Expression data from RNA-sequencing can differentiate breast cancer histological grade

The histologic grade (HG) of breast cancer is an established prognostic factor. The grade is usually reported on a scale ranging from 1 to 3, where grade 3 tumours are the most aggressive. However, grade 2 is associated with an intermediate risk of recurrence, and carries limited information for clinical decision-making. Patients classified as grade 2 are at risk of both under- and over-treatment.

Researchers from the Karolinska Institutet conducted RNA-sequencing analysis in a cohort of 275 women diagnosed with invasive breast cancer. Multivariate prediction models were developed to classify tumours into high and low transcriptomic grade (TG) based on gene- and isoform-level expression data from RNA-sequencing. HG2 tumours were reclassified according to the prediction model and a recurrence-free survival analysis was performed by the multivariate Cox proportional hazards regression model to assess to what extent the TG model could be used to stratify patients. The prediction model was validated in N=487 breast cancer cases from the The Cancer Genome Atlas (TCGA) data set. Differentially expressed genes and isoforms associated with HGs were analysed using linear models.

The classification of grade 1 and grade 3 tumours based on RNA-sequencing data achieved high accuracy (area under the receiver operating characteristic curve = 0.97). The association between recurrence-free survival rate and HGs was confirmed in the study population (hazard ratio of grade 3 versus 1 was 2.62 with 95 % confidence interval = 1.04-6.61). The TG model enabled us to reclassify grade 2 tumours as high TG and low TG gene or isoform grade. The risk of recurrence in the high TG group of grade 2 tumours was higher than in low TG group (hazard ratio = 2.43, 95 % confidence interval = 1.13-5.20). The researchers found 8200 genes and 13,809 isoforms that were differentially expressed between HG1 and HG3 breast cancer tumours.

Heat map of 34 frequently selected genes in the TG-Gene model


In the Clinseq data set, the TG-Gene model was cross-validated 100 times to optimise parameters. In 100 rounds of CV, 34 genes were selected in the models in more than 92 out of the 100 CV rounds. Value of colour key is log2 (normalised RNA-seq count). ER oestrogen receptor, PR progesterone receptor, RNA-seq RNA sequencing

Gene- and isoform-level expression data from RNA-sequencing could be utilised to differentiate HG1 and HG3 tumours with high accuracy. Researchers identified a large number of novel genes and isoforms associated with HG. Grade 2 tumours could be reclassified as high and low TG, which has the potential to reduce over- and under-treatment if implemented clinically.

Wang M, Klevebring D, Lindberg J, Czene K, Grönberg H, Rantalainen M. (2016) Determining breast cancer histological grade from RNA-sequencing data. Breast Cancer Res 18(1):48. [article]

One comment

  1. can you please share which software you used to make the heatmap/visualization?

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