Cell-lineage heterogeneity and driver mutation recurrence in pre-invasive breast neoplasia

Abstract

BackgroundAll cells in an individual are related to one another by a bifurcating lineage tree, in which each node is an ancestral cell that divided into two, each branch connects two nodes, and the root is the zygote. When a somatic mutation occurs in an ancestral cell, all its descendants carry the mutation, which can then serve as a lineage marker for the phylogenetic reconstruction of tumor progression. Using this concept, we investigate cell lineage relationships and genetic heterogeneity of pre-invasive neoplasias compared to invasive carcinomas.MethodsWe deeply sequenced over a thousand phylogenetically informative somatic variants in 66 morphologically independent samples from six patients that represent a spectrum of normal, early neoplasia, carcinoma in situ, and invasive carcinoma. For each patient, we obtained a highly resolved lineage tree that establishes the phylogenetic relationships among the pre-invasive lesions and with the invasive carcinoma.ResultsThe trees reveal lineage heterogeneity of pre-invasive lesions, both within the same lesion, and between histologically similar ones. On the basis of the lineage trees, we identified a large number of independent recurrences of PIK3CA H1047 mutations in separate lesions in four of the six patients, often separate from the diagnostic carcinoma.ConclusionsOur analyses demonstrate that multi-sample phylogenetic inference provides insights on the origin of driver mutations, lineage heterogeneity of neoplastic proliferations, and the relationship of genomically aberrant neoplasias with the primary tumors. PIK3CA driver mutations may be comparatively benign inducers of cellular proliferation.Electronic supplementary materialThe online version of this article (doi:10.1186/s13073-015-0146-2) contains supplementary material, which is available to authorized users.

A population genetics perspective on the determinants of intra-tumor heterogeneity

“…Thus, tumor growth may accompany rapid genetic diversification and a small tumor can already harbor extensive diversity. This prediction is consistent with recent findings that early tumors display high-levels of genomic diversity [33, 46, 178]. …”

“…Multiple studies have revealed the early acquisition of tumor heterogeneity in non-invasive adenomas [21, 45, 47, 241]. Breast tumors also have well defined precursor lesions, facilitating studies of tumor initiation and early growth, where genetic diversity was similarly reported to occur early [178] and reconstruction of phylogenetic trees amongst pre-invasive lesions revealed lineage heterogeneity both within and between lesions [33]. …”

“…Although relatively few primary tumors of a given tissue type have been analyzed in detail via multi-region or single cell sequencing, there have been multiple reports of branched evolution [13, 17, 18, 22, 25, 29, 30, 33] (Figure 1C). Hence, these data contrast with the early view that after transformation, subsequent tumor growth typically follows a linear clonal succession model [9] (Figure 1B), wherein a selectively advantageous mutation has time to sweep through the population prior to the acquisition of addition of additional advantageous mutations.…”

“…In theory, the earlier the initial clonal expansion is detected, the less diverse and less fit the cell population (since natural selection operates on diversity), and the better the prognosis. Even relatively early tumors exhibit high genomic diversity [33, 46], which may reflect processes that were already operative for some time and likely will continue in the absence of intervention. The term “early” is indeed relative as the first clonal expansions will be invisible and the lesion must be large enough to be detected and sampled.…”

Atypical ductal hyperplasia is a multipotent precursor of breast carcinoma

“…The key limitation of previous studies is their very small sample sizes (average n = 6) [10][11][12][13][14][15][16][32][33][34], often due to a large DNA input requirement, which itself leads to a potential sample selection bias, i.e. restricted to larger ADH.…”