Variable gene expression in APC- and MUTYH mutation negative FAP and AFAP patients

Rohlin A*1, Wernersson J1, Björk J2, and Nordling M1 Dept of Clinical Genetics, Sahlgrenska University Hospital, Gothenburg, 2) The Swedish

Polyposis Registry, Department of Gastroenterology and Hepatology, Karolinska University Hospital, Solna .

Introduction

Familial adenomatous polyposis (FAP) has been linked to germline mutations in the APC tumor suppressor gene and in the case of MAP (MUTYH associated polyposis), the base-excision repair gene MUTYH. Classical FAP and AFAP (attenuated familial polyposis) show a phenotypic heterogeneity, which is partially related to the mutation site or type.

In our material, 96 unrelated FAP patients from the Swedish polyposis register were screened for mutations in the APC and MUTYH genes. Sixty-one different mutations in the APC gene were found in 81 of the families and 6 additional families were found to have biallelic MUTYH mutations. A disease-causing mutation was found in all except one of the patients with a classical phenotype (Kanter-Smoler et al. 2008). In AFAP the genetic cause remains undetected in up to 70–80% of the patients .

We used the Exon- and SNP arrays from Affymetrix in an attempt to reveal the genetic cause of the AFAP cases without identified mutations in the APC or MUTYH genes and to investigate larger deletions of the APC region previous found with mlpa. The exon-arrays reveal the expression levels and the differences in isoforms generated by alternative splicing events. Additionally, we used this platform to investigate if expression of different isoforms might in part explain the variable penetrance of FAP observed within families and between families with the same mutation.

Methods

Two families with AFAP with two and three patients respectively were analyzed with the 1.0 HuEx arrays from Affymetrix. The exon-arrays include over 40 probes for each gene and four probes (one probeset) for every exon for all well annotated genes. The robust multi-array analysis (RMA) algorithm was used for probeset (gene-level) and (exon-level) intensity analysis. This generates a core gene list with 17800 transcripts for analysis regarding expression and alternative splicing events.

Five deletions including at least the entire APC region have been found with mlpa. The 250K SNP array was used to reveal the extension of the deletions.

Conclusions

A combination of exon-arrays and SNP-arrays can be used in order to get a more detailed picture of copy number changes and its correlation with differentially expressed/alternative spliced transcripts. This will give valuable information about regulation of genes and add information regarding new mutational mechanisms.

Results

Subsequent to ANOVA analysis a threshold cutoff was set to p-values less than 0.001 and at least a 2-fold geometric change in gene-level expression between controls and patients. This yielded 6 downregulated genes and 2 upregulated genes in total. The alternative splice analysis showed a significant difference in splicepattern for 5 genes (cutoff p-value 0.001). Two different spliced genes are shown i fig1 a and b.

1A

1B

A microarray (Affymetrix 250K) analysis of APC entire gene deletion previously identified with mlpa, shows that the deletion extends at least 5 genes 5´ of the APC gene and includes a region of 7.7Mb (fig2a and fig2b).

2A

2B

anna.rohlin@vgregion.se