Energy profile and secondary structure impact shRNA efficacy

<p>Abstract</p> <p>Background</p> <p>RNA interference (RNAi) is a cellular mechanism in which a short/small double stranded RNA induces the degradation of its sequence specific target mRNA, leading to specific gene silencing. Since its discovery, RNAi has become a powerful biological technique for gene function studies and drug discovery. The very first requirement of applying RNAi is to design functional small interfering RNA (siRNA) that can uniquely induce the degradation of the targeted mRNA. It has been shown that many functional synthetic siRNAs share some common characteristics, such as GC content limitation and free energy preferences at both terminals, etc.</p> <p>Results</p> <p>Our three-phase algorithm was developed to design siRNA on a whole-genome scale based on those identified characteristics of functional siRNA. When this algorithm was applied to design short hairpin RNA (shRNA), the validated success rate of shRNAs was over 70%, which was almost double the rate reported for TRC library. This indicates that the designs of siRNA and shRNA may share the same concerns. Further analysis of the shRNA dataset of 444 designs reveals that the high free energy states of the two terminals have the largest positive impact on the shRNA efficacy. Enforcing these energy characteristics of both terminals can further improve the shRNA design success rate to 83.1%. We also found that functional shRNAs have less probability for their 3' terminals to be involved in mRNA secondary structure formation.</p> <p>Conclusion</p> <p>Functional shRNAs prefer high free energy states at both terminals. High free energy states of the two terminals were found to be the largest positive impact factor on shRNA efficacy. In addition, the accessibility of the 3' terminal is another key factor to shRNA efficacy.</p

Designing of highly effective complementary and mismatch siRNAs for silencing a gene

In past, numerous methods have been developed for predicting efficacy of short interfering RNA (siRNA). However these methods have been developed for predicting efficacy of fully complementary siRNA against a gene. Best of author's knowledge no method has been developed for predicting efficacy of mismatch siRNA against a gene. In this study, a systematic attempt has been made to identify highly effective complementary as well as mismatch siRNAs for silencing a gene. Support vector machine (SVM) based models have been developed for predicting efficacy of siRNAs using composition, binary and hybrid pattern siRNAs. We achieved maximum correlation 0.67 between predicted and actual efficacy of siRNAs using hybrid model. All models were trained and tested on a dataset of 2182 siRNAs and performance was evaluated using five-fold cross validation techniques. The performance of our method desiRm is comparable to other well-known methods. In this study, first time attempt has been made to design mutant siRNAs (mismatch siRNAs). In this approach we mutated a given siRNA on all possible sites/positions with all possible nucleotides. Efficacy of each mutated siRNA is predicted using our method desiRm. It is well known from literature that mismatches between siRNA and target affects the silencing efficacy. Thus we have incorporated the rules derived from base mismatches experimental data to find out over all efficacy of mutated or mismatch siRNAs. Finally we developed a webserver, desiRm (http://www.imtech.res.in/raghava/desirm/) for designing highly effective siRNA for silencing a gene. This tool will be helpful to design siRNA to degrade disease isoform of heterozygous single nucleotide polymorphism gene without depleting the wild type protein

Role of epidermal growth factor receptor in feline oral squamous cell carcinoma

Feline oral squamous cell carcinomas (FOSCCs) are locally aggressive tumours and a common cause of mortality and morbidity. Current treatment options are rarely successful and animals are frequently euthanised upon diagnosis due to their grave prognosis. Epidermal Growth Factor Receptor (EGFR) is a tyrosine kinase receptor which is frequently dysregulated in SCC of the head and neck (HNSCC) in man. Recent advances in human medicine have identified EGFR as a therapeutic target in HNSCC. In this study the role of EGFR in FOSCC was investigated. Sixty seven biopsy samples were immunohistochemically labelled for EGFR and Ki67, a proliferation marker. The tyrosine kinase region of feline EGFR was cloned and sequenced, and six small interfering RNAs (siRNAs) targeting the tyrosine kinase region were developed. The most effective siRNA as well as an EGFR specific tyrosine kinase inhibitor, gefitinib, was then used on a feline SCC cell line (SCCF1), and the effect of EGFR targeting alone, or in combination with irradiation, on the cell line was determined. The majority of the biopsy samples were labelled positively for EGFR and Ki67, and high proliferation corresponded with poor prognosis. The siRNA caused reduction in EGFR mRNA by Real-Time Polymerase Chain Reaction and protein levels as assessed by western blot analysis. Reduced cell proliferation and migration were also observed by proliferation assays and scratch assays respectively. Combining EGFR knockdown with irradiation caused an additive effect on the ability of the cell line to form colonies. These results support the role of EGFR as a potential therapeutic target in FOSCCs