SureSelectXT RNA Direct: A Technique for Expression Analysis Through Sequencing of Target-Enriched FFPE Total RNA.

Gene expression profiling of samples from biobanks requires a method that can be used with intact as well as partially degraded RNA. High throughput applications can benefit from reducing the number of processing steps including eliminating the poly(A) selection and ribosomal depletion steps. When performing targeted capture, we have found that we can eliminate the upfront poly(A) selection/ribosomal depletion steps that cause bias in standard mRNA-Seq workflows. This target enrichment solution allows for whole transcriptome or customized content to characterize differential gene expression patterns (especially for mid/low level transcripts). Protocol modifications to the Agilent Strand-Specific RNA Library Prep kit resulted in a new workflow called "RNA Direct" that generates RNA-Seq data with minimal ribosomal contamination and good sequencing coverage. Using RNA isolated from a set of matched samples including fresh frozen (FF) or formalin-fixed, paraffin-embedded (FFPE) from tumor/normal tissues we generated high-quality data using a protocol that does not require upfront ribosomal depletion or poly(A) selection. Using SureSelectXT RNA Direct protocol (RNA Direct) workflow, we found transcripts to be upregulated or downregulated to similar degrees with similar confidence levels in both the FF and FFPE samples, demonstrating the utility for meaningful gene expression studies with biobank samples of variable quality.

Chronic mechanistic target of rapamycin inhibition: preventing cancer to delay aging, or vice versa?.

Cancer and aging appear to be inexorably linked, yet approaches to ameliorate them in concert are lacking. Although not (easily) feasible in humans, years of preclinical research show that diet and growth factor restriction each successfully address cancer and aging together. Chronic treatment of genetically heterogeneous mice with an enteric formulation of rapamycin (eRapa) extended maximum lifespan of both genders when started in mid or late life. In part, cancer amelioration in treated mice suggested that long-term eRapa, like diet restriction, could be a pharmacological approach feasible for use in the clinic. We review the current understanding of the role of the mechanistic target of rapamycin (mTOR) in cancer and aging. We also discuss the tumor immune surveillance system, and the need for a better understanding of its responses to mTOR inhibitors. We also address the issue of the misperception that rapamycin is a potent immunosuppressant. Finally, we review the current state of mTOR inhibitors in the cancer clinic. Because of the burgeoning elderly population most at risk for cancer, there is a great need for our eRapa findings to be a proof of concept for the development of new and more comprehensive approaches to cancer prevention that are safe and also mitigate other deleterious effects of aging.