MAY 09, 2019 12:00 PM PDT

A Metagenomic Assay to Interrogate the Role of Virome and Microbiome in Cancer

SPONSORED BY: Agilent
Speakers
  • Harry P. Schenck Endowed Chair Professor, Vice-Chair, Department of Otorhinolaryngology, Perelman School of Medicine, University of Pennsylvania
    Biography
      Erle S. Robertson obtained his Dr. Robertson received his doctorate degree from Wayne State University in Microbiology and Molecular Genetics where he studied interaction of the T-phages with bacterial hosts by mapping their infection proteome. He then completed his post-doctoral studies at Harvard Medical School and Brigham and Women's Hospital in the Department of Medicine/Infectious Disease Division as a Cancer Research Institute Fellow and an Leukemia and Lymphoma Society Special Fellow. There he studied the role of EBV in driving the oncogenic process in human cells using genetic and biochemical approaches. In 1994 he was promoted to Instructor in Medicine and was recruited to the University of Michigan Medical School in 1997. He was promoted to Associate Professor with tenure in 2002 in the Department of Microbiology. He was recruited to the Perelman School of Medicine with tenure in 2002, quickly achieving the rank of Full Professor with tenure in 2006. His awards include the Scholar Award of the Lymphoma and Leukemia Society, named Fellow of the American Academy of Microbiology, Fellow of the American Association for the Advancement of Sciences, and Fellow of the College of Physicians of Philadelphia. He was also selected as a Penn Fellow by the President and Provosts office of the University in recognition of his contribution to the cross-disciplinary activities that can bridge and enhance greater activities related to research and scholarship between different schools at Penn. In 2016, Dr. Robertson was recruited to the Department of Otorhinolaryngology to serve as Vice-Chair for Research and Director of Head and Neck Sciences in the Department of Otorhinolaryngology - Head and Neck Surgery. Since joining the department, Dr. Robertson has contributed significantly to building an internationally recognized research program in head and neck sciences with increased interactions and collaborations with the Abramson Cancer Center and across our collective clinical and basic science departments.

    Abstract:

    Screening to identify all known viruses and other pathogenic microorganisms including bacteria, fungus and parasites in human tumor tissues will provide a more comprehensive understanding of the contributory role of the microbiome in the associated cancer. Metagenomic assays will require rapid and economical processing of large numbers of samples and data analysis pipeline. The PathoChip platform was developed by targeting viral, prokaryotic and eukaryotic genomes with multiple DNA probes in a microarray format that can be combined with a variety of upstream sample preparation protocols and downstream data analyses. PathoChip screening of DNA and RNA from formalin-fixed, paraffin embedded tumor tissues demonstrated the utility of this platform, and the detection of oncogenic viruses was validated using independent PCR and deep sequencing methods. These studies demonstrate the use of the PathoChIP technology combined with PCR and deep sequencing as a valuable strategy for identification of microbial pathogens in human cancers and other diseases. Furthermore, we were able to rapidly identify a zygomycetous fungi, Rhizomucor, a challenging organism for microbial testing laboratories, in a subject with acute myelogenous leukemia using this pan pathogen array technology. We highlight the value of PathoChip as a tool to identify micro-organisms to the species or strain level, especially for those difficult to identify in most microbial testing laboratories. Additionally, human cancers are associated with a wide range of microbes making infections the third highest cancer risk. We used the PathoChIP technology to identify the viruses, bacteria, fungi and parasites associated with breast cancer using formalin-fixed paraffin embedded (FFPE) archival tissues. Results were validated by PCR and next-generation sequencing. We define the signatures in a specific type of breast cancer tissue which was underrepresented in normal tissue. These include viruses as well as families of bacteria, fungi and eukaryotic parasites. Hierarchical clustering analysis identified two signature patterns, one with predominant bacteria and parasites and the other predominant for viruses. The contribution of these microbial signatures to cancer is yet to be determined. However, these microbes may contribute or exist in the tumor microenvironment and impact cancer biology. 

    For Research Use Only. Not for use in diagnostic procedures.

    Learning Objectives: 

    1. Understand the importance of screening as it relates to the microbiome in cancer. 
    2. Gain an understanding as to how the PathoChIP technology can be used as a valuable tool to identify micro-organisims during testing. 


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