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Intra-tumor genetic heterogeneity and alternative driver genetic alterations in breast cancers with heterogeneous HER2 gene amplification.

Ng CK, Martelotto LG, Gauthier A, Wen HC, Piscuoglio S, Lim RS, Cowell CF, Wilkerson PM, Wai P, Rodrigues DN, Arnould L, Geyer FC, Bromberg SE, Lacroix-Triki M, Penault-Llorca F, Giard S, Sastre-Garau X, Natrajan R, Norton L, Cottu PH, Weigelt B, Vincent-Salomon A, Reis-Filho JS - Genome Biol. (2015)

Bottom Line: HER2 is overexpressed and amplified in approximately 15% of invasive breast cancers, and is the molecular target and predictive marker of response to anti-HER2 agents.In a subset of these cases, heterogeneous distribution of HER2 gene amplification can be found, which creates clinically challenging scenarios.Our results indicate that even driver genetic alterations, such as HER2 gene amplification, can be heterogeneously distributed within a cancer, and that the HER2-negative components are likely driven by genetic alterations not present in the HER2-positive components, including BRF2 and DSN1 amplification and HER2 somatic mutations.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA. ngk1@mskcc.org.

ABSTRACT

Background: HER2 is overexpressed and amplified in approximately 15% of invasive breast cancers, and is the molecular target and predictive marker of response to anti-HER2 agents. In a subset of these cases, heterogeneous distribution of HER2 gene amplification can be found, which creates clinically challenging scenarios. Currently, breast cancers with HER2 amplification/overexpression in just over 10% of cancer cells are considered HER2-positive for clinical purposes; however, it is unclear as to whether the HER2-negative components of such tumors would be driven by distinct genetic alterations. Here we sought to characterize the pathologic and genetic features of the HER2-positive and HER2-negative components of breast cancers with heterogeneous HER2 gene amplification and to define the repertoire of potential driver genetic alterations in the HER2-negative components of these cases.

Results: We separately analyzed the HER2-negative and HER2-positive components of 12 HER2 heterogeneous breast cancers using gene copy number profiling and massively parallel sequencing, and identified potential driver genetic alterations restricted to the HER2-negative cells in each case. In vitro experiments provided functional evidence to suggest that BRF2 and DSN1 overexpression/amplification, and the HER2 I767M mutation may be alterations that compensate for the lack of HER2 amplification in the HER2-negative components of HER2 heterogeneous breast cancers.

Conclusions: Our results indicate that even driver genetic alterations, such as HER2 gene amplification, can be heterogeneously distributed within a cancer, and that the HER2-negative components are likely driven by genetic alterations not present in the HER2-positive components, including BRF2 and DSN1 amplification and HER2 somatic mutations.

No MeSH data available.


Related in: MedlinePlus

Gene copy number alterations in HER2-positive and HER2-negative components of HER2 heterogeneous breast cancers. (A) Frequency plots of copy number gains and losses (top) and of amplifications (bottom) in HER2 non-amplified and HER2-amplified components of 12 HER2 heterogeneous breast cancers. The proportion of cases in which each bacterial artificial chromosome (BAC) clone is gained/amplified (green) or lost (red) is plotted (y-axis) for each BAC clone according to its genomic position (x-axis). Inverse Log10 values of the Fisher’s exact test P-values are plotted according to genomic location (x-axis) at the bottom of each graph. The only statistically significant difference identified between the genomic profiles of HER2 non-amplified and HER2-amplified components of 12 HER2 heterogeneous breast cancers was HER2 itself. (B) Hierarchical clustering of the genomic profiles of HER2-positive and HER2-negative components of 12 HER2 heterogeneous breast cancers. Hierarchical cluster analysis was performed with categorical states (that is, gains, losses, and amplifications) using Euclidean distance metric and the Wards algorithm. Amp, amplification; Del, deletion; NC, normal copy number.
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Fig2: Gene copy number alterations in HER2-positive and HER2-negative components of HER2 heterogeneous breast cancers. (A) Frequency plots of copy number gains and losses (top) and of amplifications (bottom) in HER2 non-amplified and HER2-amplified components of 12 HER2 heterogeneous breast cancers. The proportion of cases in which each bacterial artificial chromosome (BAC) clone is gained/amplified (green) or lost (red) is plotted (y-axis) for each BAC clone according to its genomic position (x-axis). Inverse Log10 values of the Fisher’s exact test P-values are plotted according to genomic location (x-axis) at the bottom of each graph. The only statistically significant difference identified between the genomic profiles of HER2 non-amplified and HER2-amplified components of 12 HER2 heterogeneous breast cancers was HER2 itself. (B) Hierarchical clustering of the genomic profiles of HER2-positive and HER2-negative components of 12 HER2 heterogeneous breast cancers. Hierarchical cluster analysis was performed with categorical states (that is, gains, losses, and amplifications) using Euclidean distance metric and the Wards algorithm. Amp, amplification; Del, deletion; NC, normal copy number.

