AvantGen Awarded SBIR Phase II Contract to Develop High-Affinity, Anti-Peptide Rabbit Monoclonal Antibodies for SISCAPA Assays from the NIH/NCI

AvantGen Awarded SBIR Phase II Contract to Develop High-Affinity, Anti-Peptide Rabbit Monoclonal Antibodies for SISCAPA Assays from the NIH/NCI

AvantGen, a leader in novel antibody discovery and engineering, in collaboration with SISCAPA Assay Technologies (SAT), was awarded a SBIR Phase II contract from the National Cancer Institute (NCI) to develop high-affinity, anti-peptide rabbit monoclonal antibodies for mass-spectrometry-based cancer biomarker detection and quantification assays, or so called SISCAPA (Stable Isotope Standards and Capture by Anti-Peptide Antibodies) assays.

Antibodies with high affinity and specificity suitable for cancer biomarker measurements are essential, since there are more than 2,000 potential biomarkers that have been discovered, but only about 100 of them are currently approved by the FDA for clinical diagnostic use.

Prior to this Phase II contract, AvantGen successfully completed a Phase I contract (HHSN261201300023C) using its novel rabbit monoclonal antibody generation platform which enables AvantGen to isolate the highest affinity antibody clones from an immunized rabbit with the desired specificity for the target peptide antigen.  All of the rabbit monoclonal antibody clones developed during Phase I exhibit very high affinity (10-10 to 10-11 M) and specificity for their respective antigens.

AvantGen’s technology bypasses the low efficiency of fusion between antibody-producing cells (B cells) and myeloma used with hybridoma technologies. Fusion is particularly inefficient with rabbit myeloma lines with an estimated fusion rate of 1 in 1 million. The isolated antibodies with AvantGen’s technology will be sequenced and expressed in mammalian cell systems, therefore also overcome the instability and low antibody yield issues of rabbit monoclonal antibody cell lines

The Phase II contract (HHSN261201500044C) will support the development of novel rabbit monoclonal antibodies against 100 additional peptides derived from cancer biomarkers.  The developed antibodies will be evaluated in SISCAPA assay.

SISCAPA combines antibody-based peptide enrichment with quantitative mass spectrometry to provide accurate quantitation of target proteins. The assay requires high affinity and highly specific antibodies and enables measurements of biomarkers from biological samples with unprecedented precision and throughput.

AvantGen is also providing services to generate high quality rabbit monoclonal antibody research reagents for the research community.

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faq Want to learn more?

  • Why Yeast?

    Yeast, or Saccharomyces cerevisiae aka brewer’s yeast to be exact, has the best of both worlds as a model organism for drug discovery. In selecting the right model, two opposing factors are: 1) finding an organism that can be used cost-effectively and ethically, and 2) being physiologically relevant by having it as similar as humans, the intended patients. This is where yeast has all the advantages: 1) it is unicellular, grows incredibly fast at a doubling rate of 90 minutes, and is easy and safe (non-pathogenic) to culture, meanwhile 2) as a eukaryote it can properly express, fold, and glycosylate proteins such as antibodies similar to mammals.

  • Yeast is “similar” but not the same as in humans with regards to post-translation modification (PTM) of proteins such as glycosylation?

    Correct, there are slight differences in the PTM profiles of proteins expressed in yeast versus mammals. However, we recombinantly express our lead antibodies in HEK293 or CHO cells and rarely observe a loss in activity. This is in stark contrast with E. coli-based systems like phage or cell-free, where bacteria lack protein glycosylation machinery.

  • Is affinity maturation required after using one of your platforms?

    Due to our large size rationally-designed Germliner™ library collection coupled with our rapid cell sorting based screening, we consistently obtain single-digit and subnM affinity antibodies with optimal developable characteristics. Interestingly, our popular AvantGeneer affinity maturation platform has been frequently used to optimize client antibodies that were originally discovered with hybridoma and human transgenic mouse platforms.

  • My target is a GPCR. Will your platform work?

    We have had success with multi-transmembrane proteins such as GPCRs, by using virus-like-particles (VLPs), nanodiscs, and client-designed variants with increased solubility.

  • What materials should I provide?

    We typically use various amounts of biotinylated, DyLight™ 650 conjugated, and unlabeled antigens for all projects. It’s important that both labeled and unlabeled antigens are QC’ed by provider, third party, and/or AvantGen. >0.5 mg/mL concentration, >80% monomer percentage, and >90% purity. Preferred buffer is PBS and no tris-based buffers please.

    Estimated Material Amounts*

    Application Stage Discovery Affinity Maturation Rabbit mAb
    All stages 1.5-2 mg biotinylated or 2-3 mg unlabeled 0.5 mg biotinylated or 1 mg unlabeled 2 mg unlabeled and 1 mg biotinylated
    FACS and screening 0.5-1 mg biotinylated or 1-2 mg unlabeled 0.2-0.5 mg biotinylated or 0.5-1 mg unlabeled 1 mg biotinylated and 0.2 mg unlabeled
    Screening only 0.2 mg biotinylated or 0.2-0.5 mg unlabeled 0.2 mg biotinylated or 0.2-0.5 mg unlabeled 0.2-0.5 mg unlabeled

    *Assuming 50 kDa antigen. AvantGen can bioconjugate and QC as needed.

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