NEW YORK – Eyeing the vastly untapped epitranscriptome analysis market, Alida Biosciences this week commercially launched EpiPlex, a next-generation sequencing library prep technology that promises to enable multiplex RNA modification analysis.
The San Diego-based company's first products include the EpiPlex RNA reagent kit, which can detect and quantify 6-methyladenosine (m6A) and inosine modifications in one workflow, and the EpiScout analysis suite, an automated cloud analysis software for users to interpret and share the EpiPlex data.
To use the EpiPlex library prep kit, researchers start with purified RNA from cell lines, blood, or frozen or formalin-fixed paraffin-embedded (FFPE) tissue samples.
According to Alida Cofounder and CEO Gudrun Stengel, the input requirement for the kit is 20 ng polyA-selected or 100 ng of total RNA, a low requirement that could enable customers to analyze clinically relevant samples with a scant RNA amount, she noted.
The EpiPlex RNA reagent kit currently comes in two configurations: eight or 24 samples. According to the company, a lab can process up to 24 samples in a single-day library prep workflow with three hours of hands-on time. Overall, an EpiPlex experiment can take about three days, Stengel said, with one day for sequencing and another day for data analysis on top of a day for library preparation.
For the 24-sample kit, Stengel said the list price is $350 per sample. She also noted that the company is "actively pursuing collaborations on research topics of mutual interest and offer exclusive pricing agreements for these projects."
Mechanistically, the EpiPlex reagent uses a so-called proximity barcoding strategy developed by Alida. During the EpiPlex workflow, a pool of beads, each containing a distinct RNA modification barcode and protein binder, is mixed with the fragmented RNA. Once the binder molecule conjugates to the target modification, the barcode is enzymatically transferred to the captured RNA, which then undergoes reverse transcription and library preparation for sequencing.
While the EpiPlex technology has the potential to interrogate a slew of epitranscriptome features in one reaction, Stengel said the company made a "strategic decision" to focus on two of the most common RNA modifications — m6A and inosine — for the first product.
Customers who purchase the EpiPlex reagent kit will also get access to the EpiScout analysis software for free. Available on DNAnexus as a cloud-based app, the software processes the FASTQ files from the sequencing run and can conduct automated RNA modification peak calls and genome alignment, generating a detailed summary report of the modifications for streamlined data reviewing and analysis, Stengel said.
If customers desire, there is also an option to run the software locally as a command line tool, Stengel noted.
During EpiPlex's R&D stage, Stengel said Alida conducted a beta testing program with researchers at four institutions, including the Fred Hutchinson Cancer Center, the Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium site at Stanford University, Jefferson University, and Baylor College of Medicine.
The company in June last year subsequently initiated an early-access program for the technology, where Alida shipped out the EpiPlex products to over 20 research labs in the US and abroad.
EpiPlex "opens up an alternative approach for RNA modification to the traditional methods … and the more options a researcher has, the better," said Daniel Kraushaar, director of the Genomic and RNA Profiling Core at the Baylor College of Medicine.
According to Kraushaar, whose core is one of the early-access users of EpiPlex, RNA modification experiments are traditionally done using immunoprecipitation-based methods with home-brew reagents. Therefore, there has been a void when it comes to commercially available products that can achieve multiplex epitranscriptome analysis.
"As a core facility, we are limited in the bandwidth," Kraushaar noted. "Having a kit that is batch-tested and is ready to go is key for us."
In their hands, Kraushaar said the EpiPlex product has so far performed reproducibly. The protocol is also fairly straightforward with no extra instrumentation requirement compared to a standard RNA sequencing workflow.
Currently, the Baylor Genomic and RNA Profiling Core is also an Alida certified service provider, where customers can send samples for multiplexed RNA modification sequencing using EpiPlex. According to Kraushaar, the turnaround time for the service is about two to three weeks from sample drop-off, and the listing price is $800 per sample.
While the core does not provide analysis for EpiPlex, Kraushaar said customers using the sequencing service will receive data analysis support from Alida.
In addition to EpiPlex, Kraushaar's core also does nanopore sequencing, which can also capture RNA modifications.
"I think they are both great methods," Kraushaar said. As nanopore sequencing reads native RNA molecules, it has the potential advantage of capturing many more modifications, he noted. However, analyzing the nanopore data for modifications can be "a little bit more involved," Kraushaar said.
To that end, Kraushaar also said he hopes Alida continues improving EpiPlex to accommodate more modifications as well as further bring the cost down.
Commenting on nanopore sequencing, Stengel said the additional advantages of EpiPlex are the low RNA input requirement as well as the assay's compatibility with FFPE samples.
She also noted that Alida plans to add pseudouridine analysis to EpiPlex later this year, with more modifications to come down the road. The company is also working to improve the kit to achieve single-base resolution for all modifications beyond inosine, Stengel said.
Furthermore, Stengel said the company is interested in developing targeted assays for clinically relevant samples, tailoring the assay to specific biomarker genes that are known to be differentially modified in diseases.
Since its inception, Alida has raised $5.1 million in VC seed funding. Last June, the company secured $7.5 million in Series A funding. Additionally, the company has been awarded several National Institutes of Health Small Business Innovation Research (SBIR) grants, totaling more than $7.2 million.
Stengel said the company plans to raise more money in 2026, but she declined to disclose a target amount.
With the full commercial launch of EpiPlex, Stengel said the company, which currently has 20 employees, is also building a commercial team, though she said Alida is "pacing" its growth and expanding its workforce "very deliberately."