Mentions: To determine if there would be a common alternative gene copy number alteration (CNA) present in the HER2-negative components, which would account for the lack of HER2 gene amplification, the microdissected HER2-positive and HER2-negative components of each case were subjected to DNA extraction and aCGH analysis (Figure 1B). When the copy number gains, losses and amplifications of the HER2-positive components were compared with those of the HER2-negative components from all 12 HER2 heterogeneous breast cancers, we observed that the patterns of CNAs were highly similar (Figure 2A). In fact, Fisher’s exact test revealed that the only recurrent CNA present at significantly different frequencies between the HER2-positive and HER2-negative components of the HER2 heterogeneous breast cancers studied here was the HER2 amplicon itself (that is, 17q12). Furthermore, hierarchical cluster analysis of the categorical gene copy number states revealed that the HER2-positive and HER2-negative components of a given HER2 heterogeneous breast cancer clustered together, rather than all HER2-positive and all HER2-negative components clustering together (Figure 2B). These data suggest that the HER2-positive and HER2-negative components of each case are clonally related and that there is no highly recurrent alternative CNA in the HER2-negative components of HER2 heterogeneous breast cancers that compensates for the lack of HER2 gene amplification.Figure 2


Intra-tumor genetic heterogeneity and alternative driver genetic alterations in breast cancers with heterogeneous HER2 gene amplification.

Ng CK, Martelotto LG, Gauthier A, Wen HC, Piscuoglio S, Lim RS, Cowell CF, Wilkerson PM, Wai P, Rodrigues DN, Arnould L, Geyer FC, Bromberg SE, Lacroix-Triki M, Penault-Llorca F, Giard S, Sastre-Garau X, Natrajan R, Norton L, Cottu PH, Weigelt B, Vincent-Salomon A, Reis-Filho JS - Genome Biol. (2015)

Gene copy number alterations in HER2-positive and HER2-negative components of HER2 heterogeneous breast cancers. (A) Frequency plots of copy number gains and losses (top) and of amplifications (bottom) in HER2 non-amplified and HER2-amplified components of 12 HER2 heterogeneous breast cancers. The proportion of cases in which each bacterial artificial chromosome (BAC) clone is gained/amplified (green) or lost (red) is plotted (y-axis) for each BAC clone according to its genomic position (x-axis). Inverse Log10 values of the Fisher’s exact test P-values are plotted according to genomic location (x-axis) at the bottom of each graph. The only statistically significant difference identified between the genomic profiles of HER2 non-amplified and HER2-amplified components of 12 HER2 heterogeneous breast cancers was HER2 itself. (B) Hierarchical clustering of the genomic profiles of HER2-positive and HER2-negative components of 12 HER2 heterogeneous breast cancers. Hierarchical cluster analysis was performed with categorical states (that is, gains, losses, and amplifications) using Euclidean distance metric and the Wards algorithm. Amp, amplification; Del, deletion; NC, normal copy number.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4440518&req=5

