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Quantitative Nuclease Protection Assay from Archival FFPE Discovers Systematic Downregulation of Nuclear Receptors in Lung Cancer

Join us Tuesday, June 27, 2017 at 1:00 pm EDT, 10:00 am PDT, 12:00 pm CDT for a Genomeweb Webinar.
This webinar will demonstrate 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, will describe 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.

Attendees 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.

Kenneth Huffman Ph.D.
Senior Research Scientist, Hamon Center for Therapeutic Oncology Research
University of Texas Southwestern Medical Center at Dallas

Dr. Kenneth Huffman is a Senior Research Scientist in the Hamon Center for Therapeutic Oncology and The Simmons Cancer Center at the University of Texas Southwestern Medical School. Dr. Huffman has spent six years as a member of Dr. John Minna’s lab and during that time has been an author on more than 12 peer-reviewed papers in lung and breast cancer research. Dr. Huffman received a BA in Biochemistry and a Ph.D. in Cell Biology/Biophysics at The University of Texas. He was the recipient of Ruth L. Kirchstein NIH fellowship as a postdoctoral researcher at UT Southwestern.

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