June 27, 2017
Sponsored by
HTG Molecular

Optimized qNPA Expression Analysis Yields Biological Insight in Lung Cancer FFPE

GenomeWebinar

Senior Research Scientist, Hamon Center for Therapeutic Oncology Research
University of Texas Southwestern Medical Center at Dallas

This webinar demonstrates that a quantitative nuclease protection assay (qNPA) produces consistent, high-quality expression data in formalin-fixed, paraffin-embedded (FFPE) patient samples, which is of use both in the clinic and as a discovery tool at the bench.

Most clinically annotated biopsied or resected tumor specimens are archived as FFPE blocks, which have proven difficult to assay for quantitative RNA expression. Our speaker, Kenneth Huffman of the University of Texas Southwestern Medical Center at Dallas, describes a study that used a qNPA assay to to assess the expression of 48 nuclear receptors (NRs) and 72 closely associated co-regulators (CoRegs) in non-small cell lung cancer (NSCLC) FFPE samples.

NRs and CoRegs play key regulatory roles in normal developmental and homeostatic biology but are also known as important functional and targetable proteins in several cancers. After successful development and implementation of a tissue specific endogenous control program for qNPA analysis of FFPE samples, Dr. Huffman and colleagues examined NR/CoReg mRNA expression in FFPE embedded tumor and normal matched samples from 230 lung cancer patients. They noted that expression of 10 NRs was frequently lower in tumor versus normal comparisons. Examination of TCGA lung cancer datasets as well as more than 14 other published datasets confirmed the down-regulation of these NRs in tumor-normal comparisons. Furthermore, retrospective analysis of a 2347-sample meta dataset revealed a significant overall survival benefit for patients with higher expression of these receptors. Multivariate analysis of patient data showed an association between NR loss and increasing tumor stage.

Viewers of this webinar will learn the following:

  • How to develop assays and validate HTG’s quantitative methodology for reliably measuring mRNA expression levels in clinical FFPE samples.
  • How to measure NR/CoReg mRNA expression in cell lines and 227 lung tumor/normal matched FFPE patient samples.
  • How to identify NRs and CoRegs that are potentially dysregulated in NSCLC.
  • How to define relationships between NR/CoReg expression and important clinical or molecular correlates.


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