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INanoBio Nabs $5.4M From DARPA for Silicon Nanopore Sequencer Development

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NEW YORK – INanoBio said today that it will receive up to $5.4 million over four years from the Defense Advanced Research Projects Agency (DARPA) to develop a nanopore technology for epigenetic sequencing.

The funding is part of a contract worth up to $27.8 million to a research consortium led by Mount Sinai's Icahn School of Medicine under DARPA's epigenetic characterization and observation (ECHO) program. Its objective is to develop a device for rapid epigenetic marker analysis using blood samples in order to detect an individual's exposure to weapons of mass destruction. The device might allow the user to identify WMD exposure through epigenetic signatures even in the absence of symptoms and to discriminate between a victim and a maker of WMDs.

INanoBio CEO Bharath Takulapalli said the firm will use the funds to develop its solid-state field effect nanopore transistor (FENT) technology for methylation sequencing. "We have been working on this for the past few years. It is capital intensive to make the initial prototype," he said. "We have been making progress, but this grant gives us a boost." The firm is also seeking to raise over $40 million in private investment in 2020. 

The grant is the latest development for a firm that is trying to enter the diagnostics market with its solid-state nanotechnologies. INanoBio is also developing a proteomic nanowire diagnostic platform and hopes to enter the cancer diagnostics market, potentially with both technologies.

Founded in 2007, INanoBio licensed electrical sensor technology from Arizona State University that Takulapalli developed when he was at the school's Biodesign Institute. The firm is developing the FENT using concepts he described in a 2010 ACS Nano paper, concerning sensors that used capacitive charge-coupling mechanisms to increase electrical signals from an analyte.

"Everything's in silicon," Takulapalli said. Unlike potential competitor Oxford Nanopore Technologies, which currently uses protein nanopores but holds IP to solid-state nanopore technology, the FENT combines solid-state pores with semiconductor transistor technology. The device will "enable epigenetic and DNA sequencing at a rate of up to a million bases per second per pore, which is over a thousand times faster than other state-of-the-art nanopore sequencing platforms," he said. INanoBio's transistor should be able to detect the electrical signals from the analyte at the speed at which it passes through the nanopore.

INanoBio can already make the silicon nanopores, which are between 2 and 5 nanometers across. "Now we are working on building the transistor around it," Takulapalli said. "We have the design, we have analytically developed the theory behind it, now we need to build it to show it works." 

Takulapalli said the firm is developing the prototype at a semiconductor foundry with the aim of having its proof-of-concept device ready by the end of 2020. But the firm has given year-out launch time frames before: In 2014, Takulapalli told GenomeWeb he hoped to have his prototype by the end of that year.

"This first-of-a-kind 3D transistor is structurally unique. That's why it takes time," Takulapalli said. "We have been developing improved semiconductor fabrication methods to make the device with the nanopore at the center." 

In addition to detecting DNA bases, INanoBio believes the device will be able to detect the methylation states as well. That's what drew Mount Sinai Icahn School of Medicine Professor Stuart Sealfon to the firm. 

As principal investigator for a consortium applying to participate in the DARPA ECHO program, Sealfon said he saw INanoBio's presentation at a pre-meeting in February 2018. "I thought their approach looked exciting and reached out to them about joining our application," he said in an email.  

"The human body logs exposures in a rich biographical record that we carry around with us in our epigenomes," he explained. "The ECHO technology we're developing will enable us to quickly read someone's epigenome from a small amount of blood and measure any changes in the cells to accurately predict exposure to hazardous agents or materials."

Fluidigm said last month that it is also part of the Mount Sinai-led consortium, which further includes researchers from Princeton University, Yale University, Stanford University, the University of Pittsburgh School of Medicine, the University of Hawaii, and the University of Texas Medical Branch.

While much about the epigenetic signatures left by WMD-type events remains to be discovered, the Mount Sinai-led consortium believes the work it's doing for DARPA could also be applied in infectious disease. Sealfon said they already have data, albeit unpublished, that infections show epigenetic signatures, as does at least one heavy metal chemical exposure.

"It could be valuable in the field of infectious disease, for example, to quickly and reliably predict if someone has a bacterial or viral infection during the influenza season, giving patients a point-of-care benefit," Sealfon said in a statement. "It's likely that medical applications from this research program will be realized in a shorter time frame than those on the military side, which are more demanding."

"Another novel aspect of the ECHO program is its approach to profile epigenetic signatures at the single-cell level, treating each cell as a sample," Takulapalli said. "A FENT array chip integrated with microfluidics will enable single-cell analysis, reading out epigenetic patterns from tens of thousands of cells in a few minutes. While the presence of cells with a specific epigenetic signature indicates exposure, the distribution of cellular signatures in the blood sample may inform on the period or time of exposure."

In addition to providing some funds, the DARPA award will help INanoBio develop a technology platform that it thinks could be immediately applicable to cancer diagnostics. Cell-free DNA has been a hot topic, leading to the development of liquid biopsy tests, "but people are starting to look at the epigenome," Takulapalli said.

Though he hasn't spoken yet with liquid biopsy firms about partnerships, Takulapalli said he's held informal conversations with other life science and pharma companies about the FENT technology, although he declined to name them. Partnerships, he said, is something the firm would "want to get into going forward."

INanoBio is also working on developing a nanowire protein diagnostic platform, with a focus on cancer. "Grail is leading with DNA biomarkers and then came about adding epigenetic markers to the panel," Takulapalli said. "We are going the other way; we believe phenotype is a better way to diagnose disease early. And proteomics is closer to what we can access phenotypically." 

For cancer diagnostics, the firm's initial focus will be on a proteomic biomarker panel for early-stage diagnosis, he said, adding that "we will later augment the panel with epigenetic and genomic biomarkers for improving it further." 

For the DARPA grant, methylation signature detection is just the first phase. "Following that, we will be doing DNA sequencing as part of the grant," he said.

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