NEW YORK – Just when you thought microarray-based diagnostics were a thing of the past, they are being resurrected, and in Israel. JaxBio Technologies, a Tel Aviv-based company, recently received an €8.5 million ($9 million) EU Horizon Europe grant to support the development of a new array-based platform for diagnosing hematological malignancies.
According to Yuval Ebenstein, a chemistry professor at Tel Aviv University and founder of the company, the grant was recently awarded through the EU's Cancer Mission, a funding program to reduce cancer cases throughout the EU by 2030. The project, called Sanguine and coordinated by Tel Aviv University, commenced Jan. 1, 2023, and will run through 2026. In addition to JaxBio, the Sanguine Consortium involves participants from Belgium, Czechia, Germany, Greece, Lithuania, and Spain.
The purpose of the project is to develop a liquid biopsy-based test that can classify a set of hematological malignancies, according to the grant abstract. The test involves the detection of epigenetic markers in peripheral blood cells and cell-free DNA. The markers are labeled using fluorescence and analyzed using a custom microarray, dubbed the HemaChip. As part of the project, the participants will explore the medical, technical, and social aspects of the new test.
All of this will pave the way for the eventual deployment of the test in clinical settings, with stated project goals being the provision of validated reagents, arrays, and data analysis software ready for large-scale screening and early-stage commercialization within three years.
Ebenstein said the reason the researchers have been able to win funding to develop the technology is that it is a "completely orthogonal methodology for detection, compared to bisulfite sequencing or real-time PCR." By running analysis on custom microarrays, JaxBio can assess higher numbers of markers in parallel, making it less costly than sequencing and more scalable than PCR, he said.
"We are bringing arrays back from the grave, we are resurrecting them," Ebenstein said. His lab is housed within Tel Aviv University's school of chemistry, and his research has focused on pursuing single-molecule genomics using optical mapping, epigenetic analysis technologies, and high-throughput single molecule detection.
A recent paper, "Chemoenzymatic labeling of DNA methylation patterns for single-molecule epigenetic mapping," appeared in Nucleic Acids Research in September. In it, Ebenstein and fellow authors described a procedure to enable epigenetic profiling of single DNA molecules spanning hundreds of thousands of base pairs.
Specifically, they used a CpG methyltransferase with a synthetic S-adenosyl-l-methionine cofactor analog to transfer an azide to cytosines instead of the natural methyl group. A fluorophore was clicked onto the DNA, reporting on the amount and position of non-methylated CpGs. They also used the method to determine the decline in global DNA methylation in a chronic lymphocytic leukemia patient.
Though JaxBio's technology was developed in Ebenstein's lab, he said that the company's approaches have not yet been published. "There is a lot of know-how we don't want to expose," he said, "but in essence it is a custom microarray in combination with a magic sauce we developed."
Using this "reagent sauce," users can detect DNA methylation using the array, and with the addition of some deep-learning tools, a readout is produced that supplies information of disease type, subtype, stage, and response to therapy. Ebenstein said that the company has "amazing preliminary results" and that JaxBio is gearing up for a series A round within a few months.
JaxBio began operating in 2022 with seed financing of $6 million. Other cofounders include CEO Shahar Zirkin as well as Dror Feldheim and Joel Bar-El. Feldheim and Bar-El are the president of corporate development and executive chairman of Trax Retail, a Singaporean technology firm with operations worldwide. Ebenstein said the cofounders met via personal contacts and noted that Feldheim and Bar-El's experience with Trax could be useful to JaxBio as it expands into other markets.
In addition to the new Horizon Europe funding, Ebenstein's group at Tel Aviv University recently received a €150,000 European Research Council grant to carry out a project called Base6. That effort commenced Dec. 1 and will run through May 2024. The goal of Base6 is to develop a custom microarray targeted to 5-hydroxymethylcytosine, an oxidized form of 5-methylcytosine, which is an indicator of epigenetic changes in genomic DNA that might be caused by cancer.
The effort will see the researchers employ direct fluorescent labeling of 5hmC in combination with commercially available genome-wide arrays to create maps of the distribution of the marker in health and disease. The investigators intend to use such arrays to discover cancer biomarkers.
In a second phase, a subset of genomic loci containing modulation in 5hmC will be printed on a custom array. By using such a smaller array, the investigators believe they can reduce screening costs associated with large-scale research and high-volume testing. Ultimately, they envision their chips being used for 5hmC research, biomarker discovery, and companion diagnostics.
Ebenstein said that his team has a partnership with an undisclosed array manufacturer, and for the Base6 and Sanguine projects, they will use customized versions of commercial arrays, but in the future, they will develop their own pathway for printing custom chips.
He said that JaxBio's arrays will require a "special configuration that is not the standard," one that relies on a "completely new contrast mechanism," or means of detection. What that means is that the data generated in a JaxBio assay cannot be generated by any commercial microarrays. "It has a unique, optical readout," commented Ebenstein.
Back from the dead?
Microarrays emerged as the workhorse technology for genetic research in the early 2000s and quickly transitioned into the diagnostics arena. But next-generation sequencing came quickly after, and as sequencing costs dropped, many diagnostic companies have opted to either migrate their array-based tests to next-generation sequencing or to reduce the number of markers they assess to make multiplex real-time PCR platforms an inexpensive and more scalable alternative.
Yet though some industry insiders have talked about the "death of arrays" for some time, the fact is that they have never fallen out of favor, and JaxBio's platform aims to address a gray area between sequencing and PCR in terms of number of markers and throughput that its founders believe only microarrays can fill.
Alastair Malcolm, CEO of Phoenix-based Applied Microarrays, agrees. According to him, tests based on custom arrays, just like the ones being developed by JaxBio, are thriving. He noted that AMI, which manufactures such arrays for a diverse customer base, was acquired by Schott in October 2021 to "take advantage of that trend."
AMI was established in 2007 when it acquired GE Healthcare's Codelink microarray business at a time when several established players in the market were exiting it. AMI turned its focus to the custom market, where Malcolm said there has been increased adoption of multiplex biosensors and arrays for diagnostics. He said that arrays offer better economics than other technologies, such as sequencing, and that in the case of protein-based tests, arrays can out-multiplex lateral flow devices, while being more efficient than mass spectrometry.
Arrays also have a faster turnaround time, often with results delivered in an hour, which is "similar to lateral flow devices but with many more analytes being detected," Malcolm said.
Ebenstein said that based on an internal analysis, JaxBio's array-based tests would probably cost about as much as consumer genomics providers like MyHeritage or 23andMe pay per analysis, or about $30. It is this cost point that makes an array-based approach competitive with PCR and sequencing, Ebenstein maintained.
"With PCR, each reaction assesses a single biomarker, which makes it cheap per marker, but if you want to work on a panel containing hundreds or thousands of markers, it's useless," he said. Sequencing in contrast can enable a high level of multiplexing but is more expensive and involves burdensome data analysis.
"We are avoiding this because our technology is noiseless," said Ebenstein. "It's noise free, because we are only looking at the markers we are interested in" on a custom array, he said.
He noted that hematological malignancies are just one indication for JaxBio's technology and said that the company is looking into different aspects of cancer, from diagnosis through analysis of minimal residual disease, tumor biopsies, and response to therapy. The company is already working with several medical centers in Europe and Israel in the Sanguine project, such as the Tel Aviv Sourasky Medical Center, Vilnius University Hospital Santaros Klinikos in Lithuania, and Germany's FZMB Research Center for Medical Technology and Biotechnology.
As for when its array-based cancer tests might hit the market, Ebenstein said it was too early to speculate. "We need a serious R&D phase and our business model is under discussion," he said.