Substantial Genomic Heterogeneity Characterises TNBC Molecular Subtypes

An integrative multiomic analysis identifies several candidate targets

A group of researchers led by Dr. Christos Sotiriou of the Institut Jules Bordet in Brussels, Belgium found a substantial biological heterogeneity that characterises triple negative breast cancer (TNBC) molecular subtypes, allowing the identification of several candidate targets for potential development of anticancer therapeutics. In particular the study team showed that TNBC could be partitioned into five stable transcriptional subtypes. The study was carried out by using copy-number aberrations, somatic mutations and gene expression data derived from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) and The Cancer Genome Atlas. In total, 550 TNBC samples were classified according to Lehmann’s molecular subtypes. The findings are published in the Annals of Oncology.  

The authors wrote in study background that recent efforts of genome-wide gene expression profiling analyses have improved understanding of the biological complexity and diversity of TNBC. At least six different molecular subtypes of TNBC have been reported: basal-like 1 (BL1), basal-like 2 (BL2), immunomodulatory (IM), mesenchymal (M), mesenchymal stem-like (MSL) and luminal androgen receptor (LAR). However, little is known regarding the potential driving molecular events within each subtype, their difference in survival and response to therapy.

In this study, the researchers classified TNBC samples according to Lehmann’s molecular subtypes using the TNBCtype online subtyping tool. Each subtype showed significant clinicopathological characteristic differences.

Using a multivariate model, IM subtype showed to be associated with a better prognosis (HR = 0.68; p = 0.043) whereas LAR subtype was associated with a worst prognosis (HR = 1.47; p = 0.046).

BL1 subtype was found to be most genomically instable subtype with high TP53 mutation (92%) and copy-number deletion in genes involved in DNA repair mechanism (BRCA2, MDM2, PTEN, RB1 and TP53).

LAR tumours were associated with higher mutational burden with significantly enriched mutations in PI3KCA (55%), AKT1 (13%) and CDH1 (13%) genes.

M and MSL subtypes were associated with higher signature score for angiogenesis.

IM showed high expression levels of immune signatures and checkpoint inhibitor genes such as PD1, PDL1 and CTLA4.

The largest study to characterise in depth TNBC subtype-specific alterations

BL1, IM and M tumours were classified as basal-like tumours whereas a substantial proportion of LAR and MSL tumours were classified as HER2-enriched and normal-like, respectively. LAR tumours were associated with higher mutational burden with significantly enriched mutations clustered in the PI3K pathway and MSL tumours were the ones showing the lowest mutational load that could partially explain their pertaining to HER2-enriched and normal-like subtypes by PAM50, respectively.

Although this TNBC series was mostly represented by invasive ductal carcinomas, the researchers observed some differences with the LAR and IM subtypes being enriched with invasive lobular and medullary carcinomas, respectively. Similarly to LAR tumours, lobular cancers harbour high mutation frequency in PIK3CA, AKT1 and CDH1 genes whereas medullary breast cancers, like IM tumours, are enriched with tumour infiltrating lymphocytes which are captured by high expression levels of immune checkpoint genes and immune response signatures.

The study team found specific differences in mutational and copy number profiles characterising each TNBC molecular subtype offering novel therapeutic avenues for TNBC patients.

For instance, they demonstrated that BL1 tumours were characterised by high genomic instability, high copy number losses for TP53, BRCA1/2 and RB1 genes, as well as high copy number gains for PPAR1 gene suggesting that these tumours may be sensitive to PARP inhibitors. In addition, they may also be potential candidates for MEK1/2 inhibitors since 90% of BL1 tumours displayed copy number gains for KRAS, NRAS and BRAF with significant mRNA overexpression of the corresponding genes. A high proportion of BL1 may also benefit from PI3K/AKT inhibitors since they showed a high frequency of PIK3CA copy number gains with significant overexpression of PIK3CA, AKT2 and AKT3 genes.

The study team also demonstrated that LAR and MSL tumours retained RB1 while showing significantly lower CDK4 and CDK6 mRNA expression level. Since RB1, CDK4 and CDK6 expression was shown to be associated with response to CDK4/6 inhibitors, patients diagnosed with LAR and MSL tumours may be potential candidates to CDK4/6 inhibitors. Moreover, 75% of LAR tumours exhibited somatic mutations in PI3K signalling pathway, suggesting a potential benefit to PI3K and AKT inhibitors as previously reported in preclinical models.

Despite being genetically more stable, MSL tumours showed a significant mRNA overexpression of PDGFR and VEGFR suggesting that these tumours may derive benefit from an antiangiogenic therapy in contrast to unselected TNBC population.

EGFR and Notch signalling pathways were found to be enriched in M subtype, with high level of mRNA expression for EGFR and NOTCH1, NOTCH3 suggesting that targeting EGFR and Notch pathways may be an option for these tumours. Similarly to anti-VEGF inhibitors, EGFR inhibitors failed to demonstrate a survival advantage in unselected TNBC.

What differentiated IM to other TNBC subtypes was the presence of high expression levels of immune related signatures as well as high mRNA expression levels of immune checkpoint inhibitor genes such as PD1, PDL1 and CTLA4 suggesting that these tumours may mostly benefit from checkpoint inhibitors.

MYC was the most frequently gained/amplified gene in almost all TNBC subtypes but MSL, in association with a significant mRNA overexpression in the BL1 and M subtypes. It has been recently shown that selective inhibition of CDK1/2 and spliceosomal core component BUD31 was found to induce synthetic lethal mortality in MYC overexpressing TNBC tumours suggesting a potential benefit of inhibiting CDK1/2 and the spliceosome, in particular in the BL1 and M subtypes.


In view of limited clinical benefit with targeted therapies in unselected TNBC patients, there is a research impetus towards optimising treatment through molecular subtyping. Despite the large number of past and ongoing clinical trials investigating therapeutic targets in TNBC, chemotherapy is still the only standard treatment option. In this integrative in silico analysis by using publicly available datasets, the researchers were able to reproduce Lehmann’s TNBC classification. The analysis allowed identification of several candidate targets.

The researchers were supported by the Télévie, the Fonds National de la Recherche Scientifique (F.R.S.-FNRS) and by a grant of the Région Wallonne. The study was supported by a grant from Breast Cancer Research Foundation (BCRF). 


Bareche Y, Venet D, Ignatiadis P, et al. Unravelling triple-negative breast cancer molecular heterogeneity using an integrative multiomic analysis.Annals of Oncology, Published online 22 January 2018.