Dr. Kristin Anderson, who works as a Postdoctoral Research Fellow at the University of Washington and Fred Hutchinson Cancer Research Center in Seattle, is developing molecular engineering strategies to improve tumor eradication with genetically engineered cells in ovarian cancer with the ultimate goal of translating her findings into treatment protocols for patients. In order to establish appropriate models, she uses transcriptome profiling together with other cutting-edge technologies to characterize the human and murine tumor microenvironment. “We think that analysis by transcriptome profiling of appropriate immunocompetent models and human tissues can be used to predict obstacles to therapeutic human T cell function,” says Dr. Anderson. She recently presented her results in a webinar: “Preclinical T cell immunotherapy strategies for overcoming immunosuppression in solid tumors,” the full presentation is available to watch on-demand.
Often, cancer researchers, like Dr. Anderson, who work with biopsies extracted from solid tumors may access only small quantities of material that is usually further split in order to perform multiple analyses. The ability to reliably profile transcriptomes from quantities as low as 100 pg of RNA enables researchers to extract the maximum of information from those precious samples, including from FFPE, fresh/fresh-frozen tissues, and whole blood that are commonly used in oncology research.
“We chose whole transcriptome profiling with Applied Biosystems™ Clariom™ D Pico assays because we had RNA from particular tissues that were limited in quantity and we needed an assay that was good with very low input level”, said Dr. Anderson. “In addition, Clariom D is one of the most recent microarray design with coverage of exons and exon junctions, allowing to get information on isoforms and non-coding RNA as well.”
Dr. Anderson used Applied Biosystems Services labs to process her samples. “Sample submission was very simple. They did all the quality testing and this one of the reasons we used these services. No one in my lab is an expert at deep transcriptome profiling and because we had such limited and valuable samples, we wanted to make sure that there would be a thorough QC done and the data we got back would be of really good quality.”
For data analysis, Dr. Anderson used the transcriptome analysis console (TAC) that is available at no cost with the Clariom microarray products, to look at what normal samples look like compared to tumors, which genes were up or down. “We got so much data out of this assay. I am not a bioinformatics expert; my training was in immunology as graduate student, cancer biology and molecular biology as a postdoc. TAC software was really intuitive and easy to use.” Clariom D for deep transcriptome profiling of over 500,000 transcripts from limited samples together with TAC intuitive software enables immune-oncology researchers to overcome the bottleneck of bioinformatics analysis and get deep insights quickly.
Dr. Anderson’s research is featured in a webinar on pre-clinical T cell immunotherapy strategies for overcoming immunosuppression in solid tumors. While her findings are intended to inform the development of new immunotherapies for treating ovarian cancer patients, the mechanisms under investigation are operative in many solid tumors and her advances will likely have applicability to many other malignancies.
To learn more about this research study, watch the webinar presented by Dr. Kristin Anderson
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