Technology and IP portfolio

The core of InteRNA's technology position is the use of proprietary, highly advanced bioinformatics methods to analyze, predict and validate miRNA sequences. This has led to the identification of a large population of novel miRNAs and subsequent patent applications. InteRNA applies the following technologies:

• Identification of novel miRNAs by massive parallel sequencing
• Profiling on miRNAs from human tissue
• Computational analyses of large sets of small RNA sequencing data
• Biological validation of candidate miRNAs by (modified) RAKE assay and other molecular biology techniques
• Bioinformatical integration of multiple molecular datasets
• Tools to perform functional assays
• Functional assays for validation of miRNAs

IP Portfolio

At present, InteRNA has patented approximately 1,000 mature human miRNA sequences and over 4,000 human hairpin sequences. In addition, we have patented novel microRNAs identified in various tissues of mouse and primates. Approximately 750 miRNA sequences discovered by us can be found in the miRNA database miRBase 10.
Our IP portfolio is continuously being expanded by validation of the above described human miRNAs in disease tissue.

Discovery and validation process

Novel miRNA candidates were identified by a number of different methods. Computational prediction resulted in the identification of a great number of novel miRNAs. These miRNA candidates were confirmed using microarray based RAKE (RNA-primed, array-based Klenow enzyme assay) and other molecular biological techniques, such as detection by Northern Blot and Q-PCR. Most of our proprietary miRNA sequences do not originate from computational predictions, but were experimentally cloned from small RNA of various sources. Further computational approaches - including stable hairpin formation and phylogenetic conservation criteria - resulted in the classification of candidate miRNAs. Additional biological validation of a subset of candidate miRNA sequences in human tumor samples was achieved by microarray profiling.

Tools

We are currently pursuing various experimental approaches to identify biological roles of the candidate miRNAs. Functional assays employing both miRNA overexpression and knockdown techniques are being implemented.

Data analyses platform

Recent advances in DNA sequencing technology make it possible to read billions of DNA bases in a single run. These ultra-high-throughput (U-HTP) sequencing technologies are changing the approaches to genome-related research and open up an era of personalized genomics, where each individual can have its own genome sequenced. Today, these new technologies enable novel approaches for small RNA discovery and detection, gene expression profiling, ChIP-SEQ, etc. These developments have lead to the generation of novel software tools by our bioinformatics experts. These new tools for analyses of large sets of raw sequencing data are exploited by InteRNA Genomics, a subsidiary of InteRNA Technologies. InteRNA Genomics offers services and software for processing, analyzing and presenting U-HTP sequencing data generated by various platforms. Our informatics solutions convert large sets of raw sequencing data into interpretable formats and integrate this information with existing proprietary and public data resources.

Opportunities

We are open to discussions on collaborations with academic as well as commercial partners. Opportunities for licensing also exist outside InteRNA's focal area, such as the development of diagnostic and prognostic assays.

References

• Berezikov, E., Guryev, V., van de Belt, J., Wienholds, E., Plasterk, R. H. and Cuppen, E. (2005) Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120, 21-24
• Berezikov, E., van Tetering, G., Verheul, M., van de Belt, J., van Laake, L., Vos, J., Verloop, R., van de Wetering, M., Guryev, V., Takada, S., van Zonneveld, A. J., Mano, H., Plasterk, R. and Cuppen, E. (2006) Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis. Genome Res 16, 1289-1298
• Berezikov, E., Thuemmler, F., van Laake, L., Kondova, I., Bontrop, R., Cuppen, E. and Plasterk, R. H. (2006) Diversity of microRNAs in human and chimpanzee brain. Nat Genet 38, 1375-1377
• Kloosterman, W. P., Steiner, F. A., Berezikov, E., de Bruijn, E., van de Belt, J., Verheul, M., Cuppen, E. and Plasterk, R. H. A. (2006) Cloning and expression of new microRNAs from zebrafish. Nucleic Acids Res 34, 2558-2569
• Takada, S., Berezikov, E., Yamashita, Y., Lagos-Quintana, M., Kloosterman, W. P., Enomoto, M., Hatanaka, H., Fujiwara, S., Watanabe, H., Soda, M., Choi, Y. L., Plasterk, R. H. A., Cuppen, E. and Mano, H. (2006) Mouse microRNA profiles determined with a new and sensitive cloning method. Nucleic Acids Res 34, e115
• Berezikov, E., Cuppen E. and Plasterk, R.H. (2006) Approaches to microRNA discovery. Nat Genet 38 suppl: S2-7