RNA Takes Center Stage
siRNA programs dominate the research and preclinical arena, with antisense and miRNA molecules and aptamers also well represented. The number of clinical RNAi programs rose from 2 in 2004 to 14 at present, with the number of RNAi programs in the research and preclinical stages soaring from 17 to 100 during that same time period.
With the completed expansion of its GMP facility in Boulder, CO, Agilent’s oligo manufacturing capacity has increased to hundreds of kilograms a year, according to Gary Carter, manager of business development and marketing, nucleic acids solutions division at Agilent. “We are seeing more big pharma involvement through an increase in the number and size of collaborations,” he adds. As a result, biotech customers have access to more funding for their oligo programs.
Cost of goods remains a major market driver. Based on cost modeling, current large-scale synthesis processes for DNA are economically viable, according to James Powell, GM, Agilent nucleic acids solutions division. However, raw materials, and especially amidites, are much more expensive for RNA synthesis, and “we need a two- to three-order decrease in cost to make RNA commercially viable,” he says.
The higher costs often associated with novel therapeutics may be justified if the new drugs fulfill an unmet market need. Carter predicts that in the next wave of oligo products, which will include siRNA therapeutics, “we will definitely see more targeted to areas of unmet need.”
As GMP oligo production increases to commercial scale, the main cost driver relates to the building blocks used for nucleic acid synthesis. At the upcoming “TIDES” conference, Agilent will introduce its new ST-RNA (streamlined RNA) technology for therapeutic RNA production, which relies on a more cost-effective, large-scale process.
Applied Biosystems, a division of Life Technologies, continues to add to its portfolio of genomic assay products, which includes TaqMan® Gene Expression assays for real-time PCR, genotyping assays, and the recently launched TaqMan® Copy Number Assays.
In particular, in the gene-expression sector, “the miRNA market has exploded,” says Criss Walworth, director of Applied Biosystems’ expression assays and arrays. miRNA assays were initially being used mainly for mechanistic studies, but with the growing recognition of their potential clinical value, “we are seeing tremendous growth across the board,” notably in pharmaceutical, clinical, and life science research, as well as in biomarker discovery and validation.
“The beauty of miRNA is the manageable number of targets; less than 1,000, compared to 30,000 or more for messenger RNA,” says Walworth. But miRNAs are a challenging target for several reasons: their small size—21 nucleotides, “not much real estate to design primers or probes to”; their homologous nature—many differ by only a single base; and the fact that an miRNA will also have a longer precursor form and a primary transcript, which can result in background noise if an assay is not well designed. This month, Applied Biosystems will introduce 89 sets of mRNA TaqMan assays preplated in optical plates, covering common pathways and target classes.
Other leading providers of oligo products including Dharmacon (a division of Thermo Fisher Scientific), Biosearch Technologies, and Sigma-Aldrich have also expanded their activity in the RNAi sector.
Dharmacon offers a variety of pre-designed and custom siRNA libraries: siGenome for whole-genome screens; On-Target plus, intended to reduce off-target effects; Accell, for siRNA delivery without a transfection reagent; and siSTABLE® stability enhanced siRNA. For shRNA applications Dharmacon technology includes its Open Biosystems microRNA-adapted shRNA libraries targeting human and mouse genomes, and the SMARTvector® shRNA lentiviral platform.
Biosearch offers GMP oligo components for use in in vitro diagnostic genetic assays. The company provides oligo synthesis supports and columns for DNA synthesis and producing modified DNA, Black Hole Quencher® DNA labeling reagents, a range of fluorophore and reporter group supports for 3´ labeling of DNA, and fluorophore and reporter group amidites for 5´ and internal labeling, as well as specialty amidites and 5´ modifiers.
In late March, Sigma-Aldrich announced an exclusive custom oligo supply agreement with Gene Oracle, a gene-synthesis company. The two companies will comarket Gene Oracle’s GeneIOS system and gene synthesis services. Sigma-Aldrich’s customized oligonucleotide services encompass DNA oligos and probes, iScale Oligos™, RNA oligos, RNAtural oligos, and siRNA oligos.
Banking on Diagnostics
Late last year, Eurogentec received ISO 13485:2003 certification for the production facility it opened earlier this year, where it is making oligos for the in vitro diagnostics market. The company is in the process of obtaining ISO 13485:2003 certification for its new DNA and RNA production facility in San Diego. Further expanding its manufacturing capacity, Eurogentec has opened an IVD facility in Japan to provide GMP oligos to the Asian in vitro diagnostics market.
Eurogentec recently introduced its first cGMP Taq DNA polymerase for the molecular diagnostics market. Called Diagnostic Taq, the recombinant enzyme produced in E. coli is more than 98% pure, with low residual DNA content (typically <1 fg/Taq unit) and low bioburden (0–10 CFU/mL), according to the company.
Avecia OligoMedicine, known for its expertise in large-scale, GMP oligo production, has responded to customer demand and improved its offering in the nonGMP preclinical market for all oligo classes. Demand is high, in particular for RNAi products, which Detlef Rethage, president of Avecia Biotechnologies, describes “as the fastest growing oligo market sector.”
Integrated DNA Technologies (IDT) also views diagnostics as an important growth market. IDT launched its GMP/ISO 1345 manufacturing group in May 2008, and it has been “working with diagnostics players to convert them from legacy methods used for research products to scalable methods appropriate for a more controlled environment,” says Trey Martin, COO.