Mechanisms of Genomic Instabilities Underlying Two Common Fragile-Site-Associated Loci, PARK2 and DMD, in Germ Cell and Cancer Cell Lines

Abstract

Common fragile sites (CFSs) are specific chromosome regions that exhibit an increased frequency of breaks when cells are exposed to a DNA-replication inhibitor such as aphidicolin. PARK2 and DMD, the causative genes for autosomal-recessive juvenile Parkinsonism and Duchenne and Becker muscular dystrophy, respectively, are two very large genes that are located within aphidicolin-induced CFSs. Gross rearrangements within these two genes are frequently observed as the causative mutations for these diseases, and similar alterations within the large fragile sites that surround these genes are frequently observed in cancer cells. To elucidate the molecular mechanisms underlying this fragility, we performed a custom-designed high-density comparative genomic hybridization analysis to determine the junction sequences of approximately 500 breakpoints in germ cell lines and cancer cell lines involving PARK2 or DMD. The sequence signatures where these breakpoints occur share some similar features both in germ cell lines and in cancer cell lines. Detailed analyses of these structures revealed that microhomologies are predominantly involved in rearrangement processes. Furthermore, breakpoint-clustering regions coincide with the latest-replicating region and with large nuclear-lamina-associated domains and are flanked by the highest-flexibility peaks and R/G band boundaries, suggesting that factors affecting replication timing collectively contribute to the vulnerability for rearrangement in both germ cell and somatic cell lines.

Comprehensive oligonucleotide array-comparative genomic hybridization analysis: new insights into the molecular pathology of the DMD gene

“…In our study, microhomology was present in 60.6% of breakpoints being comparable to the findings of Mitsui et al (2010) 5 for the DMD gene. There were no breakpoint clustering noticed and different families of known repetitive sequences, whose role has already been demonstrated 8,9 in other diseases, were found in 48.5% of the junctions.…”

“…Despite the high incidence of detected alterations in the DMD gene, [5][6][7] little is known about their causative molecular mechanisms. In our study, microhomology was present in 60.6% of breakpoints being comparable to the findings of Mitsui et al (2010) 5 for the DMD gene.…”

Common fragile sites and genomic instability

“…Germline genomic alterations in CFSs seem also to lead to other human illnesses of nonmalignant origin. In support of this possibility is the recent sequencing of breakpoint junctions in the CFS genes PARK2 at FRA6E and DMD at FRAXC in many patients affected, respectively, by juvenile Parkinsonism and muscular dystrophies (Mitsui et al, 2010). Somatic breakpoints in cancer cell lines and germline breakpoints within PARK2 and DMD shared some features that suggested involvement of common mechanisms in the generation of CFS rearrangements.…”

Predominance of constitutional chromosomal rearrangements in human chromosomal fragile sites

“…Namely, Burrow et al [17] reported that most of the breakpoints in pairs of genes involved in cancer-specific recurrent translocations are located in human chromosomal fragile sites, supporting a causal role for fragile sites in the generation of chromosomal rearrangements in somatic cells. Using a custom-designed high-density CGH analysis to study the junction sequences of approximately 500 breakpoints in germ cell lines and cancer cell lines involving PARK2 or DMD, Mitsui et al [11,18] suggested that a common mechanism may be involved in the generation of rearrangements in both types of cell lines. Our results extend the findings of these authors, adding evidence that chromosomal fragility associated with CFSs plays a role in constitutional chromosomal rearrangements as well.…”

“…The recently obtained evidence that chromosomal instability associated with CFSs plays an important role in gross deletions and duplications in germ cell lines, considered causal in human diseases [11], led us readdress this old issue.…”