Analyses of apoptotic regulators CASP9 and DFFA at 1P36.2, reveal rare allele variants in human neuroblastoma tumours

Abstract

The genes encoding Caspase-9 and DFF45 have both recently been mapped to chromosome region 1p36.2, that is a region alleged to involve one or several tumour suppressor genes in neuroblastoma tumours. This study presents an update contig of the 'Smallest Region of Overlap of deletions' in Scandinavian neuroblastoma tumours and suggests that DFF45 is localized in the region. The genomic organization of the human DFF45 gene, deduced by in-silico comparisons of DNA sequences, is described for the first time in this paper. In the present study 44 primary tumours were screened for mutation by analysis of the genomic sequences of the genes. In two out of the 44 tumours this detected in the DFFA gene one rare allele variant that caused a non-polar to a polar amino acid exchange in a preserved hydrophobic patch of DFF45. One case was hemizygous due to deletion of the more common allele of this polymorphism. Out of 194 normal control alleles only one was found to carry this variant allele, so in respect of it, no healthy control individual out of 97 was homozygous. Moreover, our RT -PCR expression studies showed that DFF45 is preferably expressed in low-stage neuroblastoma tumours and to a lesser degree in high-stage neuroblastomas. We conclude that although coding mutations of Caspase-9 and DFF45 are infrequent in neuroblastoma tumours, our discovery of a rare allele in two neuroblastoma cases should be taken to warrant further studies of the role of DFF45 in neuroblastoma genetics.

A novel 1p36.2 located gene, APITD1, with tumour-suppressive properties and a putative p53-binding domain, shows low expression in neuroblastoma tumours

“…The 500 kb deletion partly overlaps the most proximal part of the consensus LOH region determined by us in our set of tumours. We have previously screened all annotated genes within this 500 kb region for mutations in neuroblastoma patients (Ejeskär et al, 2000;Abel et al, 2002;Krona et al, 2003). In this study, we have further explored this genomic region by the characterisation of a predicted gene, APITD1.…”

“…Further evidence for the localisation of a neuroblastoma tumour suppressor gene to this region came from the finding of a 500 kb homozygous deletion within our SRO in a neuroblastoma cell line (Ohira et al, 2000). Mutation analysis of the coding sequences of all known genes within this 500 kb region indicated a low frequency of amino-acid changes, implying the presence of yet unidentified genes in the region which might be involved in the development and/or progression of neuroblastoma tumours (Ejeskär et al, 2000;Abel et al, 2002;Krona et al, 2003).…”

Definition and characterization of a region of 1p36.3 consistently deleted in neuroblastoma

“…However, these studies have not identified a consistent region of deletion. Furthermore, these and other studies have proposed over 20 genes within these regions as candidate neuroblastoma tumor suppressors, none of which have yet been proven to play a significant causative role in neuroblastoma tumor development (Ejeskar et al, 2000;Judson et al, 2000;De Toledo et al, 2001;Huang et al, 2001;Abel et al, 2002;Cerignoli et al, 2002;Krona et al, 2003;Thompson et al, 2003;Mathysen et al, 2004). Our current work was designed to determine the location and extent of 1p deletion in a very large primary tumor cohort by extensive genotyping, sequencing, gene identification, and transcript characterization.…”

Genetic and epigenetic changes in the common 1p36 deletion in neuroblastoma tumours

“…As an overlapping homozygous 500 kb deletion of 1p36.2 -3 was found in an NB cell line (Ohira et al, 2000), the region has been analysed in further detail. In our study of the genes within this region, all seven were screened for mutations and a few were indeed discovered (Ejeskär et al, 2000;Abel et al, 2002Abel et al, , 2004Krona et al, 2003Krona et al, , 2004. We have also explored the expression and methylation status of these genes.…”