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Alida Biosciences Commercializing Library Prep Tech for Multiplex Epitranscriptome Analysis


NEW YORK – Genomics startup Alida Biosciences said it is commercializing a next-generation sequencing library prep technology that can simultaneously detect multiple epitranscriptomic signatures in one workflow.

Named EpiPlex, the assay promises to detect and quantify 6-methyladenosine (m6A), 5-methylcytidine (m5C), pseudouridine, and inosine modifications in long coding or noncoding RNA molecules. San Diego-based Alida said it is currently offering the assay as a service to early-access customers before launching it as a kit product mid-next year.

"Alida Bio is an epigenomics company," said Cofounder and CEO Gudrun Stengel. "The mission behind the company is really making epigenomic sequencing as easy as the primary [DNA] sequence."

Stengel established the company in late 2020 with Byron Purse, an organic chemistry professor at San Diego State University. Before Alida, Stengel said she held leadership roles at Element Biosciences and Illumina helping them develop sequencing platforms.

According to Stengel, Alida's EpiPlex assay is built upon a so-called proximity barcoding strategy developed by the company.

During the EpiPlex workflow, fragmented RNA is mixed with a pool of beads such that each contains a distinct RNA modification barcode and protein binder, which Stengel said has been evolved for "very high affinity" with minimized sequence bias. Once the binder conjugates to the target modification, the barcode is enzymatically transferred to the captured RNA, which then undergoes reverse transcription and library preparation for sequencing.

Because each modification has its own barcode, the approach can interrogate multiple epitranscriptomic features in one reaction, Stengel said, adding that the exact location of certain modifications can also be determined informatically downstream. In addition, the assay includes spike-in controls as a reference to infer the relative quantity for different modifications.

Compared with the existing methods to study RNA modifications, such as antibody-mediated immunoprecipitation or deamination-based approaches, Stengel said one selling point for EpiPlex is its scalability and ability to detect multiple targets.

"Current methods tend to be fairly tedious and with little bioinformatics support," she said. "They usually focus on one modification and don't allow you to take a more comprehensive approach to detecting multiple modifications."

In addition, Stengel said there are few commercial solutions available for RNA modification analysis, given most methods are still academic protocols and "haven't been developed to full robustness."

To validate EpiPlex's performance, in one internal benchmarking study, the company applied the method to measure responses to the inhibition of METTL3, a writer enzyme responsible for installing m6A modifications, in HEK293T cells. Stengel said company researchers observed a "dramatic drop" of the m6A peak after METTL3 knockdown, indicative of the EpiPlex's high accuracy.

Currently, Alida is offering EpiPlex to early-access customers as a service, where the company performs the assay and reports the data back to the researchers. By mid-next year, the company is slated to release its first kitted product based on the technology, Stengel noted.

According to her, the library prep kit, with an input requirement of 20 ng of RNA, will be catered to detect m6A, m5C, pseudouridine, and inosine modifications in mRNA molecules in a six-hour benchtop workflow.

While the first product will be developed for Illumina sequencing, Stengel said it could also be "fairly easily" adapted to other platforms. In addition, she said the company has not decided on the asking price for the kit yet.

With the launch of the product, Stengel said Alida will also release accompanying analysis software to enable users to perform streamlined analysis.

As the EpiPlex technology continues to roll out, Stengel said she anticipates the early adopters to be academic researchers, which is one category of the company's target customers.

In addition, she said the company is also having "interesting discussions" with companies in the RNA therapeutics space, particularly RNA editing companies that are interested in detecting global changes in the epitranscriptome. Beyond that, she said RNA drug developers could also be the company's potential customers.

In recent years, single-molecule native RNA sequencing technology, such as nanopore sequencing, has also gained traction for comprehensively detecting RNA modifications.

Commenting on that, Stengel said while the nanopore sequencing-based approach is "very elegant conceptionally," she believes "it will be a long time for the technology to really become a tough competitor."

For one, Stengel said nanopore sequencing requires unmodified reference or training sets to help interpret the epitranscriptomic signals with advanced bioinformatics, which is still largely lacking. In addition, she noted that Alida's focus is currently on mRNA molecules, which tend to only exhibit a small fraction of modifications, making it "a particularly tough target" for nanopore sequencing to handle given its limited data output.

Besides the mRNA kit, Stengel said Alida is also interested in developing targeted analysis kits tailored for detecting RNA modifications related to particular diseases.

In addition, she said the company is interested in tackling DNA modifications. To that end, Stengel said company researchers also demonstrated EpiPlex's feasibility for detecting histone modifications, which Alida plans to further develop down the road.

Eventually, she said the company plans to "link the different epigenomic layers," producing an assay that can detect DNA methylations, histone modifications, and RNA modifications in one reaction.

So far, Alida is supported by $5.1 million of VC seed funding from Palo Alto, California-based General Inception and Vertical Venture Partners as well as San Diego-based FusionX Ventures, Stengel said. Additionally, the company has secured six Small Business Innovation Research (SBIR) grants from the National Institutes of Health, totaling $5 million.

As its early-access program starts to take off, the company also plans to start raising Series A funding during Q4 this year, Stengel noted. The firm currently has 17 employees and plans to grow its workforce by one-third during next year as it builds up the commercial team, she said.

IP-wise, Stengel said the company has filed three provisional patent applications in the US pertaining to its ​​EpiPlex technology, one of which has been granted this year.