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Extensive Transcriptomic and Genomic Analysis Provides New Insights about Luminal Breast Cancers.

Tishchenko I, Milioli HH, Riveros C, Moscato P - PLoS ONE (2016)

Bottom Line: Our results indicate that the separation between the molecular luminal A and B subtypes-per definition-is not associated with intrinsic characteristics evident in the differentiation between other subtypes.The comparison with the current separation into luminal A and B subtypes revealed a substantially improved survival stratification.A proposition for a revisited delineation is provided in this study.

View Article: PubMed Central - PubMed

Affiliation: Information-based Medicine Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia.

ABSTRACT
Despite constituting approximately two thirds of all breast cancers, the luminal A and B tumours are poorly classified at both clinical and molecular levels. There are contradictory reports on the nature of these subtypes: some define them as intrinsic entities, others as a continuum. With the aim of addressing these uncertainties and identifying molecular signatures of patients at risk, we conducted a comprehensive transcriptomic and genomic analysis of 2,425 luminal breast cancer samples. Our results indicate that the separation between the molecular luminal A and B subtypes-per definition-is not associated with intrinsic characteristics evident in the differentiation between other subtypes. Moreover, t-SNE and MST-kNN clustering approaches based on 10,000 probes, associated with luminal tumour initiation and/or development, revealed the close connections between luminal A and B tumours, with no evidence of a clear boundary between them. Thus, we considered all luminal tumours as a single heterogeneous group for analysis purposes. We first stratified luminal tumours into two distinct groups by their HER2 gene cluster co-expression: HER2-amplified luminal and ordinary-luminal. The former group is associated with distinct transcriptomic and genomic profiles, and poor prognosis; it comprises approximately 8% of all luminal cases. For the remaining ordinary-luminal tumours we further identified the molecular signature correlated with disease outcomes, exhibiting an approximately continuous gene expression range from low to high risk. Thus, we employed four virtual quantiles to segregate the groups of patients. The clinico-pathological characteristics and ratios of genomic aberrations are concordant with the variations in gene expression profiles, hinting at a progressive staging. The comparison with the current separation into luminal A and B subtypes revealed a substantially improved survival stratification. Concluding, we suggest a review of the definition of luminal A and B subtypes. A proposition for a revisited delineation is provided in this study.

No MeSH data available.


Related in: MedlinePlus

Molecular signature of ordinary-luminal subgroups.Heat maps in this figure show relative expression of the top ten list of genes used to define four quantiles within ordinary-luminal tumours: Q1 (yellow), Q2 (orange), Q3 (spring-green) and Q4 (blue), in the METABRIC training (a), validation (b) and ROCK (c) data sets (n = 629, 629 and 975, respectively). The 600 probes identified to be related to survival outcomes, split into groups Gup-positive, Gdown-negative, Gup-negative and Gdown-positive, show co-expression among each other, and with the top ten list. In the METABRIC data set, the red colour corresponds to an over-expression relative to controls, green—to an under-expression, and the black colour stands for the mean expression levels of controls. In the ROCK data set, the scale black-red was used, as the controls are not available. The expression levels of same probes for the HER2-amplified luminal (n = 51, 51 and 90, respectively, shown in purple) groups are also shown in this figure, including the corresponding IHC HER2-status (negative in blue and positive in pink). MKI67 expression levels and luminal A and B subtype distributions, defined using the PAM50 ensemble learning method [32], are depicted in separate bars.
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pone.0158259.g005: Molecular signature of ordinary-luminal subgroups.Heat maps in this figure show relative expression of the top ten list of genes used to define four quantiles within ordinary-luminal tumours: Q1 (yellow), Q2 (orange), Q3 (spring-green) and Q4 (blue), in the METABRIC training (a), validation (b) and ROCK (c) data sets (n = 629, 629 and 975, respectively). The 600 probes identified to be related to survival outcomes, split into groups Gup-positive, Gdown-negative, Gup-negative and Gdown-positive, show co-expression among each other, and with the top ten list. In the METABRIC data set, the red colour corresponds to an over-expression relative to controls, green—to an under-expression, and the black colour stands for the mean expression levels of controls. In the ROCK data set, the scale black-red was used, as the controls are not available. The expression levels of same probes for the HER2-amplified luminal (n = 51, 51 and 90, respectively, shown in purple) groups are also shown in this figure, including the corresponding IHC HER2-status (negative in blue and positive in pink). MKI67 expression levels and luminal A and B subtype distributions, defined using the PAM50 ensemble learning method [32], are depicted in separate bars.

Mentions: Up to this point, we have analysed the ordinary-luminal breast cancers as a heterogeneous group of samples, for which certain microarray expression levels are associated with varying patients’ prognosis. With the goal to split these tumours into further subgroups based on a subset of previously defined 600 probes, we referred to the top ten genes with the lowest Wilcoxon test p-values from Table 3. We used these probes—all belonging to the Gup-positive group associated with cell proliferation state—to order luminal samples by their average rank (section Defining a Molecular Signature of Patients at Risk). To define groups within the ordinary-luminal breast cancers we referred to four quantiles, each comprising 25% of all patients, called luminal Q1, Q2, Q3 and Q4; they are shown in Fig 5a. A corresponding heat map visualising expression levels of all 600 probes, previously defined to be related to varying survival rates, is also plotted in this figure. We would like to emphasise that there are no clear boundaries between the ordinary-luminal subgroups, and they are purely defined based on markers with approximately uniformly distributed expression values, for diagnostic and prognostics purposes.


