In a recent interview with ProteoMonitor, Swiss Federal Institute of Technology Zurich researcher Ruedi Aebersold observed that to a significant extent, proteomics has been constrained by a lack of good affinity reagents (PM 1/25/2013).
"Right now most measurements of proteins in a biological sample are done by Western blotting," he said. "And, of course, for only a relatively small fraction of protein is there an antibody [suitable for Western blotting]."
Aebersold went on to identify mass spec as a potential solution to this dilemma, suggesting that libraries of pre-built targeted assays combined with simplified, streamlined instrumentation could one day enable the technology to replace Western blots as the basic tool of protein research.
Michael Weiner, chief scientific officer and founder of biotech firm Axiomx, agrees with Aebersold's assessment. Rather than working to reduce researchers' reliance on antibodies, though, Weiner and his colleagues are pursuing improved ways of making them.
"My suspicion, and the reason we started Axiomx, is that a lot of experiments today aren't done because it takes four to six months to get the reagents to start, and that is outside the journal life cycle of publishing an article," Weiner told ProteoMonitor this week. "A graduate student starts, they've got to wait six months, then they do the experiments for a year, then they publish it the next year. So, it's like a two-and-a-half year cycle."
Weiner and Axiomx aim to compress that cycle by bringing the time required to produce custom recombinant antibodies from the four- to six-month range down to under three weeks.
Launched in March 2012, the firm began offering custom antibody services in November. According to Weiner, it is currently on track to have its antibody production process down to between six and eight weeks by June of this year and plans to have it down to less than three weeks by June 2014.
The company, which currently has 12 employees, completed an initial financing round in December, raising more than $2 million from investors including Connecticut Innovations and Elm Street Ventures.
Axiomx is the second antibody outfit founded by Weiner in recent years. In 2008, he, along with Stanford University researcher Michael Snyder (then at Yale University), Yale researcher Sherman Weissman, and Mike Sherman, launched the biotech firm Affomix, which similarly aimed to shorten antibody production timescales while increasing quality (PM 4/9/2009).
At the time, Sherman told ProteoMonitor that the company intended develop "an antibody set against virtually all proteins in the human proteome."
Affomix was acquired by Illumina in 2010, and two years later Weiner – who is also one of the inventors of 454 Sequencing and a founder of genomics firm GnuBio – launched Axiomx with a similar goal of making antibodies more broadly available for proteomics research.
"People say, 'There's no PCR for proteins," he said. "And so I think people just sort of slough off and say that that's why nucleic acids took off [and proteins haven't.] But I think that the PCR for proteins is antibodies" — and recombinant antibodies, in particular, Weiner said.
He noted that a significant advantage of these recombinant reagents is the ability to carefully control their various binding characteristics during the production process.
"The same [dissociation constants], the same affinities – these are things you can build into sets of recombinant antibodies that you can't in mouse monoclonals," he said.
Weiner highlighted several key aspects of Axiomx's efforts to bring antibody production times under three weeks. Among them is its use of an all-liquid approach to its affinity screening process, which enables the company to automate this work on liquid handling systems, speeding it while also reducing opportunities for human error.
Also key, he said, is the company's use of what it calls the AXM mutagenesis approach for its affinity maturation process. Affinity maturation involves use of error-prone PCR to create variations on initial hits with the aim of developing molecules that bind their target better than the original hit. Typically in this process the new PCR products must be ligated into a vector and then transformed into E. coli. The AXM mutagenesis, on the other hand, selectively degrades one of the strands of the error-prone PCR product, allowing it to be hybridized, eliminating the need for the ligation step, which increases throughput and lowers costs.
Additionally, Axiomx is trying to streamline the process by using PerkinElmer's AlphaScreen technology for measuring its antibodies' affinities instead of more expensive techniques like surface plasmon resonance, Weiner said.
Currently, he said, the company is aiming to be competitive on price with monoclonal reagents. He added that when Axiomx first launched its antibody production services, it "was probably losing money" on each order, but it has since brought costs down to where it is profitable.
Tom Thompson, the company's vice president of sales and marketing told ProteoMonitor that while Axiomx plans to compete primarily on quality of the "uniqueness" of its offerings, it does "foresee the potential for some price decrease with continued process improvements."
The firm is focused on the custom antibody business but is also interested in generating libraries of antibodies for particular research areas – such as transcription factors – where it perceives there to be an unmet need, Weiner said.
As for the original Affomix vision of developing antibodies against the entire human proteome, Weiner acknowledged that would be a daunting goal given the perhaps hundreds of thousands of protein forms that would need to be covered.
"Will we get to every polymorphism of a protein where an amino acid has been changed? That's unlikely," he said. However, he believes Axiomx could achieve significant coverage with its workflow.
"We know what our pipeline is. We know how much we can crank it up," he said. "The other question is, do we need the complete [proteome] right away? For instance, if we had the phosphoproteome or the secretome, that would probably be extremely useful."
Thompson said the company was looking in particular to establish catalogs of reagents in emerging research areas "where there are unmet antibody needs and strong growth potential" such as antibodies to post-translationally modified proteins.