Somagenics, a biotech company specialized in small RNA technologies, has received a second NIH grant to develop a method to quantify mRNA from degraded samples. The resQ-RNA is a quantitative real-time PCR of fragmented samples. The I-SBIR grant will be used to fund assays with a whole new range of RNA targets, including transcripts involved in breast cancer.
RNA obtained from tissue samples is often in very bad condition due to improper sample storage or collection. Formaldehyde, paraffin or the presence of RNases, among other factors, can fragment RNA to lengths incompatible with amplification by real-time quantitative PCR. Somagenics has developed a technology that would allow to amplify RNAs 23 nucleotides long, compared with the minimum of 100 nt needed with current technologies. The resQ-RNA will allow to quantify RNA from formaldehyde-fixed, paraffin-embedded (FFPE) samples collected through the years in hospitals. These biopsy collections store very valuable information that has been impossible to access so far. Every RNA sample contains biomarkers that would be linked to clinical information of a patient -disease, response to treatment, progression, etc.
RNA circularization before amplification
The resQ-RNA method starts with RNA fragments circularization, followed by rolling-circle amplification. The resultant concatemeric cDNA is then PCR-amplified. The repeated DNA allows to use primers that are similar in size to the sequence to be analyzed. A similar approach has already been used in other Somagenics applications to analyze microRNA, like miR-ID® and miR-Direct®.
resQ-RNA has been tested in some RNA samples. Somagenics will use the new funds to develop the technology and use it in new RNA targets relevant to diseases.