Extensive Transcriptomic and Genomic Analysis Provides New Insights about Luminal Breast Cancers.

Tishchenko I, Milioli HH, Riveros C, Moscato P - PLoS ONE (2016)

Molecular signature of ordinary-luminal subgroups.Heat maps in this figure show relative expression of the top ten list of genes used to define four quantiles within ordinary-luminal tumours: Q1 (yellow), Q2 (orange), Q3 (spring-green) and Q4 (blue), in the METABRIC training (a), validation (b) and ROCK (c) data sets (n = 629, 629 and 975, respectively). The 600 probes identified to be related to survival outcomes, split into groups Gup-positive, Gdown-negative, Gup-negative and Gdown-positive, show co-expression among each other, and with the top ten list. In the METABRIC data set, the red colour corresponds to an over-expression relative to controls, green—to an under-expression, and the black colour stands for the mean expression levels of controls. In the ROCK data set, the scale black-red was used, as the controls are not available. The expression levels of same probes for the HER2-amplified luminal (n = 51, 51 and 90, respectively, shown in purple) groups are also shown in this figure, including the corresponding IHC HER2-status (negative in blue and positive in pink). MKI67 expression levels and luminal A and B subtype distributions, defined using the PAM50 ensemble learning method [32], are depicted in separate bars.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4920434&req=5

pone.0158259.g005: Molecular signature of ordinary-luminal subgroups.Heat maps in this figure show relative expression of the top ten list of genes used to define four quantiles within ordinary-luminal tumours: Q1 (yellow), Q2 (orange), Q3 (spring-green) and Q4 (blue), in the METABRIC training (a), validation (b) and ROCK (c) data sets (n = 629, 629 and 975, respectively). The 600 probes identified to be related to survival outcomes, split into groups Gup-positive, Gdown-negative, Gup-negative and Gdown-positive, show co-expression among each other, and with the top ten list. In the METABRIC data set, the red colour corresponds to an over-expression relative to controls, green—to an under-expression, and the black colour stands for the mean expression levels of controls. In the ROCK data set, the scale black-red was used, as the controls are not available. The expression levels of same probes for the HER2-amplified luminal (n = 51, 51 and 90, respectively, shown in purple) groups are also shown in this figure, including the corresponding IHC HER2-status (negative in blue and positive in pink). MKI67 expression levels and luminal A and B subtype distributions, defined using the PAM50 ensemble learning method [32], are depicted in separate bars.
Mentions: Up to this point, we have analysed the ordinary-luminal breast cancers as a heterogeneous group of samples, for which certain microarray expression levels are associated with varying patients’ prognosis. With the goal to split these tumours into further subgroups based on a subset of previously defined 600 probes, we referred to the top ten genes with the lowest Wilcoxon test p-values from Table 3. We used these probes—all belonging to the Gup-positive group associated with cell proliferation state—to order luminal samples by their average rank (section Defining a Molecular Signature of Patients at Risk). To define groups within the ordinary-luminal breast cancers we referred to four quantiles, each comprising 25% of all patients, called luminal Q1, Q2, Q3 and Q4; they are shown in Fig 5a. A corresponding heat map visualising expression levels of all 600 probes, previously defined to be related to varying survival rates, is also plotted in this figure. We would like to emphasise that there are no clear boundaries between the ordinary-luminal subgroups, and they are purely defined based on markers with approximately uniformly distributed expression values, for diagnostic and prognostics purposes.

Bottom Line: Our results indicate that the separation between the molecular luminal A and B subtypes-per definition-is not associated with intrinsic characteristics evident in the differentiation between other subtypes.The comparison with the current separation into luminal A and B subtypes revealed a substantially improved survival stratification.A proposition for a revisited delineation is provided in this study.

View Article: PubMed Central - PubMed

Affiliation: Information-based Medicine Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia.

ABSTRACT
Despite constituting approximately two thirds of all breast cancers, the luminal A and B tumours are poorly classified at both clinical and molecular levels. There are contradictory reports on the nature of these subtypes: some define them as intrinsic entities, others as a continuum. With the aim of addressing these uncertainties and identifying molecular signatures of patients at risk, we conducted a comprehensive transcriptomic and genomic analysis of 2,425 luminal breast cancer samples. Our results indicate that the separation between the molecular luminal A and B subtypes-per definition-is not associated with intrinsic characteristics evident in the differentiation between other subtypes. Moreover, t-SNE and MST-kNN clustering approaches based on 10,000 probes, associated with luminal tumour initiation and/or development, revealed the close connections between luminal A and B tumours, with no evidence of a clear boundary between them. Thus, we considered all luminal tumours as a single heterogeneous group for analysis purposes. We first stratified luminal tumours into two distinct groups by their HER2 gene cluster co-expression: HER2-amplified luminal and ordinary-luminal. The former group is associated with distinct transcriptomic and genomic profiles, and poor prognosis; it comprises approximately 8% of all luminal cases. For the remaining ordinary-luminal tumours we further identified the molecular signature correlated with disease outcomes, exhibiting an approximately continuous gene expression range from low to high risk. Thus, we employed four virtual quantiles to segregate the groups of patients. The clinico-pathological characteristics and ratios of genomic aberrations are concordant with the variations in gene expression profiles, hinting at a progressive staging. The comparison with the current separation into luminal A and B subtypes revealed a substantially improved survival stratification. Concluding, we suggest a review of the definition of luminal A and B subtypes. A proposition for a revisited delineation is provided in this study.

No MeSH data available.


Related in: MedlinePlus