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Wyss Institute Spinout Pluto Biosciences Bets on Collaborative Bioinformatics Platform


CHICAGO – Pluto Biosciences, a recent spinout of the Wyss Institute, seeks to facilitate collaborations between researchers through a shared bioinformatics platform. Next week, the firm plans to announce that it has closed a seed round worth slightly more than $1 million and that it has launched a free version of its software.

The angel investors supporting the seed round for the Denver-based company include Christopher Glode, CEO and cofounder of HumanCode, which Helix bought in 2018.

Pluto makes an eponymous "digital lab space" that founder and CEO Rani Powers calls a collaboration platform for researchers. Powers said that she sometimes thinks of the technology as an operating system for a laboratory or life sciences organization to run its workflows.

"[It can be] a single source of truth and a single home for them to take their raw data, upload into Pluto, get a plot very quickly … then share that plot the same way that you would share a Google doc, for example, with anybody that you want to inside or outside of your organization," Powers explained.

Managers control access to various functions, provisioning access to users as needed, based on each person's role.

"I as a biologist could create the experiment, and then I can send a link to maybe my sequencing core so that they can add the FASTQ files and then I can finish the analysis," Powers explained. "Then my computational biologists can use our API to reap the data."

Powers called Pluto "assay-agnostic," meaning that it is flexible enough to manage multiple types of omics data, such as DNA, RNA, and metabolomic information.

"We have our users tell us what kind of data it is that they're uploading so that we can map between genes and proteins and metabolites," she explained. Users can then query across their pool of experiments.

The platform is mostly self-service, but Powers said that it features a "concierge" in the form of a chat bubble that users can click on to get live help from a Pluto bioinformatician or molecular biologist. "We can come in and actually help them format the data and then make sure that it's all plugged in to Pluto correctly," she said.

The company has eight full-time employees, plus some part-time contractors.

The scientists at Pluto can help not only with data formatting but some more advanced custom pathway analysis or mapping, according to Powers. Those services are included in Pluto's annual platform fee, which also covers data uploads, computing time, and storage.

A new offering, to be unveiled next week, is a free tier of the software, called Explorer. Users will be able to register for a free account to search and analyze low-throughput assays from more than 10,000 publicly available datasets, including RNA sequences, microarray data, metabolomics data, and quantitative polymerase chain reaction tests, according to Powers.

Pluto has licensed some of its technology from Harvard University's Office of Technology Development, though Powers herself was the developer during the year and a half she spent as a staff scientist at the Harvard-affiliated Wyss Institute.

When Powers joined the Wyss in January 2020, she pitched the idea of Pluto Biosciences to the institute, which to that point had not spun out any pure-play software companies. Powers had previous experience with several software startups, including HumanCode, where she served as senior manager of innovation before the Helix acquisition.

"I posed this idea to them of [creating] the infrastructure within the Wyss Institute to be able to develop these software platforms and then spin them out as a company," Powers said. She offered to make her own company the proof of concept of that infrastructure.

During her time at the Wyss, Powers helped build servers, designing storage systems and protocols, and creating an environment to foster app development. This effort is now a fledging program called Predictive Bioanalytics Initiative. Pluto is the first company to emerge from what the Wyss calls PredBio.

"I would think about it as a discovery and translation enablement team," said John Mercer, who joined the Wyss in February to lead PredBio. "It's really a combination of software, data engineering, [machine learning/artificial intelligence] development, and product development."

PredBio works with Wyss scientists to build data pipelines and provide modeling, analysis, and visualization services to support grant work and facilitate technology transfer. "That translational focus is an imperative of the PredBio group," Mercer said.

Mercer has been tasked with building a team and platform in an academic environment that one might find at an established bioinformatics company, with technology that is scalable, interoperable, extendable, and reproducible. It also has to support collaboration among researchers and serve the different missions of the 11 primary labs at Harvard that Wyss works with, he said.

Mercer has worked at software companies as well as the Broad Institute. While at the Broad, he was a key architect of the first large-scale machine learning platform there.

"I try to help industry people understand that there is a place for them in science. There is a place for them in biotech. There is a place for them in the biomedical space, even if you don't have a formal Ph.D. in genetics," said Mercer, who noted that Broad President Eric Lander is a mathematician by training who moved into biology.

"It is now a confluence of both lab biologists and in silico computationalists working together hand in hand to make discoveries and to build tools," Mercer said, explaining the philosophy behind PredBio. When the COVID-19 pandemic struck in March 2020, some of the PredBio infrastructure development was diverted to coronavirus research and to support Wyss researchers and their partners who were forced to work remotely. The US government's Defense Advanced Research Projects Agency provided a $16 million grant for the Wyss to advance research into COVID-19 therapeutics, in collaboration with the University of Maryland and Mount Sinai Health System in New York, but these partners initially relied on older communications technology for the work.

"A lot of time was spent emailing people back and forth to coordinate a plan for generating, storing, and analyzing results," Powers said. "If we'd had a centralized collaboration platform housing everyone's experimental data and results, our ability to respond to the pandemic would have been even greater."

The infrastructure that Powers led development of at the Wyss gave bioinformaticians near-real-time visibility into results from experiments at those three sites.

By October of last year, when Powers had shown that the COVID-19 research dashboard works, the Wyss gave her the go-ahead to create the Pluto platform, along with access to institutional resources. Harvard provided financial support for the actual software development and now licenses this technology to Pluto.

"We want to accelerate the scientific process in this collaborative era, in this digital era, and in this era where we're working asynchronously, and potentially all from home," Powers said.

She sees Pluto filling a gap between general business applications like Dropbox, Microsoft Excel, and GraphPad Prism, and true bioinformatics environments such as Terra and DNAnexus that require significant IT infrastructure. "Pluto abstracts away all of that for the types of customers that want to get into the cloud and really can't invest in those resources or are currently paying a bioinformatics core hourly," Powers said.

She added that she is particularly excited about Pluto's potential in rare disease research because investigators tend to be geographically dispersed rather than concentrated in centers of excellence and often work asynchronously. Pluto can serve as a "single source of truth" in such areas, she said.

A key customer segment for Pluto is academic laboratories. "We really see the value there in [offering] a department- or university-wide license," Powers said.

The firm is also targeting small biotech companies as well as research and development IT groups at larger pharmaceutical companies. Another potential market that Powers did not initially think about until the company fielded some inquiries includes lab incubators and contract research organizations.

At the moment, Pluto is running a lot of standard pipelines. "What we're doing is helping our users by parallelizing those processes, optimizing for speed so that they don't have to worry about any of the parameter setting," Powers said.

Pluto is a modular platform, able to take various experiment types as they are developed. The company currently offers modules for RNA-seq, simple quantitative assays, and imaging results from microscopy systems. It will soon add single-cell RNA sequencing and predictive biomarker analysis.

"If you upload any sort of omics higher-throughput assay, we can do predictive analysis," Powers said.

For her Ph.D. in computational bioscience, Powers developed an algorithm that compares how gene expression changes in different experiments. Pluto is in the early stages of molding that algorithm into a user-friendly tool to add to the platform, but the company does not have an expected release date yet.