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Multiomics Startup Pleno Targeting Sequencing, PCR Markets With New Molecular Detection Technology


NEW YORK – Backed by $15 million in pre-Series A funding, San Diego-based startup Pleno is targeting 2023 for a limited commercial launch of its molecular detection platform.

Based on so-called Hypercoding technology, the platform will be capable of detecting up to 10,000 nucleic acid targets per sample and processing up to 10,000 samples per day, according to the firm.

Pleno Founder and CEO Pieter van Rooyen said the system will offer a more streamlined, less expensive, and higher-throughput alternative to next-generation sequencing in applications where researchers, and, eventually clinicians, are looking to analyze large numbers of known nucleic acid targets.

"There are a lot of genomic tests now where you need to detect many different targets," he said, citing as examples applications like cancer screening and surveillance of multiple infectious disease variants.

He added that while the company aims initially to complement existing PCR tools, targeting primarily applications where PCR isn't able to offer high enough multiplexing, it aims to eventually compete with conventional PCR, particularly on the research side.

Pleno's platform is based on a set of reagents it calls plenoids — DNA probes to specific targets that are each linked to unique DNA-based codes called Hypercodes. Users add these probes to their sample (in a well of a 384 or 96 well plate) and after the probes hybridize to their targets they amplify the specific Hypercode linked to each probe. They then label these Hypercodes with conventional fluorophores and optically read out the specific signal generated by each of these Hypercodes. Amplification is done using a technique that Gavin Stone, Pleno's VP of product development, declined to disclose but which he said was a non-PCR nucleic acid amplification approach currently in use in the broader research community.

Stone said the system reads out all targets in a sample simultaneously, with the assay repeated "over several successive cycles to build up the patterns for each Hypercode."

The company's coding system and signal processing use techniques borrowed from the telecommunications space that Van Rooyen said allow for high levels of multiplexing, enabling the platform to deconvolute the signals specific to each individual Hypercode from out of the mass of signal generated by all the different Hypercodes in a sample.

He offered the analogy of a sports stadium filled with people, many of them using their cell phones.

"The reason they can do that [without signals getting confused] is that each phone is essentially assigned a unique code, and based on that code, the base station and network can distinguish between the different people making calls," he said. "In the same way, we assign codes to different targets, and then we have a decoding algorithm to extract the different probes and distinguish the different targets from each other. The essence is applying telecommunications principles to biochemistry."

The approach is roughly similar to the DNA barcoding techniques that are widely used for reading out various molecular and protein assays, but the telecommunications-based codes and algorithms "are incredibly powerful compared to just a DNA barcode," said Stone. "We are able to have a much better signal-to-noise ratio, so we are able to multiplex more of these codes."

Stone said the system provides high sensitivity that is not negatively impacted by increased levels of multiplexing. Using a 384-well plate format, the platform can measure 10,000 targets per sample in up to 10,000 samples per day, he said, though Pleno has not yet made any data generated on the system publicly available. He added that the company is currently working with several industry partners on applications for the system. The company has "filed extensive IP around all foundation aspects" of the technology, Stone said.

Van Rooyen began his career in the telecommunications space, first as an engineer at Alcatel-Lucent, then as a researcher at Sony, and as chief architect at Broadcom. In 2013, he founded next-gen sequencing data analysis firm Edico Genome, which Illumina acquired in 2018.

Van Rooyen said Pleno plans to have a prototype device ready in 2023 that it could roll out to early-access customers. The goal is to move into the research market first, but the firm ultimately plans to target clinical applications, as well.

Stone said the technology could prove useful as a nucleic acid analysis tool for "any application where the content you are looking for is known."

"Anything that is pure discovery, where you don't know the markers you are looking for, would stay in the realm of sequencing," he said.

Pleno also expects its platform will be applicable to other omics research, including proteomics, where it could be used to read the DNA barcodes or aptamers used by companies like Olink and SomaLogic in their large-scale proteomics assays. This could be a hard sell, though, given that both companies — currently the clear leaders in label-based proteomics — have recently moved to NGS for readout of their assays.

SomaLogic announced a deal with Illumina in January to use the sequencing company's NovaSeq instrument for its SomaScan assay, which employs a library of proprietary aptamers called Somamers to measure 7,000 proteins per sample. As part of the deal, Illumina is developing its own NGS-based proteomics assay using the SomaScan system that it plans to release in 2024.

Before moving to NGS, SomaLogic used a microarray readout, which offered significantly less sensitivity than NGS and which some in the field considered a major disadvantage for the company in its competition with Olink, which in 2020 began moving its high-plex Explore assay, which measures around 3,000 proteins per sample, to NGS on Illumina's NovaSeq platform. Olink previously used qPCR as the readout for the system, and it still uses qPCR, on Standard BioTools' BioMark instrument, for readout of its lower-plex Signature Q100 assays.

Olink has indicated openness to expanding readout of Explore to platforms beyond NovaSeq, with CEO Jon Heimer noting during its recent Q1 earnings call that it is collaborating with "multiple partners" to allow users to read out data from the Explore platform on "several of the new sequencing instruments entering the market."

"This effort will translate into increased flexibility as customers will be able to choose from a menu of detection platform alternatives," he said.

Pleno's recent funding round was led by investors including Medical Excellence Capital and Alexandria Venture Investments.

The company has appointed Greg Lucier, a biotech industry veteran and former CEO of Life Technologies, as chairman of its board of directors. It currently has 14 employees and plans to add another 25 to 30 employees by the end of the year.