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Advanced molecular tools for array-based analyses of genomes, transcriptomes, proteomes, and cells

Final Report Summary - MOLTOOLS (Advanced molecular tools for array-based analyses of genomes, transcriptomes, proteomes, and cells)

The EU project MOLTOOLS was designed to establish key tools for research and diagnostic analyses of DNA, RNA, proteins and cells, by coordinating a wide range of expertise in some of Europe's leading groups in academic or industrial technology development. The success of the MOLTOOLS project has had important consequences by providing a wide range of valuable new research tools in academia and industry, a prerequisite for progress in all biomedicine. Moreover, the output of the research programme has already given rise to important applications in industry and will continue to do so.

MOLTOOLS partners rapidly seized upon the need for isolating all sequences of special interest from genomic DNA samples for priority sequencing using emerging DNA sequencing techniques. Between them, they have pioneered and patented several of the major approaches considered by DNA sequencing companies, including selector probes, MegaPlex PCR and padlock probes. Similarly, techniques invented by the partners and perfected during MOLTOOLS have proven valuable for measuring and distinguishing gene sequences, as exemplified by the padlock probes licensed by the Uppsala group to the company Affymetrix for their targeted genotyping platform.

Regarding medical applications of nucleic acid technologies, the TAcKLE RNA amplification protocol is used in clinical breast cancer studies and aPRIMES is used in genetic studies of medulloblastoma. Furthermore, the nanowell real-time PCR platform will be used for miniaturised gene expression profiling in research settings in particular for clinical samples available at very low amount and the need of a flexible assay set-up.

Numerous contributions were also made to the central problem of measuring proteins in biological specimens with ever-higher sensitivity and precision. The in situ protein arrays established by the partners provide an efficient means of constructing planar arrays of many different proteins for parallel analyses of their properties. Proximity ligation represents a new and quite general test mechanism that offers unprecedented sensitivity for protein measurements in patient samples. Some aspects of the technology have been licensed to Applied Biosystems, while others will be commercialised by the start-up Olink, spun out by a partner during MOLTOOLS.

Another very important trend where MOLTOOLS has made contributions that will prove important in biomedicine concerns the measurement of even single nucleic acid or protein molecules in individual cells. A proximity ligation based strategy to detect interacting proteins in patient samples was established and published during MOLTOOLS, and is now commercially available from Olink. In a related fashion, another partner developed technology allowing single molecules to be imaged on arrays.

As a final example, several partners of MOLTOOLS contributed to establishing technologies that permit parallel analyses of many cell populations modified to influence their susceptibility to drug treatment. Another partner has used their miniature cell arrays to successfully identify potential targets for drug therapy in cancer, of great interest to the drug industry.

The groups brought together in this programme are experienced inventors of tools for molecular analysis. An excellent indicator of the scientific novelty of the MOLTOOLS project is the large number of patents and patent applications that have been filed during the course of the project so far, many of which are being exploited commercially. As far as generation of start-up companies is concerned, Olink, founded by a partner to exploit proximity ligation technology. Similarly, another partner founded a new company (In Situ RCP A/S) for exploiting the IPR generated by this group, and BI is in the process of establishing Discerna Ltd, in order to commercialise ribosome display and in situ protein array systems.

Results of the work in the MOLTOOLS project have been disseminated through our public website (please see online), which has been accessed on average by 200 visitors a day. The work has also been presented for the scientific community through research articles, conference presentations, and through 14 MOLTOOLS symposia and workshops that have been arranged by the consortium. Hands-on practical training in our techniques has been made available through the MOLTOOLS training courses arranged in Uppsala, Berlin, Paris, and Heidelberg.