NEW YORK – Partillion Bioscience, a spinout from the University of California, Los Angeles, is looking to expand its customer base with the launch of an early-access program for its new sequencing-based assays for detecting proteins secreted by cells.
The firm's new multicell assays build upon its nanovial technology, developed in the lab of UCLA's Dino Di Carlo. Partillion launched with the ability to isolate single cells and analyze secreted proteins, captured by the droplet-emulsified, bowl-like glass particles. Now, bigger particles allow researchers to perform studies "where the precise colocalization of cells is essential for studying complex cell-to-cell interactions or screening for therapeutic molecules released by one cell that act on another," said Joe de Rutte, CEO and cofounder of Partillion.
"By enabling these complex screens, we're enabling scientists to scale studies of how cells interact with other cells, whether it's better understanding tumors in the context of immune cells in their microenvironment, [analyzing] host-pathogen interactions, or developing next-generation therapies."
A major application of the firm's technology is antibody discovery, and the multicell nanovials will enable researchers to look at how secreted proteins affect neighboring cells. Importantly, the firm's kits allow this without the use of specialized instrumentation, de Rutte said.
Company researchers posted a preprint to BioRxiv in mid-August in collaboration with partner Alloy Therapeutics, presenting a method for discovering monoclonal antibodies from plasma B cells. Proof-of-concept experiments paired antibody-secreting cells with cells expressing a target protein. Single-cell sequencing of the isolated antibody-producing cells yielded the heavy- and light-chain sequences. An antibody discovery campaign targeting the immune checkpoint protein PD-1 yielded molecules with similar binding affinities to the therapies pembrolizumab and nivolumab, the authors wrote.
"Secreted proteins represent something like 20 percent of the proteome, and we don't really understand a lot of the factors that lead to their regulation of other cells," said Richard James, an immunology researcher at the University of Washington and a Partillion collaborator. His lab is one of several that are using Partillion's technology to investigate this area of biology.
De Rutte founded Partillion in the spring of 2020 at the end of his doctoral studies under Di Carlo, a bioengineering professor and the firm's other cofounder. Di Carlo's lab specializes in microfluidics and has also helped develop a handheld magnet-driven molecular diagnostics device. It has spun out other startups, including Cytovale, a diagnostics company commercializing a sepsis test.
The lab was looking for a way to do microfluidics in small reaction chambers to isolate cells "but in a way that lets people use the tools they have in their lab," de Rutte said. The biotinylated nanovials were a solution that helped them not just isolate cells but also capture the information around them.
At first, they designed them to be compatible with flow cytometers, of which there are thousands in labs around the world. The instruments could capture certain cells and allow researchers to perform single-cell assays on them. "We did a lot around proteins being secreted by cells. Not just cell surface proteins, but cytokines and antibodies," de Rutte said.
Their proof of concept was in cell line development. After talking to scientists in that field, de Rutte said he realized they were hesitant to adopt complex new instrumentation, such as the Berkeley Lights Beacon, which was launched in 2016. (That firm went public in 2020, but struggled to place instruments and was ultimately acquired by Bruker a year ago for $108 million.)
At first, the technology was used mostly for screening cells, but the "aha!" moment came with being able to link functional information with a cell's gene expression. "There are a lot of applications where you want to isolate cells but keep them alive to do downstream sequencing," de Rutte said. Partillion also found that it could simply load its nanovials into a 10x Genomics Chromium single-cell instrument to get gene expression data.
Partillion has now raised "a few hundred thousand dollars" in pre-seed financing, followed by a December 2022 seed round of approximately $5 million, led by ND Capital and joined by Vertical Venture Partners and Paladin Capital. The company has also obtained National Institutes of Health Small Business Innovation Research grants totaling approximately $3 million. "We've been lean and efficient," de Rutte said, adding that he may consider looking at raising funds sometime next year. The company has 15 full-time employees and has licensed IP from UCLA and developed its own IP.
Several Di Carlo lab collaborators have published papers using the nanovial technology, including James, who is trying to turn antibody-secreting cells into factories for other proteins. Proof-of-concept studies have shown that "some of them have the features we want, and others don't," he said. "We really wanted a way to understand the basis of that heterogeneity."
The lab had engaged with Berkeley Lights about buying a Beacon, "but I just didn't want to spend a million dollars on their piece of equipment that didn't do everything we wanted to do," James said. "Partillion's technology is really flexible."
The nanoparticles are available for sale on their own and can work with commercially available antibodies and flow cytometers. Partillion offers them in two sizes: a 35-micron outer diameter for single cells and 50 microns with larger cavities for the multicell assays or larger cells.
Tubes of Nanovials start at $1,000 and contain enough to process 200,000-400,000 cells. Larger kit formats are available and come at a bulk discount. Partillion also has ready-to-use kits for certain applications, such as antibody discovery. The kits include Nanovials, validated antibodies for certain cell targets, detection antibodies for secreted targets and other reagents needed for the workflow, "typically in the $2,000 to $3,000 range," de Rutte said.
The firm's customer base "skews towards pharma," he said, with only about 25 percent of customers in academic labs. For the new early-access program, Partillion is looking to work with between five and 10 labs, which will receive free reagents and antibodies for particular validated workflows. The firm has already begun with certain early-access customers; it is primarily focused on advancing antibody discovery applications. The new multicell kits solve some problems of antibody discovery against certain targets that maintain their physiological structure only in their native cellular context, such as G-protein coupled receptors and immune checkpoint proteins, de Rutte said, adding that chimeric antigen receptor T-cell screening and cytokine profiling of immune cells are other areas the company is exploring for future commercial offerings.
James framed his experience with nanovials as a collaboration that began with Di Carlo's lab and continued with Partillion. He noted that he did a lot of troubleshooting early on alongside de Rutte. Issues included nonspecific binding to the particles and cell loading issues, including loading efficiency. However, he said the company has been optimizing these aspects of its technology.
In May, James posted a preprint to BioRxiv with Di Carlo and UCLA epigenetics researcher Kathrin Plath on the use of nanovials to link single-cell transcriptomes with secretion. They used the method, dubbed "Secretion amount of a target protein encoded by thousands of single cells with transcriptional sequencing (SEC-seq)" to link T-cell receptor sequences to cytokine secretion amounts, surface marker gene expression in "highly secreting" mesenchymal stromal cells, and plasma cell transcriptomes with high immunoglobulin secretion levels.
The authors used the 35-micron nanovials in their experiments but noted that 10x's new GEM-X chips may be compatible with the larger, 50-micron nanovials. "Additionally, other single-cell RNA sequencing technologies that rely on split-pool reactions and do not use microfluidic chips are also expected to be compatible," they wrote.
James has several specific uses planned for nanovials. "One of them is doing perturb-seq-like applications" introducing CRISPR guide libraries into B cells to explore regulatory regions that might affect protein secretion or cell differentiation, he said. Another is simply optimizing secretion of therapeutic products. "We're finding that the primary sequence actually makes a huge difference in the amount of antibody that gets secreted."
Partillion's multicell tech could also help slot in amid the drive to bridge single-cell studies with spatial ones. "With spatial biology, there are so many interactions; it's sometimes hard to piece out what's important, [and] what's actually driving cause and effect between these different cell types," he said. "Pairing them in a more purposeful way, being able to look at cells together, can help you unravel how cell-cell interactions are causing different gene expression [patterns]."