The late Sanjiv (Sam) Gambhir, MD, PhD, spent his life fighting cancer. A pioneer in cancer imaging, Gambhir helped develop Positron emission tomography (PET) reporter gene technology. Gambhir, a distinguished professor at the Stanford University School of Medicine and an advisor to numerous companies, was never content with the sensitivity of cancer detection technologies when it came to finding early-stage cancers. With 70 percent of all cancers discovered at Stage 3 or 4, waiting for symptoms is usually too late, with a five-year survival rate of only 25 percent.
After losing his son Milan to glioblastoma when he was just 16 years old, Gambhir’s motivation reached new heights. He devised a solution that flipped the paradigm of cancer detection on its head—instead of waiting for cancer to produce biomarkers, why not make cancer reveal itself? Can cancers be engineered to produce a biomarker when they are still in their early stages of malignancy?
After being diagnosed with the “emperor of all maladies” himself in 2020, Gambhir never got to witness his goal of getting cancer cells to express detectable “synthetic” biomarkers. He passed away in July 2020. However his legacy lives on in Earli, a company he co-founded, which presented its first data at AACR 2024 this week.
Earli researchers, under the direction of co-founder and chief scientific officer (CSO) David Suhy, PhD, demonstrated a robust screening platform to identify response elements that can be activated by uncontrolled cancer pathways. With this platform, the team designed a DNA construct with binding sites for transcription factor combinations found only in active cancers. This construct drives the expression of a biomarker that can be quantified in cancer cells while remaining transcriptionally silent in adjacent healthy tissues and benign lesions.
Based in Redwood City, California, Earli developed the platform technology in stealth. In January 2021, the company announced that it had raised a $40 million Series A, with financing led by Khosla Ventures. Additional investors included Perceptive Advisors, Casdin Capital, Andreessen Horowitz, Sands Capital, and top individuals, including Midas List investors Jim Breyer/Breyer Capital and Rahul Mehta, Goldman Sachs’s former CFO and CIO R. Martin Chavez, and biomedical device entrepreneur Shlomo Ben-Haim, MD.
Earli’s advisory board includes a remarkable group of A-list researchers, including Nobel Laureates Jim Allison, PhD, and Lee Hartwell, PhD, as well as Bob Langer, Sangeeta Bhatia, MD, PhD, Phil Greenberg, MD, Padmanee Sharma, MD, PhD, Charlie Rudin, MD, PhD, and Alan Ashworth, PhD.
Gene therapy constructs in cancer
After selling his company ShopKick for $250 million in 2014, serial entrepreneur Cyriac Roeding was coming back into the business fold and looking to strike at the intersection of technology and disease. When confronted with the opportunity, Gambhir told Roeding that he had a solution to one of medicine’s most important problems—early cancer detection.
Although Roeding didn’t bite at first, Gambhir persisted. In 2018, Roeding and Gambhir co-founded Earli with the idea of developing a technology for identifying cancers at Stages 1 or 2 and localizing them for precise treatment, which would save more than one million lives annually.
Earli raised $19.5 million in a seed investment in 2018, led by Andreessen Horowitz’s a16z Bio Fund and Marc Benioff, and supported by Menlo Ventures and ZhenFund. Jorge Conde is the Earli board member from a16z, and Marc Andreessen serves as a board observer.
There was just one problem: Gambhir was adamant about staying on the faculty at Stanford, necessitating the recruitment of a CSO.
“At the time, I was the CSO of a small gene therapy company called Benitec Biopharma, the company that put the first virally encoded RNA into human beings,” recalls Suhy. “[Roeding and I] met for coffee, and Cyriac breaks out a slide deck. The first slide was a Tylenol-like capsule with DNA inside of it. I looked at it and almost got up and walked out because no one puts DNA inside of a capsule!”
Roeding, who would go on to assume the role of Earli’s CEO, cut to the chase and presented Gambhir’s idea of “synthetic” cancer biomarkers, which Suhy said was fundamentally game-changing for him.
“The idea that Sam had was, ‘Can we tap into these pathways already dysregulated within cancer and express something using a gene therapy construct?’” Said Suhy. “For the first time, we wouldn’t be treating or trying to detect cancers by using blunt-force instruments like toxins or even targeted therapies that only recognize things on the outside of cells.”
Suhy, who was in a financially successful and scientifically captivating position, had a big decision to make: should he walk away from his position as CSO at Benitec?
“I was making a lot of money, doing a lot of great science, putting a lot into the clinic,” Suhy recalled. “Before we had even raised a single cent, one day I was talking with Cyriac and Sam and said, ‘That’s it, I’m in!’. This is too intriguing for me to pass up.” Suhy promptly told his board of directors that was resigning. “It’s been an exciting ride since.”
