Modeling the Genomic Landscape of HER2-Positive Breast Cancer

The second major research project in the Hormones and Cancer Laboratory is to model the genomic landscape of HER2-positive breast cancer. Dr. Thompson's Hormones and Cancer Lab is conducting a deep-sequence analysis of the transcriptome of HER2-positive cell lines and tumors using paired end-tagged RNA sequence (RNA-seq) technology.

Dr. Thompson and his research team have completed RNA-seq analysis of a survey panel of tumors, including ER positive, HER2-positive and triple negative tumors. In addition, the lab has carried out RNA sequence analysis of a panel of benign breast tumors used to build a HER2 transcriptome map.

In parallel to that work, the research team isolated and characterized trastuzumab-resistant HER2 cell lines (BT474 and SKBR3). The lab completed RNA-seq analysis of both sensitive and resistant cell lines after treatment with trastuzumab and after ERBB2 knockdown with two independent shRNA constructs. These data are being analyzed to identify HER2-regulated genes, which will be evaluated for mechanistic insight, as biomarkers of HER2 activity and as potential therapeutic targets.

Dr. Thompson's team is also carrying out deep sequence analysis of genomic rearrangements in HER2-positive tumors and patient-matched normal DNA using mate-pair tagged genomic sequence technology. The lab has invested a considerable amount of time and effort into developing analytical workflows to identify genomic rearrangements using mate-pair genomic sequence analysis.

Two major research conclusions

Two major conclusions are derived from these studies:

  • First, the majority of fusion transcripts arise from genomic rearrangements. This outcome substantiates the lab's view that fusion transcripts can be used as surrogate markers of chromosomal instability.
  • Second, the research team is satisfied that mate-pair sequencing does not produce sufficient depth of coverage for detailed mapping of genomic rearrangements. Future directions in this regard will therefore focus on whole-genome sequencing, which is becoming increasingly cost-effective.

The ability to integrate various types of genomic data remains a major challenge in cancer genomics.

Developing new analytic tools

The Hormones and Cancer Lab has completed the construction of genomic interactome maps of HER2-positive breast cancer. The evolution of this landscape model has required the development of new analytical tools for quantifying splice variants, and for identifying and quantifying expressed single nucleotide sequence variants (eSNVs) in tumor RNA.

Using these tools, the lab team has been able to build a landscape model that incorporates differential mRNA expression, alternative splicing and HER2-specific eSNVs. Components of this pathway have been linked to therapeutic response, using the lab's genomic data from the North Central Cancer Treatment Group N9831 HER2 adjuvant trial.

These data are also being used to interrogate the functional HER2 signaling model that is being built using data from sensitive and resistant cell lines treated with trastuzumab and after ERBB2 knockdown.

Dr. Thompson and his team are also interrogating phosphoproteomic data (generated along with external collaborator Emanuel Petricoin, Ph.D.) in an effort to link genomic changes to changes in protein phosphorylation status. These studies are currently exploratory.