NEW YORK – Proteomics firm NanoMosaic is looking to aptamers to build out content for its Tessie label-free biosensing system.
According to Qimin Quan, cofounder and chief scientific officer of the Woburn, Massachusetts-based company, it plans to launch an early-access program for the platform in the next few weeks and is aiming for a broad commercial release in early 2022.
Quan said that upon release the platform will, in theory, be able to multiplex 94,000 measurements in a single experiment. In practice, however, this multiplexing capability will be limited by the availability of high-quality affinity reagents to targets of interest. Given this constraint, NanoMosaic has been exploring whether aptamers could prove effective reagents for the system.
The Tessie platform uses arrays of silicon "nanoneedles" functionalized with antibodies or other affinity reagents to detect and quantify proteins. The system's measurements are based on changes in optical resonances that occur when target molecules bind to the functionalized needles.
Because the needles are close in scale to the targets they are measuring, the perturbation of a needle's light-scattering spectrum upon binding of the target protein to the antibody triggers a color change in the needle that can be detected using an inexpensive color camera and correlated to the amount of the protein present.
The needles are arrayed in sub-500-µm sections each devoted to a single target. Within each of these sections are thousands of nanoneedles divided between a "digital detection" region and an "analog" region. In the digital region, the nanoneedles capture one target molecule per needle, which, according to the company, allows the platform to detect very low-abundance proteins and quantify them at the single-molecule level.
At higher concentrations, however, the nanoneedles in the digital region become saturated. At this point, the platform begins using the analog section, which consists of larger nanoneedles that can capture multiple proteins each. The amount of protein captured by these nanoneedles correlates with their change in color, allowing researchers to quantify the amount of target present at these higher abundances, as well.
To maintain assay specificity, particularly at higher levels of multiplexing, NanoMosaic uses paired antibodies for detection. However, there are relatively few well-validated antibody pairs, Quan noted, which will limit researchers' ability to make full use of Tessie's multiplexing capabilities.
"There are a lot of antibodies, but not a lot of good antibody pairs that can give you good specificity and sensitivity," he said. "That limits the content."
Using aptamers "could really open that up," he added, noting that the small size of aptamers compared to antibodies could make it easier to develop good antibody-aptamer pairs than antibody-antibody pairs.
"One of the reasons it is hard to find a [good antibody] pair is that antibodies are so large," Quan said. "You have to target epitopes that are not too far away or too close together, otherwise you can't form the sandwich."
"When you combine antibodies and aptamers, because aptamers are much smaller, it is much easier to form the sandwich pair," he said. "With antibodies and aptamers you can create a much larger [library of] content, and you can start thinking about doing proteome-wide discovery work," he said.
Quan said that the company has done a substantial amount of in-house validation work testing how antibody-aptamer pairs work on the Tessie platform.
"So far it looks like the antibody-aptamer combinations are in many cases outperforming [traditional] antibody pairs," he said. "We're pretty excited."
He said NanoMosaic plans to begin offering the aptamer reagents to an early-access user in the next several weeks.
While the aptamer-antibody reagents will help the company expand its content library, it will still fall far short of the 94,000-plex Quan said the platform is theoretically capable of. That figure is based on calculations of how close together antibodies can be spotted on the nanoneedle arrays.
Quan said, however, that reagent availability and the ability to deal with cross-reactivity issues would ultimately determine how close the system would come to hitting that theoretical multiplexing limit. Previously, the company said it had built chips capable of multiplexing around 1,000 protein targets.
Somalogic, which uses proprietary aptamer reagents called Somamers, multiplexes 7,000 protein measurements per experiment, though it uses single Somamers, as opposed to sandwich assays. Olink, which uses antibody pairs as part of its proximity extension assay technology, can measure around 3,000 proteins per experiment on its Explore platform.
NanoMosaic has placed Tessie systems with two early-access users, Massachusetts General Hospital and the New York Stem Cell Foundation Research Institute.
At MGH, researchers have used the system to run clinical samples as part of work developing a diagnostic test for post-operative delirium. The MGH team functionalized the Tessie chips with their own reagents to their proteins of interest, running around 100 patient samples on the system and identifying several potential markers for the delirium syndrome, Quan said, adding that translating the markers into a laboratory-developed test was under consideration.
The NYSCF work, he noted, is focused more on demonstrating the system's potential for high-throughput as well as integrating liquid handling with the platform to make for a "walkaway solution." The institute will use the system to characterize the proteome of stem cells at various stages of differentiation.
NanoMosaic has also put together a panel of proteins to enable proteome-wide association studies, which measure proteins across the proteome to identify relationships between genes and phenotypes mediated by changes in protein function or abundance. It detailed the panel in a presentation at the American Association of Cancer Research annual meeting in April.