Research - CLIC Sargent Group
The work of the CLIC Sargent research unit
The CLIC Sargent Research Unit was set up in 1985 to study the fundamental changes that cause cancers to develop in children. During that time many exciting discoveries have been made around the world, and the CLIC Sargent Research Unit has made important contributions to this increased understanding of cancer. This work is vital to ensure that more children are cured of their cancers, and to improve on the treatments already in use, so that unpleasant side effects can be avoided.
The changes that lead to cancers are defects in the genetic information, which is present in (almost) every cell in the body, in the form of a complex chemical known as DNA. The DNA constitutes a sort of library of plans, with each book representing a gene. There are about 30,000 human genes. Each gene codes for the production of a specific protein that performs a function in the cell, such as providing a supporting structure, an enzyme that makes an essential chemical, or a controlling factor that tells cells when to grow. So cells need this genetic information to tell them how to replicate themselves and perform their day-to-day functions. Genes can become defective either because the DNA becomes damaged (mutated), or because too much or too little protein is made from them. If defects occur in a gene that tells a cell how and when to divide, then it can start to grow uncontrollably, and so develop into a tumour.
Identifying the exact genes that may become altered during the development of childhood cancer is a major aim of much current research, including that of the CLIC Sargent Research Unit.
In the CLIC Sargent Research Unit, up until recently we have concentrated on one particular type of childhood cancer, a tumour of the kidney, called Wilms' tumour, which affects about one in 10,000 children (this translates to approximately 6 cases per year in the Southwest region). In particular, we have studied the genes involved in the development of Wilms' tumour.
- Our short-term aims are to identify the genes involved in childhood tumours and to how they cause cancer when they go wrong.
- Our long-term aims are to translate this knowledge into new rational therapies for childhood cancer.
Our work has shown that there are many different genes that can cause Wilms' tumour when defective i.e. there are several routes to the same kind of tumour, and that there are several different sorts of changes by which these genes become defective.
One project in the Research Unit is the cloning of a novel gene involved in the development of Wilms' tumour. This was identified because of the discovery of a very rare DNA abnormality in a child with Wilms' tumour. This involves a visible rearrangement of the organisation of the DNA, known as a chromosome translocation (chromosomes represent large sections of the library of genetic information). We have found one gene that is disrupted by this rearrangement, and we are now studying how often this gene is defective in Wilms' tumour.
Analysis of the Wilms' tumour epigenome. (A) shows a region of long-range epigenetic silencing (LRES) on human chromosome 5q31 identified by human genome promoter arrays. (B) Clustered paralogous protocadherin genes at chromosome 5q31 are hypermethylated in Wilms' tumour. (Click image for larger version.)
The major project in the Research Unit, which has just received new funding from CLIC Sargent, involves the identification of novel genetic defects in Wilms' tumour and other childhood cancers. These changes are called epigenetic alterations and are caused by subtle changes in the DNA that alter the activity of genes so that too much or too little protein in made. We are studying epigenetic changes in genes that we already know are important in Wilms' tumour, as well as other new genes that we have found. The project expands the work of the unit from its previous studies on Wilms' tumour into most major types of childhood cancer. One of our major aims in this project is to develop cutting-edge technologies for screening childhood cancers for alterations in thousands of genes simultaneously. This will provide invaluable information for clinical diagnosis as well as identifying new targets for therapy. One of the very attractive properties of epigenetic changes is that they are potentially reversible, unlike other alterations in cancer. So studies of epigenetic changes could lead to completely new ways of treating childhood cancer.
The identification of new genes and new epigenetic changes should allow the design of new diagnostic and therapeutic methods.
On a day-to day basis this work involves a great deal of laboratory experimentation using cutting edge techniques of genetic engineering and tissue culture. We isolate the genes of interest as fragments of DNA, which must then be 'cloned' i.e. multiplied in bacteria so that we can get enough pure DNA to work with. We can then use this DNA as a tool to investigate the corresponding region in cancers, and to introduce the genes into cultured cells, to begin to understand what function they perform in cells.
As well as the laboratory work, we present our work to other scientists, both as publications in scientific journals, and as talks at scientific meetings. In this way our results become part of the scientific literature and contribute to a worldwide bank of knowledge. Publication in a scientific journal is also an important measure of the quality of our work, because all such publications have to pass through a rigorous review process ('peer review').
In the longer term, we have to plan our future studies by writing applications to grant-giving bodies (such as CLIC Sargent), in which we set out what we want to achieve in the next grant period (usually 3-5 years). If these applications receive a favourable review by a panel of external experts, then we are granted money for the programme of study that we have proposed. Progress is reported to the grant-giving body by annual reports and by giving them copies of all our publications during the period of the grant.
What problems do we face in our work? Naturally, our jobs involve solving intellectual and scientific problems, but there are some other non-scientific difficulties. A major one is that all childhood tumours are rare. This means that it takes time to accumulate sufficient material to do meaningful studies, and so most investigations on childhood cancers have to be carried out in paediatric oncology centres. Fortunately Bristol Children's Hospital is the paediatric oncology centre for the whole of the Southwest, and in addition we can get access to material from other centres via the United Kingdom Children's Cancer Study Group (UKCCSG). The excellent collaboration that we have with paediatric oncologists and pathologists has allowed us to build a large bank of Wilms' tumours and other childhood cancer samples to work on.
Our work will have important implications for childhood cancer and has already shown practical benefits, including the establishment of a molecular diagnostic laboratory as a result of collaboration between scientists and clinicians in the CLIC Sargent Research Unit and department of Paediatric Pathology. In addition many scientists and clinicians have been trained in research methods in the CLIC Sargent laboratories, often gaining a MD or PhD as a result.
