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Stanford Spinout Earli Developing Synthetic Genetic Constructs for Cancer Detection


NEW YORK – Stanford University spinout Earli aims to use synthetic genetic reporters to aid in the early detection of cancer by programming tumor cells to selectively express markers that can then be detected by imaging or other readouts.

The company plans to focus initially on lung cancer, where its technology may help doctors evaluate indeterminate lesions detected via low-dose computed tomography (LDCT), said David Suhy, Earli's cofounder and CSO.

Earli's genetic constructs consist of DNA-binding sequences for transcription factors dysregulated in the cancer of interest along with a cancer-activated synthetic promoter that drives high expression of a reporter molecule. These constructs can be delivered to a patient using a carrier like a lipid nanoparticle. Once in the patient's body, the constructs will bind to the dysregulated transcription factors present in any tumor cells and produce the reporter, which will indicate the presence of cancer.

"Instead of searching for biomarkers that cancer naturally produces … why not instead tap into the genetic circuitry itself and understand how to usurp the very dysregulated pathways to, at a genetic level, activate either the expression of a biomarker or a therapeutic protein?" Suhy said.

Earli launched in 2018 to commercialize technology developed in the lab of late Stanford professor Sanjiv Gambhir. In a 2015 Proceedings of the National Academy of Sciences study, Gambhir and colleagues used a synthetic DNA molecule consisting of the tumor-specific promoter pSurv and the reporter gene SEAP to detect melanoma in mice and produce SEAP in response. In a study of seven mice injected with melanoma cells and six that had not been injected, the researchers were able to distinguish between the two groups with an area under the curve of 0.92.

In 2019, Gambhir's lab published a paper in Nature Biotechnology in which he and his colleagues used engineered macrophages to detect tumors.

Suhy noted that while Earli has rights to the intellectual property covering both approaches, it is not currently pursuing the macrophage-based approach given the high cost of producing those engineered cells.

Devising the genetic reporters requires identifying transcription factors that are dysregulated in a large proportion of the cancers the reporters are meant to detect. To do this, Earli examines transcriptomic, proteomic, and phosphoproteomic data across tumors of interest.

In a poster presented at the American Association for Cancer Research annual meeting last year, the company detailed this process. Using data generated by the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium, Earli researchers looked at RNA-seq data along with mass spec-based proteomic and phosphoproteomic data from 211 paired tumor and normal adjacent tissue samples collected from patients with non-small cell lung cancer (NSCLC). They used an unsupervised multiomics factor analysis to identify dysregulated transcription factors, looking for factors exhibiting high expression levels compared to normal tissue in at least two out of the three data types they analyzed.

The researchers then produced constructs featuring binding sequences to a set of those dysregulated transcription factors and transfected them into various cell lines, including cancer cells, patient-derived xenograft cells, and normal cells, finding that the cancer cells expressed reporter molecules at high levels while normal cells showed low expression.

The company has since moved to testing its constructs in mouse and pig models, Suhy noted. It is also working to validate its constructs in cell lines derived from patient samples collected via collaborations with partners including Stanford University and the Mayo Clinic, he said.

Earli plans to position its lung cancer test as a tool to help doctors determine whether a nodule picked up on an LDCT scan is malignant. In this case, the construct will produce a reporter that can be detected using PET imaging. In general, Suhy said, the company plans to use reporters that are already clinically validated and, when possible, sold commercially.

Suhy said the company is planning an initial clinical trial in lung cancer in which it will use its constructs in patients who are scheduled to undergo biopsy of a suspicious nodule. Ultimately, the goal is to use its technology in place of a biopsy. Earli aims to conduct Phase I and II studies for the test within the next few years.

To date, Earli has raised $82 million from investors including Andreessen Horowitz and Khosla Ventures, which should provide it sufficient runway for these efforts, although it recently launched a new funding round targeting $40 million.

Injecting individuals with synthetic genetic constructs, even in small doses, comes with certain risks, Suhy said, citing concerns like the possibility of integration into the individual's genome and the potential for immuno-toxicity. Given these risks, the company doesn't view the technology as a good fit for broad population-scale cancer screening but plans instead to target it to reflex testing applications helping doctors evaluate potential malignancies, Suhy noted.

The company's novel approach also brings with it a level of regulatory complexity.

"There are clear biology implications for us [introducing] nucleic acids," Suhy said, noting that oversight of the company's tests will likely fall under several different sub-agencies at the US Food and Drug Administration. "We've yet to get a clear ruling [from the FDA] in terms of how this will be regulated moving forward."

Perhaps the closest example of a comparable technology is Cambridge, Massachusetts-based Glympse Bio's synthetic peptide diagnostics. Glympse's tests work by injecting patients with peptide substrates to proteases that are known to be dysregulated by particular disease states. When these peptides are cleaved by their proteases they are excreted in the patient's urine and can be measured, with changes in quantities indicating protease dysregulation reflective of a given disease. The technology was developed in the lab of Massachusetts Institute of Technology professor Sangeeta Bhatia, who sits on Earli's scientific advisory board. Last year, Glympse merged with Singapore-based biotech firm Sunbird Bio.

If and when Earli does bring its lung cancer test to market, it will likely face a fair amount of competition. Several companies are pursuing similar applications using more traditional approaches. Biodesix's Nodify Lung test is a blood-based protein test for assessing the likelihood that an LDCT-detected lung nodule is malignant. Other tests targeting the same use case include BioAffinity Technologies' CyPath Lung and Veracyte's Percepta Nasal Swab.