Cancer Letters

Cancer Letters

Volume 232, Issue 1, 28 January 2006, Pages 48-57
Cancer Letters

Mini Review
Common fragile sites, extremely large genes, neural development and cancer

https://doi.org/10.1016/j.canlet.2005.06.049Get rights and content

Abstract

Common fragile sites (CFSs) are large regions of profound genomic instability found in all individuals. They are biologically significant due to their role in a number of genomic alterations that are frequently found in many different types of cancer. The first CFS to be cloned and characterized was FRA3B, the most active CFS in the human genome. Instability within this region extends for over 4.0 Mbs and contained within the center of this CFS is the FHIT gene spanning 1.5 Mbs of genomic sequence. There are frequent deletions and other alterations within this gene in multiple tumor types and the protein encoded by this gene has been demonstrated to function as a tumor suppressor in vitro and in vivo. In spite of this, FHIT is not a traditional mutational target in cancer and many tumors have large intronic deletions without any exonic alterations. There are several other very large genes found within CFS regions including Parkin (1.37 Mbs in FRA6E), GRID2 (1.47 Mbs within 4q22.3), and WWOX (1.11 Mbs within FRA16D). These genes also appear to function as tumor suppressors but are not traditional mutational targets in cancer. Each of these genes is highly conserved and the regions spanning them are CFSs in mice. We have now examined lists of the largest human genes and found forty that span over one megabase. Many of these are derived from chromosomal bands containing CFSs. BACs within these genes are being utilized as FISH probes to determine if these are also CFS genes. Thus far we have identified the following as CFS genes: CNTNAP2 (2.3 Mbs in FRA7I), DMD (2.09 Mbs in FRAXC), LRP1B (1.9 Mbs in FRA2F), CTNNA3 (1.78 Mbs in FRA10D), DAB1 (1.55 Mbs in FRA1B), and IL1RAPL1 (1.36 Mbs in FRAXC). Although, these genes are also not traditional mutational targets in cancer they do exhibit loss of expression in multiple tumor types suggesting that they may also function as tumor suppressors. Many of the large CFS genes are involved in neurological development. Parkin is mutated in autosomal recessive juvenile Parkinsonism and deletions in mice are associated with the mouse mutant Quaking (viable). Spontaneous mouse mutants in GRID2 and DAB1 are associated with Lurcher and Reelin, respectively. In humans, alterations in IL1RAPL1 cause X-linked mental retardation and loss of WWOX is associated with Tau phosphorylation. We propose that the instability-induced alterations in these genes contribute to cancer development in a two-step process. Initial alterations will primarily occur within intronic regions, as these genes are greater than 99% intronic. These are not benign. Instead, they alter the repertoire of transcripts produced from these genes. As cancer progresses deletions will begin to encompass exons resulting in gene inactivation. These two types of alterations occurring in multiple large CFS genes may contribute significantly to the heterogeneity observed in cancer. There are also important potential linkages between normal neurological development and the development of cancer mediated by alterations in these genes.

Section snippets

FRA3B and FHIT

The common fragile sites (CFSs) are distinct from the rare fragile sites (RFSs) because they are found in all individuals and not in some small proportion of people who have altered DNA sequences [1]. The RFSs are expressed only after sufficient expansion of unstable repeat sequences [2]. In contrast, the CFSs are presumably unstable because of something inherent within their DNA sequence. Over 90 CFSs have been described throughout the human genome and these vary in their frequency of

FRA16D and WWOX

The second most active CFS is FRA16D (16q23.2). This chromosomal region is frequently deleted in a variety of different cancers and approximately 25% of multiple myelomas have a translocation between sequences in this region and those on chromosome 14. We localized the FRA16D CFS using a FISH-based approach with large insert YAC and BAC clones from the chromosome 16q23 region as probes. We then completely characterized the FRA16D CFS to identify the ends of this CFS region as well as the

FRA6E and Parkin

A number of different methods have been used to localize and characterize CFS regions. Both FRA3B and FRA16D were localized by using large insert clones as FISH probes to triangulate and eventually uncover each CFS region. This strategy was also utilized to localize a number of other CFS regions including FRA7G [27], FRAXB [28], and FRA2G [29]. An alternative strategy to localize many other CFS regions was based upon the observation that human papillomaviruses, HPV16 and HPV18, were

GRID2 and FRA4?? (4q22)

GRID2 is another extremely large gene (1.46 Mbs) and Michelle Debatisse and co-workers demonstrated that this gene is localized within a CFS region in both humans and mice [38]. In addition, the mouse gene is a hot-spot for spontaneous deletions resulting in the mouse neurological mutant Lurcher. There is also considerable homology between the mouse and human GRID2 genes even within the introns. Recurrent deletions of subregions of band 4q22 has been described in human hepatocellular carcinomas

Not all CFS regions are associated with extremely large genes

Our observations with several of the most active of the CFS regions and their association with large genes are not applicable to all CFS regions. Indeed more of the characterized CFS regions are not associated with extremely large genes. This includes FRA7G [27], FRAXB [28], FRA7H [40], FRA2G [29] and FRA6F [41]. Some of the CFS regions contain several smaller genes, such as FRA7G, FRAXB, FRA2G and FRA6F, while the 300 kb region spanned by FRA7H is not associated with any genes [40].

The largest human genes

In spite of the fact that not all CFS regions are associated with genes that span vast genomic stretches, we were interested in whether there were other very large genes that could also be derived from CFS regions. We were also curious how large FHIT, Parkin and WWOX were relative to the largest human genes. We obtained lists of the largest known human genes from Dr Robert Kuhn (UCSC Database) and after carefully curating those lists to remove redundant genes discovered that there were 40 human

Many of the largest human genes are localized to chromosomal regions that contain CFSs

An examination of the Table 1 reveals that many of the largest known human genes do indeed map to chromosomal bands that contain a CFS. Although only a few of the CFS regions have been completely characterized we do know the approximate location of 20 additional CFS regions. These were delineated either by the identification of a viral integration site in a cervical tumor or because gene(s) within those regions frequently lost expression in primary ovarian tumors. Although we do not know where

Examining very large genes as possible CFS genes

We used several criteria to determine which large genes to test as potential CFS genes. Since we were particularly interested in genes that could play an important role in the development of cancer, we chose the 1.2 Mb deleted in colorectal cancer (DCC) gene, as well as the 677 kb RAD51L1 gene, which is the human homolog of the bacterial recA gene. The DCC gene is derived from 18q21.1 and the Rad51L1 gene is derived from 14q24.1. We treated lymphocytes with 0.4 uM aphidicolin for 24 h and prepared

Large genes and neurological development

The first large CFS gene that was identified to be involved in neurological development was Parkin, which is mutated in some patients with autosomal recessive juvenile Parkinsonism. In mice there is a spontaneous deletion of Parkin and the immediately distal PARCG gene that results in the Quaker (viable) phenotype [42].

A second large CFS gene is the delta2 glutamate receptor gene (GRID2) which is localized within a chromosomal region in the mouse where there are frequent spontaneous

Role of the CFSs and the large genes contained within them in normal cells

Since the genes within the CFS regions are highly susceptible to genomic instability especially within developing cancer cells, most of the studies on the CFS genes have been in the context of what role they could play in cancer development. A number of these studies have revealed that many of the large CFS genes do play important roles in cancer development and several of the large CFS genes appear to function as tumor suppressors, even if they are not traditional mutational targets in cancer.

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