, germline mutations in telomere-regulating proteins and their interacting partners have been found to underlie a variety of diseases and cancer-predisposition syndromes. These syndromes can be characterized by progressively shortening telomeres, in which carriers can present with organ failure due to stem cell senescence among other characteristics, or can also present with long or unprotected telomeres, providing an alternative route for cancer formation. This review, summarizes the critical roles that telomere-regulating proteins play in cell cycle control and cell fate and explores the current knowledge on different cancer-predisposing conditions that have been linked to germline defects in these proteins and their interacting partners.

    Funded by: Cancer Research UK: 13031

    Molecular cancer research : MCR 2014

  • BRAF/NRAS wild-type melanoma, NF1 status and sensitivity to trametinib.

    Ranzani M, Alifrangis C, Perna D, Dutton-Regester K, Pritchard A, Wong K, Rashid M, Robles-Espinoza CD, Hayward NK, McDermott U, Garnett M and Adams DJ

    Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.

    Funded by: Cancer Research UK: 13031

    Pigment cell & melanoma research 2014

  • POT1 loss-of-function variants predispose to familial melanoma.

    Robles-Espinoza CD, Harland M, Ramsay AJ, Aoude LG, Quesada V, Ding Z, Pooley KA, Pritchard AL, Tiffen JC, Petljak M, Palmer JM, Symmons J, Johansson P, Stark MS, Gartside MG, Snowden H, Montgomery GW, Martin NG, Liu JZ, Choi J, Makowski M, Brown KM, Dunning AM, Keane TM, López-Otín C, Gruis NA, Hayward NK, Bishop DT, Newton-Bishop JA and Adams DJ

    1] Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK. [2].

    Deleterious germline variants in CDKN2A account for around 40% of familial melanoma cases, and rare variants in CDK4, BRCA2, BAP1 and the promoter of TERT have also been linked to the disease. Here we set out to identify new high-penetrance susceptibility genes by sequencing 184 melanoma cases from 105 pedigrees recruited in the UK, The Netherlands and Australia that were negative for variants in known predisposition genes. We identified families where melanoma cosegregates with loss-of-function variants in the protection of telomeres 1 gene (POT1), with a proportion of family members presenting with an early age of onset and multiple primary tumors. We show that these variants either affect POT1 mRNA splicing or alter key residues in the highly conserved oligonucleotide/oligosaccharide-binding (OB) domains of POT1, disrupting protein-telomere binding and leading to increased telomere length. These findings suggest that POT1 variants predispose to melanoma formation via a direct effect on telomeres.

    Funded by: Cancer Research UK: 13031, C1287/A9540, C588/A10589, C588/A4994, C8197/A10123; Wellcome Trust: WT091310, WT098051

    Nature genetics 2014;46;5;478-81

  • Cross-species analysis of mouse and human cancer genomes.

    Robles-Espinoza CD and Adams DJ

    Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1HH, United Kingdom.

    Fundamental advances in our understanding of the human cancer genome have been made over the last five years, driven largely by the development of next-generation sequencing (NGS) technologies. Here we will discuss the tools and technologies that have been used to profile human tumors, how they may be applied to the analysis of the mouse cancer genome, and the results thus far. In addition to mutations that disrupt cancer genes, NGS is also being applied to the analysis of the transcriptome of cancers, and, through the use of techniques such as ChIP-Seq, the protein-DNA landscape is also being revealed. Gaining a comprehensive picture of the mouse cancer genome, at the DNA level and through the analysis of the transcriptome and regulatory landscape, will allow us to "biofilter" for driver genes in more complex human cancers and represents a critical test to determine which mouse cancer models are faithful genetic surrogates of the human disease.

    Funded by: Cancer Research UK: 13031

    Cold Spring Harbor protocols 2014;2014;4;350-8

  • Cake: a bioinformatics pipeline for the integrated analysis of somatic variants in cancer genomes.

    Rashid M, Robles-Espinoza CD, Rust AG and Adams DJ

    Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK.

    We have developed Cake, a bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone. Cake can be run on a high-performance computer cluster or used as a stand-alone application. Availabilty: Cake is open-source and is available from http://cakesomatic.sourceforge.net/

    Funded by: Cancer Research UK: 13031; Wellcome Trust

    Bioinformatics (Oxford, England) 2013;29;17;2208-10

  • Jdp2 downregulates Trp53 transcription to promote leukaemogenesis in the context of Trp53 heterozygosity.

    van der Weyden L, Rust AG, McIntyre RE, Robles-Espinoza CD, del Castillo Velasco-Herrera M, Strogantsev R, Ferguson-Smith AC, McCarthy S, Keane TM, Arends MJ and Adams DJ

    Wellcome Trust Sanger Institute, Cambridge, UK.

    We performed a genetic screen in mice to identify candidate genes that are associated with leukaemogenesis in the context of Trp53 heterozygosity. To do this we generated Trp53 heterozygous mice carrying the T2/Onc transposon and SB11 transposase alleles to allow transposon-mediated insertional mutagenesis to occur. From the resulting leukaemias/lymphomas that developed in these mice, we identified nine loci that are potentially associated with tumour formation in the context of Trp53 heterozygosity, including AB041803 and the Jun dimerization protein 2 (Jdp2). We show that Jdp2 transcriptionally regulates the Trp53 promoter, via an atypical AP-1 site, and that Jdp2 expression negatively regulates Trp53 expression levels. This study is the first to identify a genetic mechanism for tumour formation in the context of Trp53 heterozygosity.

    Funded by: Cancer Research UK: 13031; Wellcome Trust: 095606

    Oncogene 2013;32;3;397-402

* quick link - http://q.sanger.ac.uk/expcan