NEW YORK – David Johnson, CEO and cofounder of GigaMune, had planned to spend the months of March and April developing business opportunities for his firm's T cell receptor (TCR) profiling method.
Earlier this month, GigaMune and its academic collaborators published a paper in Nature Biotechnology, describing a way to capture single primary T cells from human repertoires, sequence the TCR components, and express those proteins in an immortalized cell line, thus creating a reusable assay for reactivity to particular antigens. For their study, they captured approximately 2.9 million TCR alpha and beta pairs from six cytomegalovirus seropositive human donors.
Specifically, Johnson was hoping to court pharmaceutical companies working on cellular therapies in oncology, the firm's primary application for its tech. "We do a few million cells per hour," he said, while competing technologies can only do tens of thousands at a time. Also, the method enables functional screening, "rather than making some guesses based on sequencing," he added.
Instead, on March 18, the Bay Area company was facing the region's shelter-in-place order, enacted two days earlier in response to the COVID-19 outbreak, and all three employees were occupied trying to make sure their antigen-reactive TCR libraries, which Johnson claims are worth millions of dollars, would survive.
He had just learned the firm's liquid nitrogen supplier would only serve hospitals going forward. "We spent a full day calling around to see if we could get it ourselves," Johnson said last week. "We finally found a supplier willing to deliver, but that was only after a lot of scares, and now I don't even believe that supply chain is going to happen. There's no work going on in the lab, we're pretty much just in triage."
Meanwhile, the situation facing GigaMune has stabilized a little. Johnson said this week that he and his colleagues were able to find a liquid nitrogen supplier to keep their cell libraries intact. "Supply chains are stable for now," he said, "though who knows what the future might entail."
It's a moment of adversity for the startup, which has no revenues or partnerships on the books. "We're really disappointed the paper came out in the midst of everything else," Johnson said. "We were hoping to make a splash and that potential partners would see us, but I don't think anybody knows about it, so too bad. But I do think our technology is going to be useful for a lot of bigger companies working in cell therapies."
"The method is capable of processing more cells than other methods," such as 10x Genomics' immune cell profiling assay on its Chromium platform, said Andre Franke, an expert on T cell receptor sequencing at the Institute of Clinical Molecular Biology at Germany's Kiel University who was not involved in the publication. He agreed that the firm's reusable cell receptor libraries "may be a great advantage" for antigen screening, compared to primary cell-based libraries, which only have a single use.
GigaMune's TCR profiling technology traces back to its older sibling, GigaGen, which Johnson also cofounded. After originally planning to make a diagnostic platform, around 2016, GigaGen pivoted to immune repertoire sequencing for pharmaceutical development and has since changed directions again to work on antibody therapeutics. In 2018, after GigaGen received $50 million in Series A financing, it spun off GigaMune to carry on its TCR profiling work.
Johnson said GigaMune has licensed intellectual property related to TCR sequencing from GigaGen in a stock-for-technology swap, while GigaGen held on to the antibody-related technology.
Though technically separate entities, in practice the firms are closely related, occupying the same lab space in South San Francisco, California. So far, GigaMune's only funding has been a Phase I Small Business Innovation Research grant from the National Cancer Institute totaling $300,000, awarded in 2018 and expiring in August.
GigaMune's closest competitor may be Adaptive Biotechnologies, the publicly traded Seattle firm whose next-generation sequencing-based method for immune repertoire profiling has been picked up by Genentech, under a partnership last year that is worth $300 million in upfront payments and potentially billions more. But unlike Adaptive, GigaMune seems to have given up on diagnostic applications.
"Our method is probably too expensive to apply in the diagnostics space," Johnson said. Specifically, the firm uses droplet microfluidics to prepare single-cell libraries for sequencing on an Illumina MiSeq instrument. The GigaMune method captures RNA from the cells and amplifies the TCR components within the droplet. The method also tweaks the Illumina sequencing, using custom primers to sequence the amplicons. They also developed their own informatics pipeline to deal with TCR sequences that confused the Illumina image and error processing algorithms, due to homogeneity in those sequences.
The firm then pairs the TCR-alpha and beta sequences, stitches them into lentiviral vectors, and expresses the TCRs in a Jurkat cell line.
Franke said the method looked "laborious" and difficult to implement, and added that it doesn't supply RNA-seq information in parallel, like 10x's immune cell profiling assay. "The most interesting part, in my opinion, is the lentiviral TCR alpha-beta library," he said.
But Johnson said GigaMune's method was highly optimized for one thing: discovering TCRs that are rare within a patient sample. Also, the number of cells per sample it affords may make up for any perceived shortcomings. "Some of the reactive TCRs we capture are as rare as one in 10,000," he said. "If you're only doing 20,000 cells [at a time], you're not really doing much better than you would with 96-well plates."
"Our tech is much better than [Adaptive's] for that sort of [therapeutic discovery] work," Johnson added. Adaptive's method can process many samples, but "the info you get isn't as deep as what we can do," he said. Adaptive did not immediately respond to a request for comment.
Franke said GigaMune's method was more "qualitative than quantitative, having the goal of identifying new clonotypes rather than quantifying them in the primary sample." Without using unique molecular identifiers (UMIs), the method may not be able to distinguish PCR artifacts from true biological diversity, he added.
But GigaMune tried UMIs and found them to be unhelpful. "One problem is that UMIs have their own high error rates," Johnson said, adding that they would also negatively impact TCR expression in the Jurkat cell line.
And while the GigaMune method may not be used for diagnostics, Johnson hopes it can be a useful resource in basic immunology research. The method could "greatly accelerate the pace of identifying natively paired TCRαβ sequences and their cognate antigen specificities," the study's author wrote in their paper. The scale provides "an opportunity to comprehensively profile human TCR reactivity to a diverse set of antigens," they added.
Johnson said the dataset from the Nature Biotechnology paper has already been posted, although he wasn't sure if anybody had downloaded it yet.