mRNA profiling reveals determinants of trastuzumab efficiency in HER2-positive breast cancer

PLoS One. 2015 Feb 24;10(2):e0117818. doi: 10.1371/journal.pone.0117818. eCollection 2015.

Abstract

Intrinsic and acquired resistance to the monoclonal antibody drug trastuzumab is a major problem in the treatment of HER2-positive breast cancer. A deeper understanding of the underlying mechanisms could help to develop new agents. Our intention was to detect genes and single nucleotide polymorphisms (SNPs) affecting trastuzumab efficiency in cell culture. Three HER2-positive breast cancer cell lines with different resistance phenotypes were analyzed. We chose BT474 as model of trastuzumab sensitivity, HCC1954 as model of intrinsic resistance, and BTR50, derived from BT474, as model of acquired resistance. Based on RNA-Seq data, we performed differential expression analyses on these cell lines with and without trastuzumab treatment. Differentially expressed genes between the resistant cell lines and BT474 are expected to contribute to resistance. Differentially expressed genes between untreated and trastuzumab treated BT474 are expected to contribute to drug efficacy. To exclude false positives from the candidate gene set, we removed genes that were also differentially expressed between untreated and trastuzumab treated BTR50. We further searched for SNPs in the untreated cell lines which could contribute to trastuzumab resistance. The analysis resulted in 54 differentially expressed candidate genes that might be connected to trastuzumab efficiency. 90% of 40 selected candidates were validated by RT-qPCR. ALPP, CALCOCO1, CAV1, CYP1A2 and IGFBP3 were significantly higher expressed in the trastuzumab treated than in the untreated BT474 cell line. GDF15, IL8, LCN2, PTGS2 and 20 other genes were significantly higher expressed in HCC1954 than in BT474, while NCAM2, COLEC12, AFF3, TFF3, NRCAM, GREB1 and TFF1 were significantly lower expressed. Additionally, we inferred SNPs in HCC1954 for CAV1, PTGS2, IL8 and IGFBP3. The latter also had a variation in BTR50. 20% of the validated subset have already been mentioned in literature. For half of them we called and analyzed SNPs. These results contribute to a better understanding of trastuzumab action and resistance mechanisms.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antibodies, Monoclonal, Humanized / pharmacology*
  • Antibodies, Monoclonal, Humanized / therapeutic use
  • Antineoplastic Agents / pharmacology*
  • Antineoplastic Agents / therapeutic use
  • Breast Neoplasms / drug therapy
  • Breast Neoplasms / genetics*
  • Breast Neoplasms / pathology
  • Caveolin 1 / genetics
  • Caveolin 1 / metabolism
  • Cell Line, Tumor
  • Cell Survival / drug effects
  • Drug Resistance, Neoplasm / drug effects
  • Female
  • Humans
  • Polymorphism, Single Nucleotide
  • Principal Component Analysis
  • RNA, Messenger / metabolism*
  • Real-Time Polymerase Chain Reaction
  • Receptor, ErbB-2 / metabolism
  • Sequence Analysis, RNA
  • Trastuzumab
  • Up-Regulation / drug effects*

Substances

  • Antibodies, Monoclonal, Humanized
  • Antineoplastic Agents
  • CAV1 protein, human
  • Caveolin 1
  • RNA, Messenger
  • Receptor, ErbB-2
  • Trastuzumab

Associated data

  • GEO/GSE55005

Grant support

This work was supported by the German Federal Ministry of Education and Research in the platform MedSys via the project BreastSys (grant 0315396A, URL http://www.ams.med.uni-goettingen.de/breastsys/), in the platform e:Bio via the project MetastaSys (grant 0316173A, URL http://www.ams.med.unigoettingen.de/metastasys/) and in the platform e:Med via the project Her2Low (grant 031A429C, URL http://www.ams.med.uni-goettingen.de/her2low/). TB received the mentioned funding. Above that SvdH, MN, SW and DA were funded by BreastSys. AC was funded by MetastaSys. The authors also acknowledge support by the Open Access Publication Funds of the Göttingen University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.