A Sensitive NanoString-Based Assay to Score STK11 (LKB1) Pathway Disruption in Lung Adenocarcinoma

J Thorac Oncol. 2016 Jun;11(6):838-49. doi: 10.1016/j.jtho.2016.02.009. Epub 2016 Feb 23.

Abstract

Introduction: Serine/threonine kinase 11 gene (STK11), better known as liver kinase β1, is a tumor suppressor that is commonly mutated in lung adenocarcinoma (LUAD). Previous work has shown that mutational inactivation of the STK11 pathway may serve as a predictive biomarker for cancer treatments, including phenformin and cyclooxygenase-2 inhibition. Although immunohistochemical (IHC) staining and diagnostic sequencing are used to measure STK11 pathway disruption, there are serious limitations to these methods, thus emphasizing the importance of validating a clinically useful assay.

Methods: An initial STK11 mutation mRNA signature was generated using cell line data and refined using three large, independent patient databases. The signature was validated as a classifier using The Cancer Genome Atlas (TCGA) LUAD cohort as well as a 442-patient LUAD cohort developed at Moffitt. Finally, the signature was adapted to a NanoString-based format and validated using RNA samples isolated from formalin-fixed, paraffin-embedded tissue blocks corresponding to a cohort of 150 patients with LUAD. For comparison, STK11 IHC staining was also performed.

Results: The STK11 signature was found to correlate with null mutations identified by exon sequencing in multiple cohorts using both microarray and NanoString formats. Although there was a statistically significant correlation between reduced STK11 protein expression by IHC staining and mutation status, the NanoString-based assay showed superior overall performance, with a -0.1588 improvement in area under the curve in receiver-operator characteristic curve analysis (p < 0.012).

Conclusion: The described NanoString-based STK11 assay is a sensitive biomarker to study emerging therapeutic modalities in clinical trials.

Keywords: COX-2 inhibition; LKB1; NanoString; STK11; biomarker.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenocarcinoma / diagnosis*
  • Adenocarcinoma / genetics
  • Biological Assay / methods*
  • Biomarkers, Tumor / genetics*
  • Cohort Studies
  • Humans
  • Lung Neoplasms / diagnosis*
  • Lung Neoplasms / genetics
  • Mutation*
  • Nanotechnology
  • Neoplasm Staging
  • Prognosis
  • Protein-Serine-Threonine Kinases / genetics*
  • ROC Curve

Substances

  • Biomarkers, Tumor
  • STK11 protein, human
  • Protein-Serine-Threonine Kinases