Cancer is not a single disease
Suhy has jumped feet first into figuring out how to take advantage of what cancer is already doing to these cells and activate some sort of genetic programming to do something in response—whether producing an epitope on the cell surface like a flag or an oncolytic therapeutic.
Cancer is not a single disease—it is a lot of genetic diseases that fall under one umbrella, with the same physical outcome of unregulated cell growth. And within each cancer type—whether lung adenocarcinoma with an EGFR mutation or hereditary breast cancer rooted in a BRCA1/2 mutation—there’s a lot of heterogeneity within the cancer cells in a patient.
With that in mind, Gambhir’s first iteration of his technology was based on using the Survivin anti-apoptotic promoter to represent the activation of pathways specific to cancer cells.
“If we were to try and design a promoter that corresponded to each driver mutation, it would never get done,” said Suhy. “Instead, we started thinking that cancer driver mutations don’t act in a vacuum. [Cancer mutations] trigger many dysregulated pathways with the end goal of cellular proliferation. Whether it’s an EGFR mutation related to KRAS, Wnt pathways, or TGF beta, it’s all going to converge down to the same genes that are going to be highly upregulated in the context of cancer so that these cells can divide.”
The Earli team built on Gambhir’s idea by using the huge amount of bioinformatics data that has been gathered over the past few decades to do a multifactorial analysis and find the downstream transcription factors that are upregulated and cause cells to divide. These genes probably would not be active in healthy tissues, so the team was able to find them.
By combining binding sequences for transcription factors within active cancers on a plasmid, Earli created what they call a sensor that they’ve called a “synthetic” biomarker.
Lighting up the lung
As a proof of concept, Earli has been working on designing a “synthetic” biomarker plasmid for non-small cell lung cancer (NSCLC). To do this, the group used a Massively Parallel Reporter Assay (MPRA) high-throughput pooled screening (HTS) method to look for specific activity in groups of response elements. More than 2,000 different sequences of homotypic or heterotypic transcription factor binding sites for the top 100 transcription factors were arranged in a grid with different spacing and each one was given a barcode for high-throughput screening in NSCLC cell lines.
Their best hits are cloned into plasmids to make cancer-specific promoters. These are then tested on a wide range of in vitro primary tumor lines with different genetic backgrounds and transcriptional profiles. Finally, they are tested in vivo using their own imaging platform to tell the difference between benign and malignant lung nodules.
“We not only do this in the context of small animals such as mice, but more recently we’ve been using pigs and companion animal dogs through veterinary oncology clinics,” said Suhy. “The rationale is that if we can scale into a pig with a fully functional immune system, that’s a lot easier going from a pig into a human than from a mouse into a human on top of that.”
Suhy said that they’re able to pick up signal from relatively small numbers of cells, with somewhere around 62,000 cells being sufficient. Depending on the tumor, Stage I cancer falls into the ballpark of 10 mm in diameter. For breast cancer, tumors of 10 mm, 5 mm, and 1 mm have about 100 million, 10 million, and 100,000 cells, respectively.
The next steps for Earli include expanding the platform to other cancer models and indications and leveraging this to explore more complex response elements that use combinations of transcription factors and natural spacing.
“It will never be a pan-cancer screen or multi-cancer sort of screen,” said Suhy. “We limit the diagnostic portion of what we do, and even the therapeutic portion, because the specificity of the promoters is too hard to do at a very broad level. We’re not claiming that we’re going to develop a therapeutic that will cure every cancer.”
Earli is also thinking through how to properly design epitopes without setting off signaling cascades and potentially even triggering more cancer. To do so, most of the epitopes, which are membrane-bound proteins, are inactivated. If the protein has a signal transduction tail, they mute it but leave the epitope untouched.
It’s personal
Suhy said that Earli is still working out the kinks of their diagnostic platform and is finalizing work on their clinical candidate. The goal is to begin regulatory meetings with the FDA in the next 18 months, with the expectation of making it into clinical trials at the end of 2025.
“We’ve largely been in stealth mode for the last few years, but we feel confident now with our intellectual property, which is now starting to be granted, and with the capital raisings that we’ve been able to do, [that] now is sort of the time to start releasing some of the data and some of the details,” said Suhy.
Suhy said that the company, while only 30 people, is devoted to cancer. They continue the fight that Sam is no longer physically a part of.
“Sam lost his son two years before we founded the company,” said Suhy. “Two years after we founded the company, Sam died of cancer himself. His wife [Aruna] just passed away of cancer [in November 2023]. For us, it’s personal.”
