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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 separation between ordinary-luminal and HER2-amplified luminal groups.This graph shows a comparison between ordinary-luminal (n = 629, shown in green), and HER2-amplified (n = 51, in purple) types of luminal tumours in the METABRIC training set. (a) The heat map is generated from Illumina probe profiles, under a normalisation with relation to the molecular signature of control samples represented by the black colour. An over-expression relative to controls corresponds to red, while an under-expression—to green. All samples are ordered by their expression levels of HER2. (b) Expression values density distributions of the top three probes correlated to and including HER2, are shown in the first, and ordered expression values functions—in the second row. The molecular signature of HER2-amplified is delineated by an over-expression of HER2-associated genes, in relation to ordinary-luminal and controls. These graphs exhibit a clearly non-uniform behaviour of probe expression levels, allowing a rather robust separation of luminal tumours.
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pone.0158259.g004: Molecular separation between ordinary-luminal and HER2-amplified luminal groups.This graph shows a comparison between ordinary-luminal (n = 629, shown in green), and HER2-amplified (n = 51, in purple) types of luminal tumours in the METABRIC training set. (a) The heat map is generated from Illumina probe profiles, under a normalisation with relation to the molecular signature of control samples represented by the black colour. An over-expression relative to controls corresponds to red, while an under-expression—to green. All samples are ordered by their expression levels of HER2. (b) Expression values density distributions of the top three probes correlated to and including HER2, are shown in the first, and ordered expression values functions—in the second row. The molecular signature of HER2-amplified is delineated by an over-expression of HER2-associated genes, in relation to ordinary-luminal and controls. These graphs exhibit a clearly non-uniform behaviour of probe expression levels, allowing a rather robust separation of luminal tumours.

Mentions: These results demonstrate that the HER2-amplified group is an entity with consistent characteristics variant from the ordinary-luminal. To follow up this segregation in terms of the molecular signature, we plotted a heat map, shown in Fig 4a. Accordingly, the former group is associated with a well defined amplification in the subset of HER2-associated probes, absent in the ordinary-luminal tumours and controls. Interestingly, the expression of ORMDL3 in ordinary-luminal is lower than the average level of control samples, while it is higher for the HER2-amplified luminal tumours. We further plotted the density distribution functions of the top three genes associated with and including HER2, shown in Fig 4b. These functions are multimodal. However, since the minimum density value located between the two local maxima is not well defined in each plot (the absolute difference between these values is small), this segregation is not as intrinsic as the differentiation between luminal A and basal-like subtypes (Fig 1c). On the other hand, the separation between HER2-amplified and ordinary-luminal samples is clearer than between luminal A and B (Fig 1a). The functions of ordered expression values support this conclusion (Fig 4b), where the cutting point between these two subgroups is roughly located at the break point representing the change in the nearly uniform distribution corresponding to the ordinary-luminal samples (this is the point where the approximately linear segment changes its gradient/direction). Summarising, we suggest that the separation of luminal tumours into HER2-amplified and ordinary-luminal on the molecular level, correlating to the stratification based on the IHC HER2-status [6], should be given more credence.


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

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

Molecular separation between ordinary-luminal and HER2-amplified luminal groups.This graph shows a comparison between ordinary-luminal (n = 629, shown in green), and HER2-amplified (n = 51, in purple) types of luminal tumours in the METABRIC training set. (a) The heat map is generated from Illumina probe profiles, under a normalisation with relation to the molecular signature of control samples represented by the black colour. An over-expression relative to controls corresponds to red, while an under-expression—to green. All samples are ordered by their expression levels of HER2. (b) Expression values density distributions of the top three probes correlated to and including HER2, are shown in the first, and ordered expression values functions—in the second row. The molecular signature of HER2-amplified is delineated by an over-expression of HER2-associated genes, in relation to ordinary-luminal and controls. These graphs exhibit a clearly non-uniform behaviour of probe expression levels, allowing a rather robust separation of luminal tumours.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0158259.g004: Molecular separation between ordinary-luminal and HER2-amplified luminal groups.This graph shows a comparison between ordinary-luminal (n = 629, shown in green), and HER2-amplified (n = 51, in purple) types of luminal tumours in the METABRIC training set. (a) The heat map is generated from Illumina probe profiles, under a normalisation with relation to the molecular signature of control samples represented by the black colour. An over-expression relative to controls corresponds to red, while an under-expression—to green. All samples are ordered by their expression levels of HER2. (b) Expression values density distributions of the top three probes correlated to and including HER2, are shown in the first, and ordered expression values functions—in the second row. The molecular signature of HER2-amplified is delineated by an over-expression of HER2-associated genes, in relation to ordinary-luminal and controls. These graphs exhibit a clearly non-uniform behaviour of probe expression levels, allowing a rather robust separation of luminal tumours.
Mentions: These results demonstrate that the HER2-amplified group is an entity with consistent characteristics variant from the ordinary-luminal. To follow up this segregation in terms of the molecular signature, we plotted a heat map, shown in Fig 4a. Accordingly, the former group is associated with a well defined amplification in the subset of HER2-associated probes, absent in the ordinary-luminal tumours and controls. Interestingly, the expression of ORMDL3 in ordinary-luminal is lower than the average level of control samples, while it is higher for the HER2-amplified luminal tumours. We further plotted the density distribution functions of the top three genes associated with and including HER2, shown in Fig 4b. These functions are multimodal. However, since the minimum density value located between the two local maxima is not well defined in each plot (the absolute difference between these values is small), this segregation is not as intrinsic as the differentiation between luminal A and basal-like subtypes (Fig 1c). On the other hand, the separation between HER2-amplified and ordinary-luminal samples is clearer than between luminal A and B (Fig 1a). The functions of ordered expression values support this conclusion (Fig 4b), where the cutting point between these two subgroups is roughly located at the break point representing the change in the nearly uniform distribution corresponding to the ordinary-luminal samples (this is the point where the approximately linear segment changes its gradient/direction). Summarising, we suggest that the separation of luminal tumours into HER2-amplified and ordinary-luminal on the molecular level, correlating to the stratification based on the IHC HER2-status [6], should be given more credence.

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