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Sweden's Aplex Bio Gearing up to Launch 'Hyperplexed' PCR Platform

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NEW YORK – Aplex Bio this week announced that it had raised SEK 14 million ($1.5 million) to support the development and rollout of its "hyperplexed" PCR-based molecular detection platform.

The two-year-old Swedish firm, headquartered on the campus of the Karolinska Institutet in Stockholm, believes its technology has the sensitivity, specificity, and scale to challenge both digital PCR and next-generation sequencing-based applications.

The technology could eventually find use in pathogen detection and cancer diagnostics, including companion diagnostics, according to CEO Umear Naseem. Aplex Bio is currently courting numerous first adopters to take part in an early-access program, set to commence in the second quarter.

"We are probing which customers to take in because we want to have a few key opinion leaders in different applications," said Naseem. "We are talking with different players in cancer diagnostics and other applications."

Naseem founded Aplex Bio in 2020 after spending three years at Single Technologies, a company that offers a sequencing platform called Theta, most recently as director of chemistry and materials. Before that, he held roles at Sol Voltaics in Lund, Sweden, which was focused on employing nanomaterials in solar energy. His scientific background is in chemical engineering.

A partner in his development of Aplex's technology has been Mats Nilsson's laboratory at SciLifeLab, the Swedish national research center. The Nilsson lab has been a locus of innovation for multiplexing and sequencing approaches for years, and is responsible for the padlock probe technology behind HaloPlex, now commercialized by Agilent Technologies, for example.

Naseem said that while Aplex Bio's core hyperprobe technology was developed in house, the firm initiated its collaboration with SciLifeLab "almost immediately," to implement the technology for padlock probe-rolling circle amplification assays, as well as for use in spatial biology studies.

Aplex is also investigating end user applications in partnership with the Nilsson lab, he noted.

Aplex Bio has not yet published its technology, although Naseem was willing to divulge a few details. Currently, the company can analyze more than 100 biomolecules deposited on a glass surface that can be read using conventional fluorescent image detection readers. The technology can generate 100 synthetic colors and read them out in high quality in a single step, Naseem claimed. These capabilities naturally lend themselves to multiplexing, he maintained, and could empower a "completely new arsenal of molecular technologies."

Aplex Bio's approach pairs the single-nucleotide specificity of padlock probes with single-molecule sensitivity and high multiplexity. "This essentially outperforms digital PCR," said Naseem. "This is a next-generation PCR technology, what we call beyond digital PCR."

The technology also could be used in lieu of sequencing in some situations, which Naseem said has drawbacks in terms of cost, lead time, and resources. "Sequencing will never compete with multiplexing on cost, even if one pools the samples," said Naseem. "It's unavoidable, since sequencing involves multiple steps, and here the only consumable is a glass slide," he said. "Plastic tubes and biochemistry do the rest."

Naseem noted that for those familiar with microarray technology, Aplex's offering could be considered to be self-assembling arrays. Each drop deposited on a slide could be a sample or a patient, so rather than running one patient sample against a whole-genome array, for example, you could assay a hundred-plus samples or patients on the same surface using Aplex Bio's approach against more than 100 targets.

"All of a sudden you are doing high-throughput detection screening on a very large scale," commented Naseem. He said that the technology could be set out in 96-well or 384-well plates, for example, and that Aplex will be working with partners to develop an automated solution in coming years. He said that an automated approach could conceivably be on the market by 2024.

In addition to pathogen diagnostics, cancer diagnostics, antimicrobial resistance testing, and environmental surveillance, Aplex Bio envisions applications of its technology in companion diagnostics.

"This is because we hit a unique sweet spot of being able to profile around 100 biomarkers in a single step," said Naseem. "This is much more cost efficient and scalable than sequencing, allowing our technology to be used like a PCR test before giving treatment to patients with complex diseases," he said.

Wastewater testing

One initial collaborator has been the Swedish Environmental Epidemiology Center, an environmental testing unit housed within SciLifeLab. The SEEC, established during the ongoing COVID-19 pandemic as part of SciLifeLab's Pandemic Laboratory Preparedness initiative, has continuously performed analysis of Swedish wastewater to monitor the spread of SARS-CoV-2 — an application that has already proven to be a sweet spot for digital PCR.

According to Maja Malmberg, a virologist at SciLifeLab who is involved with the SEEC, the center has been using quantitative PCR for its wastewater monitoring efforts, but recently decided to try out the Aplex Bio platform in a pilot study to see if it could detect additional pathogens from wastewater within the same assay, as well as to look for SARS-CoV-2 variants of interest.

While the project is nascent, Malmberg said her team has had a "very positive experience" with Aplex Bio's technology. Initial trials focused on the ability of the Aplex platform to detect SARS-CoV-2 in wastewater, with virus present at varying levels. Now the partners are working on detecting specific variants, with an eye to multiplexing different viruses in the same sample.

"I envision this could be extremely useful in lower income countries, or places where there are more pathogens and less possibility to run lots of PCRs for many different things," said Malmberg.

Malmberg noted that wastewater is a "naturally pooled sample," which means that testing it is less expensive than testing individuals for the virus. "If you can also multiplex, and do 50 or 100 targets within one sample, it is kind of mind-blowing in potential if it really works," she said.

Naseem said the cooperation could showcase the ability of the Aplex Bio platform to detect mutations not detectable by PCR, while overcoming the sensitivity issues inherent in sequencing.

"With our solution, they can get high sensitivity and they can get point mutation detection," said Naseem. He confirmed that Aplex continues to work with SEEC to test more pathogens on its platform.

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