UMEÅ UNIVERSITY MEDICAL DISSERTATIONS New Series No.1717 ISSN 0346-6612 ISBN 978-91-7601-263-5 Wilms’ tumor gene 1 in different types of cancer Xingru Li Department of Medical Biosciences, Clinical Chemistry Umeå University, Sweden Umeå 2015 Copyright © 2015 Xingru Li ISBN: 978-91-7601-263-5 ISSN: 0346-6612 Printed by: Print & Media Umeå, Sweden, 2015 To my family Table of Contents Abstract .......................................................................................................... 1 Original Articles ............................................................................................. 2 Abbreviations ................................................................................................. 3 Introduction .................................................................................................... 4 WT1 (Wilms’ tumor gene 1) ...................................................................... 4 Structure of WT1 ..................................................................................... 4 WT1, the transcription factor ................................................................. 5 WT1 and its interacting partners ............................................................ 5 WT1 function .......................................................................................... 8 The tumor suppressor ........................................................................ 8 An oncogene ...................................................................................... 8 Mutations and single nucleotide polymorphisms (SNPs) in WT1 ............ 10 WT1 mutations ...................................................................................... 10 SNPs in WT1 ......................................................................................... 11 Methylation of WT1 ................................................................................. 11 DNA methylation .................................................................................. 11 WT1 methylation in different types of cancer ....................................... 12 Different methods for detecting DNA methylation ............................... 13 Genome-scale DNA methylation analysis methods ......................... 14 Locus-specific DNA methylation detection methods ....................... 14 Clinical relevance of the WT1 gene.......................................................... 14 WT1 in acute leukemia ......................................................................... 14 WT1 in RCC .......................................................................................... 15 WT1 in squamous cell carcinoma of the head and neck (SCCHN) ...... 15 p53/p63 in SCCHN ............................................................................... 16 Aims of the thesis ......................................................................................... 17 Materials and methods .................................................................................. 18 Tumor samples and cell culture (paper I - IV) ......................................... 18 RNA extraction and cDNA preparation (papers I - IV) ........................... 19 WT1 RNA Expression with RQ-PCR (papers I - IV) ............................... 19 Genomic DNA Preparation (papers II and III) ......................................... 19 Sequencing Analysis of the WT1 Genes (paper II) .................................. 19 Pyrosequencing (paper III) ....................................................................... 20 Transient transfection (paper IV) ............................................................. 20 siRNA transfection ................................................................................ 20 WT1D plasmid transfections ................................................................ 20 MTT assay (paper IV) .............................................................................. 21 Western blot (paper IV) ........................................................................... 21 Chromatin immunoprecipitation (ChIP)/PCR analysis (paper IV) .......... 21 Genome-wide gene expression array (paper IV) ...................................... 22 Genome-wide DNA methylation array (paper III) ................................... 22 Protein co-immunoprecipitation (paper IV) ............................................. 23 Statistical Analysis ................................................................................... 23 Results and Discussion ................................................................................. 24 Paper I ...................................................................................................... 24 Paper II ..................................................................................................... 25 Paper III .................................................................................................... 27 Paper IV ................................................................................................... 31 Conclusions .................................................................................................. 36 Acknowledgements ...................................................................................... 37 References .................................................................................................... 40 Abstract The Wilms’ tumor gene 1 (WT1) was first reported as a tumor suppressor gene in Wilms’ tumor. However, later studies have shown the oncogenic properties of WT1 in a variety of tumors. It was recently proposed that WT1 was a chameleon gene, due to its dual functions in tumorigenesis. We aimed to investigate the clinical significance of WT1 as biomarker in acute myeloid leukemia (AML) and clear cell renal cell carcinoma (ccRCC) and to elucidate the function of WT1 as an oncogene in squamous cell carcinoma of head and neck (SCCHN). In AML, it was suggested that WT1 expression was an applicable marker of minimal residual disease (MRD). In adult patients with AML, we found a good correlation between WT1 expression levels normalized to two control genes, -actin and ABL. Outcome could be predicted by a reduction in WT1 expression in bone marrow (≥ 1-log) detected less than 1 month after diagnosis, when -actin was used as control. Also, irrespective of the control gene used, outcome could be predicted by a reduction in WT1 expression in peripheral blood (≥ 2-log) detected between 1 and 6 months after treatment initiation. Previous studies in RCC demonstrated that WT1 acted as a tumor suppressor. Thus, we tested whether single nucleotide polymorphisms (SNPs) or mutations in WT1 might be associated with WT1 expression and clinical outcome in patients with ccRCC. We performed sequencing analysis on 10 exons of the WT1 gene in a total of 182 patient samples, and we identified six different SNPs in the WT1 gene. We found that at least one or two copies of the minor allele were present in 61% of ccRCC tumor samples. However, no correlation was observed between WT1 SNP genotypes and RNA expression levels. Moreover, none of the previously reported WT1 mutations were found in ccRCC. Nevertheless, we found that a favorable outcome was associated the homozygous minor allele for WT1 SNP. We then further investigated whether WT1 methylation was related to WT1 expression and its clinical significance. Methylation array and pyrosequencing analyses showed that the WT1 promoter region CpG site, cg22975913, was the most frequently hypermethylated CpG site. We found a trend that showed nearly significant correlation between WT1 mRNA levels and hypermethylation in the 5’-untranslated region. Hypermethylation in the WT1 CpG site, cg22975913, was found to be associated with patient age and a worse prognosis. One previous study reported that WT1 was overexpressed in SCCHN. That finding suggested that WT1 might play a role in oncogenesis. We found that both WT1 and p63 could promote cell proliferation. A positive correlation between WT1 and p63 expression was observed, and we identified p63 as a WT1 target gene. Furthermore, several known WT1 and p63 target genes were affected by knocking down WT1. Also, co-immunoprecipitation analyses demonstrated a protein interaction between WT1 and p53. In summary, WT1 gene expression can provide useful information for MRD detection during treatment of patients with AML. In RCC, our results suggested that the prognostic impact of WT1 SNPs was limited to the subgroup of patients that were homozygous for the minor allele, and that WT1 promoter hypermethylation could be used as a prognostic biomarker. In SCCHN, WT1 and p63 acted as oncogenes by affecting multiple genes involved in cancer cell growth. 1 Original Articles This thesis is based on the following papers and manuscripts: I. Andersson C, Li X, Lorenz F, Golovleva I, Wahlin A, Li A. Reduction in WT1 gene expression during early treatment predicts the outcome in patients with acute myeloid leukemia. Diagn Mol Pathol. 2012 Dec; 21(4):225-33. II. Li X, Wang S, Sitaram RT, Andersson C, Ljungberg B, Li A. Single nucleotide polymorphisms in the Wilms' tumour gene 1 in clear cell renal cell carcinoma. PLoS One. 8(3):e58396. doi: 10.1371/journal.pone.0058396. 2013 III. Li X, Evelönn E A, Wang S, Sitaram RT, Landfors M, Ottosson S, Andersson C, Nilsson S, Ljungberg B, Li A. Prognostic significance of hypermethylation in the promoter region of the Wilms’ tumour gene 1 in clear cell renal cell carcinoma. Manuscript. IV. Li X, Ottosson