In the immediate future, knowing what genetic alterations have caused each tumour to develop will help doctors to give a better diagnosis and prognosis. This is vital if the best sort of treatment is to be given to each and every child. In the longer term, we hope that by finding out exactly how these errors in the genetic information cause cancer, we can design completely new methods of treatment which will be more effective and less damaging than what is available now.
Major publications in last 6 years (members and ex-members of the CLIC Sargent research unit are shown in bold):
Hancock, A.L., Brown, K.W., Moorwood, K., Moon, H., Holmgren, C., Mardikar, S.H., Dallosso, A.R., Klenova, E., Loukinov, D., Ohlsson, R., Lobanenkov, V.V. and Malik, K. (2007) A CTCF-binding silencer regulates the imprinted genes AWT1 and WT1-AS, and exhibits sequential epigenetic defects during Wilms' tumourigenesis. Human Molecular Genetics 16(3), 343-354.
H-Zadeh, A.M., Collard, T.J., Malik, K., Hicks, D.J., Paraskeva, C. and Williams, A.C. (2006) Induction of apoptosis by the 16-kDa amino-terminal fragment of the insulin-like growth factor binding protein 3 in human colonic carcinoma cells. International Journal of Oncology 29, 1279-1286.
Dallosso, A.R., Hancock, A.L., Brown, K.W., Williams, A.C., Jackson, S. and Malik, K. (2004) Genomic Imprinting at the WT1 gene involves a novel coding transcript (AWT1) that shows deregulation in Wilms' tumours. Human Molecular Genetics 13, 405-415.
Vernon, E.G., Malik, K., Reynolds, P., Powlesland, R., Dallosso, A.R., Jackson, S., Henthorn, K., Green, E.D. and Brown, K.W. (2003) The parathyroid hormone-responsive B1 gene is interrupted by a t(1;7)(q42;p15) breakpoint associated with Wilms' tumour. Oncogene 22, 1371-1380.
Arhel N.J., Packham, G., Townsend, P.A., Collard, T.J., H-Zadeh, A.M., Sharp, A., Cutress, R.I., Malik, K., Hague, A., Paraskeva, C. and Williams A.C. (2003) The retinoblastoma protein interacts with Bag-1 in human colonic adenoma and carcinoma derived cell lines. International Journal of Cancer 106, 364-371.
Greenhalgh, K.L., Howell, R.T., Bottani, A., Ancliff, P.J., Brunner, H.G., Verschurren-Bemelmans, C.C., Vernon, E., Brown, K. and Newbury-Ecob, R.A. (2002) Thrombocytopenia-Absent Radius syndrome: A clinical genetic study. J. Med. Genet. 39, 876-881.
Ehrlich, M., Jiang, G., Fiala, E., Dome, J.S., Yu, M.C, Long, T.I., Youn, B., Sohn, O.S., Widschwendter, M., Tomlinson, G.E., Chintagumpala, M., Champagne, M., Parham, D., Liang, G., Malik, K. and Laird, P.W. (2002) Hypomethylation and hypermethylation of DNA in Wilms tumors. Oncogene 21, 6694-6702.
Malik, K., Yan, P., Huang, T.H-M. and Brown, K.W. (2001) Wilms' tumor: A paradigm for the new genetics. Oncology Research 12, 441-449.
Brown, K.W. and Malik, K.T.A. (2001) The molecular biology of Wilms' tumour. Expert Reviews in Molecular Medicine 14 May, http://www-ermm.cbcu.cam.ac.uk/01003027h.htm.
Cummings, M. and Brown, K.W. (2001) Low frequency of genetic lesions in Wilms tumors by representational difference analysis, Cancer Genetics and Cytogenetics 127, 155-160.
Malik, K. and Brown, K.W. (2000) Epigenetic gene deregulation in cancer. British Journal of Cancer 83, 1583-1588.
Malik, K., Salpekar, A., Hancock, A., Moorwood, K., Jackson, S., Charles, A. and Brown, K.W. (2000) Identification of differential methylation of the WT1 antisense regulatory region and relaxation of imprinting in Wilms' tumor. Cancer Research 60, 2356-2360.
Powlesland, R.M., Charles, A.K., Malik, K.T.A., Reynolds, P.A., Pires, S., Boavida, M. and Brown, K.W. (2000) Loss of heterozygosity at 7p in Wilms' tumour development. British Journal of Cancer 82, 323-329.
Moorwood, K., Salpekar, A., Ivins, S.M., Hall, J., Powlesland, R.M., Brown, K.W. and Malik, K. (1999) Transactivation of the WT1 antisense promoter is unique to the WT1[+/-] isoform. FEBS Letters 456, 131-136.
Charles, A.K., Brown, K.W. & Berry, P.J. (1998) Microdissecting the genetic events in nephrogenic rests and Wilms' tumour development. American Journal of Pathology 153, 991-1000.
Moorwood, K., Charles, A.K., Salpekar, A., Wallace, J.I., Brown, K.W. & Malik, K.T.A. (1998) Antisense WT1 transcription overlaps sense mRNA and protein in fetal kidney and can elevate protein levels in vitro. Journal of Pathology 185, 352-359.
Miyagawa, K., Kent, J., Moore, A., Charlieu, J-P., Little, M., Williamson, K.A., Kelsey, A., Brown, K.W., Hassam, S., Briner, J., Van Heyningen, V. & Hastie, N.D. (1998) Loss of WT1 function leads to ectopicis myogenesis in Wilms' tumour. Nature Genetics 18, 15-17.