The complex (sawtooth) pattern exhibits numerous low-amplitude gains/losses and copy-number transitions, and is characteristic of basal-like breast cancers. Although the underlying mechanism is not yet known, the pattern is indicative of chromosome breakage throughout the genome, suggesting a more generalized process, e.g., a defect in DNA damage repair. Indeed, an intriguing hypothesis on the underlying mechanism is suggested by noted similarities between sporadic basal-like breast cancers and hereditary breast cancers arising from germline BRCA1
]. Sporadic basal-like and BRCA1-associated tumors exhibit similar histology, with high mitotic counts, medullary features, lymphocytic infiltrates, and “pushing” margins [51
]. The vast majority of BRCA1-associated breast tumors are also triple-negative, and express basal markers and gene-expression patterns [52
]. Notably, BRCA1 tumors also exhibit complex, low-amplitude segmented profiles, with similar loci of preferential deletion (e.g. 4p, 4q, 5q) [24
]. Finally, both sporadic basal-like and BRCA1-associated breast tumors appear to lack of markers of a normal inactive X chromosome [56
]. BRCA1 has diverse functions, but its tumor suppressive activity is most often connected to its role in DNA double-strand break (DSB) repair [57
Multiple pathways exist to repair DNA damage, including for example mismatch repair, base excision repair (BER), nucleotide excision repair (NER), and DSB repair [58
]. DSBs, caused for example by ionizing radiation, reactive oxygen species (ROS), and collapsed DNA replication forks, are perhaps the most deleterious lesions. The two major pathways for DSB repair are homologous recombination (HR) and non-homologous end joining (NHEJ) [59
]. HR is an error-free process that uses the sister chromatid (or homologous chromosome) to align and repair ends, and is the preferred mode of DSB repair in S/G2
phases of cell cycle (when sister chromatids are present). By contrast, NHEJ comprises error-prone processes that join together two broken ends.
BRCA1 plays a key role in DSB repair, and in particular, in channeling repair towards error-free HR [60
]. In the context of BRCA1
mutation, dysfunction of HR repair would lead to increased error-prone repair, with resultant chromosome rearrangements and copy-number transitions. Intriguingly, BRCA1 also appears to function in breast epithelial differentiation, regulating the differentiation of ER-negative breast epithelial stem cells into ER-positive luminal progenitors [61
]. Therefore, a unifying hypothesis states that sporadic basal-like breast tumors harbor a dysfunction of BRCA1 (or BRCA1-associated pathways), leading to both a complex pattern of genomic alteration, and an ER-negative, basal-like phenotype.
Some evidence supports a BRCA1 deficiency in sporadic basal-like breast cancers. While BRCA1
mutations are rare in sporadic breast cancer [62
(17q21) deletion/LOH has been reported (though does not appear to be specific for ER-negative (including basal-like) tumors) [63
]. Decreased BRCA1
transcript levels [64
] and nuclear protein expression [65
] have also been observed in some basal-like tumors. In addition, BRCA1
promoter hypermethylation has been reported in metaplastic breast cancers (a rare type of basal-like tumor), as has overexpression of ID4, a negative regular of BRCA1 expression, in basal-like cancers [64
]. Finally, paired-end DNA sequencing analysis of rearrangements, including the tandem duplications prevalent in basal-like breast cancers, has identified short (1–4 bp) regions of overlapping microhomology (i.e. identical sequences present in the contributing DNA segments, and once at the rearrangement junction), a finding less common of amplicon-associated rearrangements in amplifier tumors [33
]. Such microhomology, guiding the alignment of broken ends, has been considered a hallmark of the NHEJ process [66
], and possibly implies a defect in error-free HR repair.
However, despite the intriguing hypothesis connecting complex genome patterns, basal-like phenotype and BRCA1 dysfunction, at least one study supports the presence of functional BRCA1 in basal-like tumors, evidenced by the common appearance of nuclear BRCA1 foci [56
]. Furthermore, to our knowledge, there is as yet no direct evidence of a HR defect in sporadic basal-like breast cancer.
Perhaps most notable, though, are the characteristics of hereditary breast cancers arising from germline mutation of BRCA2
, which also has a key function in HR repair. BRCA2
-associated tumors are typically ER-positive (not basal-like), and exhibit neither the same preferential sites of loss (e.g. 4p, 4q, 5q), nor the complex pattern of genomic alteration [33
] (though at least one study did report finding complex-pattern changes [69
]). Of note, the main function of BRCA2 appears to be in regulating RAD51 activity in HR. In contrast, BRCA1 functions more as a signal integrator of the DNA damage response, acting not only in HR but also in other DNA repair pathways (e.g., NER, BER), as well as cell-cycle (G2/M and spindle assembly) checkpoints, and more broadly in transcriptional regulation and chromatin remodeling [70
]. Therefore, it is possible that dysfunction of one or more of its other activities (in addition to or instead of HR) connects BRCA1 to the complex genome patterns in basal-like tumors. In this regard, Alli and colleagues [72
] recently reported defective BER of oxidative DNA damage (a pathway also associated with BRCA1 function) in basal-like cancer cell lines.
Alternatively, a different shared property of BRCA1-associated and sporadic basal-like breast tumors might underlie the observed complex-pattern genome rearrangements. For example, both tumor types show frequent mutation of TP53
, a master caretaker that controls cell fate in response to DNA damage, but also has a specific role in blocking HR between divergent sequences (which might otherwise lead to rearrangement) [16
]. In addition, BRCA1 and sporadic basal-like tumors both show frequent deletions at 5q, a region harboring several genes functioning in DNA damage repair, including MSH3
]. Another shared feature appears to be dysfunction of the PTEN tumor suppressor [73
]. Loss of PTEN expression has been observed in sporadic basal-like tumors, and BRCA1-deficient tumors exhibit gross mutations (inversions, deletions) at the PTEN
locus. Intriguingly, PTEN loss also results in defective HR [74
], though that dysfunction would seem superfluous in BRCA1-deficient tumors (where ostensibly the PTEN
gross mutations are themselves a likely consequence of a BRCA1-associated HR defect).
Increased DNA breakage might also contribute to the etiology of complex-pattern genomes. In this regard, another shared feature of hereditary BRCA1-associated and sporadic basal-like breast tumors is their high rates of cell proliferation. Indeed, analyzing gene-expression patterns of complex pattern breast cancers, Fridlyand and colleagues [24
] identified enrichment of gene sets relating to cell proliferation (e.g. mitosis, cell cycle, DNA replication and repair), and of E2F1 target genes. Mechanistically, oncogene-driven cell proliferation can induce DNA replication stress, where the stall and collapse of replication forks create DSBs [75
]. Of note, collapsed replication forks will create single-ended DSBs, most likely repaired by microhomology mediated break-induced replication (MMBIR) [76
], and providing an alternative explanation for the observed microhomologies at rearrangement junctions [33
]. However, we note that high proliferation rates also characterize many of the amplifier (luminal B) subtype breast tumors [77
Finally, the resultant constellation of CNAs might itself perpetuate or drive genomic instability. Analyzing the numerous gains in complex pattern genomes, Chin and colleagues [27
] noted enrichment of genes associated with RNA and cell metabolism, which might increase basal metabolism and possibly proliferation rates. In addition, widespread CNA, through the altered expression of many genes, might disrupt critical stochiometric relationships within protein complexes (e.g., the mitotic spindle), possibly further promoting genomic instability [78