Expression-Based Profiling of Challenging FFPE Tumor Samples

This webinar focused on recent advances in gene expression profiling of challenging formalin-fixed, paraffin-embedded tissue samples for cancer research and clinical practice. The presentation covered studies in non-small cell lung cancer and pancreatic cancer. 

The first presenters, Adi Gazdar and Luc Girard from UT Southwestern Medical Center, discussed an expression-based assay for the pathological classification of non-small cell lung cancer. 

Most NSCLCs are diagnosed from small specimens, and classification using standard pathology methods can be difficult. This is of clinical relevance as many therapy regimens and clinical trials are histology-dependent. Dr. Gazdar and Dr. Girard developed a 62-gene mRNA expression signature as an adjunct test for routine histopathological classification of NSCLCs, which includes many genes used in immunostains for NSCLC typing. 

In order to demonstrate the clinical practicality and cost-effectiveness of the classifier, they developed a research-use, custom assay based on the HTG EdgeSeq technology. The classifier can be applied to small FFPE samples and core-needle biopsies, demonstrating the potential for deployment of routine RNA testing in standard clinical practice. 

Next, Bryan Lo of the Ottawa Hospital discussed a method for gene expression profiling of pancreatic cancer precursors directly from FFPE tissues without nucleic acid extraction. 

Gene expression analysis of pancreatic intraepithelial neoplasia’s (PanINs), the classical pancreatic cancer precursor, has been challenging because extracting and purifying RNA from pancreatic tissue is difficult. Since the pancreas is rich in ribonucleases and PanINs are typically very small lesions, attempts to purify RNA of sufficient quality and quantity for microarray or RNAseq are usually unsuccessful. This is especially true if the starting material is FFPE tissue, where the fixation process introduces further degradation of the RNA. 

Dr. Lo and colleagues have shown in a pilot study that they can use the HTG EdgeSeq Oncology Biomarker Panel to profile approximately 2,500 genes from a cohort of microdissected low- and high-grade PanIN lesions from human pancreatic cancer resections that have been archived as FFPE tissue blocks. 

Dr. Lo and colleagues believe that most of these PanIN lesions would not have been amenable to other gene expression methodologies and that the PanIN data collected using the HTG EdgeSeq technology will contribute to a better understanding of the molecular pathways that underlie pancreatic cancer.


Dr. Adi Gazdar, MD
Dr. Luc Girard, Ph.D
Dr. Bryan Lo, MD/PhD
John Luecke

Speaker Biographies

Adi Gazdar serves as a professor of pathology and Deputy Director of the Hamon Center for Therapeutic Oncology Research at the University of Texas Southwestern Medical Center.  Dr. Gazdar is the holder of the W. Ray Wallace Distinguished Chair in Molecular Pathology Research. He is a pathologist and molecular biologist with a long standing interest in lung cancer with over 400 publications in this field.  He is among the most widely quoted scientists in medical literature (among the top 1%). He received the Mary Matthews award from the International Association of the Study of Lung Cancer for contributions to pathology excellence.  He has extensive experience with tissue procurement and processing and cell culture experience.  He has developed a new molecular classification for lung cancers.  The cell lines he has initiated are have been widely distributed worldwide and form the basis of much of the in vitro studies on lung cancer.  He has closely collaborated with numerous pathologists, investigators and clinicians for many years. He has been a member of the IASLC for over 30 years, and served on the Board of Directors and on the Pathology Panel. He was a member of the IASLC sponsored Committee that reclassified lung adenocarcinomas and serves on WHO committees reclassifying lung cancers.

Luc Girard, Ph.D. is an Assistant Professor at UT Southwestern Medical Center. Originally from Montreal, Canada, he is a molecular biologist with extensive bioinformatics experience. Over the past several years, he has taken part in multiple genomic and functional screening efforts, including the generation of a large dataset of in vitro drug sensitivity assays (n > 35,000), the creation of a multi-user (server-client) database to store these assays and automatically process them, and the derivation of expression signatures for drug response in lung cancer as well as for classification of NSCLCs. He is collaborating closely with Drs. John Minna, Adi Gazdar and multiple investigators at UT Southwestern and other institutions.

Dr. Bryan Lo received his MD/PhD from the University of Toronto, followed by a medical genetics residency at the Hospital for Sick Children from 1999 to 2004. He was a postdoctoral fellow in the Department of Cell Biology at Yale University from 2005 to 2007 when he became a research fellow in the Department of Research Oncology at the biotechnology firm Genentech in South San Francisco, California. In 2014, Dr. Lo returned to Canada to become the medical director for The Ottawa Hospital's brand new Molecular Oncology Diagnostics Laboratory. In addition, he sees patients in the Inherited Cancer Program at the Children's Hospital of Eastern Ontario and maintains a research lab in The Ottawa Hospital Research Institute investigating the basic biology of precancerous lesions.

Mr. Luecke has served in various Marketing, Scientific Affairs, and Operations roles with HTG since 2008.  He has worked extensively with drug development teams helping to develop effective biomarker strategies using HTG technology.  Prior to joining HTG, Mr. Luecke served in marketing roles with Epicentre Biotechnologies, where he was responsible for the development and commercialization of various molecular biology technologies including those for microarray, qPCR, and NGS applications. Mr. Luecke holds a Master’s Degree in Bacteriology and a Master’s Degree in Business Administration from the University of Wisconsin-Madison.

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