Molecular processes of chromosome 9p21 deletions causing inactivation of the p16 tumor suppressor gene in human cancer: Deduction from structural analysis of breakpoints for deletions
Introduction
Chromosome interstitial deletion (i.e., deletion of a chromosome segment in a chromosome arm) is a major genetic event causing inactivation of tumor suppressor genes in human cancer cells [1], [2]. Such deletions also cause activation of a few oncogenes [3], [4]. Elucidation of the mechanism(s) for chromosome interstitial deletions is, therefore, indispensable in understanding the molecular mechanisms of human carcinogenesis. Interstitial deletions are supposed to be caused by DNA double strand breaks (DSBs) and subsequent illegitimate joining of DNA ends by homologous or non-homologous end joining repair. Structural analysis of breakpoints for chromosome interstitial deletions has been thought to be a powerful way to deduce molecular processes of its occurrence, since the breakpoints retain “traces” of DSBs and their subsequent repair. The analysis gives us information on:
- (1)
Locations (clustering) of breakpoints on a genomic segment, which enables us to deduce genomic/chromosomal features making DNA susceptible to DSBs.
- (2)
Structures of breakpoint junctions, which enables us to deduce DSB repair pathways used in joining broken DNA ends.
Section snippets
Genomic sequences susceptible to DSBs triggering deletion
The p16 (also called CDKN2A) tumor suppressor gene, and two related genes, p14ARF and p15 (also called CDKN2B) are involved in regulation of the cell cycle and/or apoptosis [5], and the genes are located in a 40-kb region in 9p21 (Fig. 1A). Homozygous deletion (i.e., deletion of both alleles) at chromosome 9p21 removing the p16 gene is frequently occurs in a variety of cancers, therefore, the p16 locus was considered to be a paradigm for loci that are subjected to interstitial deletions during
Genomic/chromosomal feature(s) responsible for the susceptibity to DSBs
Only a few defined RSS-like sequences were defined as breakpoint sites in lymphoid leukemia in spite that the 9p21 segment contained thousands of such sequences. Thus, the susceptibility of a genomic fragment to DSBs by the RAG complex was unlikely to be determined by the homologies with the consensus RSS. In addition, a 10-kb region encompassing the p16 locus contained the largest number of breakpoints for deletions in solid tumors, although a variety of sites in the region were subjected to
DSB repair activities to join DNA ends giving rise to chromosome interstitial deletions
Next, structures of breakpoint junctions were studied to deduce DSB repair pathways used in the joining of broken DNA ends. In Table 1, structures of breakpoint junctions for interstitial 9p21 deletions in lymphoid leukemia and solid tumors are summarized [7], [8], [9], [23], [24], [25]. First of all, it was noted that no significant homology has been found between the distal and proximal breakpoints in any of the cases. Thus, DSBs triggering 9p21 deletions were exclusively joined by
Prospective
The fundamental molecular processes for chromosome interstitial deletions in human cancer have been deduced by the analyses of breakpoints for deletions in human cancers. However, at present the following issues remain unknown.
- (1)
Environmental and endogenous factors causing DSBs triggering deletions in the development of solid tumors.
- (2)
Molecular basis for the architecture of chromatin making DNA susceptible to DSBs.
- (3)
Molecular basis for the predominance of microhomology mediated-NHEJ in the repair of
Acknowledgement
This research was supported by Grants-in-Aid from the Ministry of Health, Labor and Welfare of Japan for the Third Term Comprehensive Control Research for Cancer, for Research on Human Genome and Tissue Engineering and for Cancer Research (16S-1).
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