Fig2: Gene copy number alterations in HER2-positive and HER2-negative components of HER2 heterogeneous breast cancers. (A) Frequency plots of copy number gains and losses (top) and of amplifications (bottom) in HER2 non-amplified and HER2-amplified components of 12 HER2 heterogeneous breast cancers. The proportion of cases in which each bacterial artificial chromosome (BAC) clone is gained/amplified (green) or lost (red) is plotted (y-axis) for each BAC clone according to its genomic position (x-axis). Inverse Log10 values of the Fisher’s exact test P-values are plotted according to genomic location (x-axis) at the bottom of each graph. The only statistically significant difference identified between the genomic profiles of HER2 non-amplified and HER2-amplified components of 12 HER2 heterogeneous breast cancers was HER2 itself. (B) Hierarchical clustering of the genomic profiles of HER2-positive and HER2-negative components of 12 HER2 heterogeneous breast cancers. Hierarchical cluster analysis was performed with categorical states (that is, gains, losses, and amplifications) using Euclidean distance metric and the Wards algorithm. Amp, amplification; Del, deletion; NC, normal copy number.
Mentions: To determine if there would be a common alternative gene copy number alteration (CNA) present in the HER2-negative components, which would account for the lack of HER2 gene amplification, the microdissected HER2-positive and HER2-negative components of each case were subjected to DNA extraction and aCGH analysis (Figure 1B). When the copy number gains, losses and amplifications of the HER2-positive components were compared with those of the HER2-negative components from all 12 HER2 heterogeneous breast cancers, we observed that the patterns of CNAs were highly similar (Figure 2A). In fact, Fisher’s exact test revealed that the only recurrent CNA present at significantly different frequencies between the HER2-positive and HER2-negative components of the HER2 heterogeneous breast cancers studied here was the HER2 amplicon itself (that is, 17q12). Furthermore, hierarchical cluster analysis of the categorical gene copy number states revealed that the HER2-positive and HER2-negative components of a given HER2 heterogeneous breast cancer clustered together, rather than all HER2-positive and all HER2-negative components clustering together (Figure 2B). These data suggest that the HER2-positive and HER2-negative components of each case are clonally related and that there is no highly recurrent alternative CNA in the HER2-negative components of HER2 heterogeneous breast cancers that compensates for the lack of HER2 gene amplification.Figure 2

Bottom Line: HER2 is overexpressed and amplified in approximately 15% of invasive breast cancers, and is the molecular target and predictive marker of response to anti-HER2 agents.In a subset of these cases, heterogeneous distribution of HER2 gene amplification can be found, which creates clinically challenging scenarios.Our results indicate that even driver genetic alterations, such as HER2 gene amplification, can be heterogeneously distributed within a cancer, and that the HER2-negative components are likely driven by genetic alterations not present in the HER2-positive components, including BRF2 and DSN1 amplification and HER2 somatic mutations.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA. ngk1@mskcc.org.

ABSTRACT

Background: HER2 is overexpressed and amplified in approximately 15% of invasive breast cancers, and is the molecular target and predictive marker of response to anti-HER2 agents. In a subset of these cases, heterogeneous distribution of HER2 gene amplification can be found, which creates clinically challenging scenarios. Currently, breast cancers with HER2 amplification/overexpression in just over 10% of cancer cells are considered HER2-positive for clinical purposes; however, it is unclear as to whether the HER2-negative components of such tumors would be driven by distinct genetic alterations. Here we sought to characterize the pathologic and genetic features of the HER2-positive and HER2-negative components of breast cancers with heterogeneous HER2 gene amplification and to define the repertoire of potential driver genetic alterations in the HER2-negative components of these cases.

Results: We separately analyzed the HER2-negative and HER2-positive components of 12 HER2 heterogeneous breast cancers using gene copy number profiling and massively parallel sequencing, and identified potential driver genetic alterations restricted to the HER2-negative cells in each case. In vitro experiments provided functional evidence to suggest that BRF2 and DSN1 overexpression/amplification, and the HER2 I767M mutation may be alterations that compensate for the lack of HER2 amplification in the HER2-negative components of HER2 heterogeneous breast cancers.

Conclusions: Our results indicate that even driver genetic alterations, such as HER2 gene amplification, can be heterogeneously distributed within a cancer, and that the HER2-negative components are likely driven by genetic alterations not present in the HER2-positive components, including BRF2 and DSN1 amplification and HER2 somatic mutations.

No MeSH data available.


Related in: MedlinePlus