Harnessing Carpool-Seq to Tackle Complex Disease: An Interview with Neptune Bio

Hanna: Ben, could you start by sharing your background and what led you to founding Neptune Bio?

Ben: I came into the biotech industry with a fairly unique background. I did my undergraduate work at Vassar College majoring in Biochemistry and while also being pre-med. I chose this path, primarily driven by my love of science, but also mistakenly believing that becoming an MD or PhD were the only two paths for people who were interested in the sciences. After graduating, I worked at Weill Cornell Medical College in New York City in the department of Human Genetics, participating in all aspects of the department’s working, including everything from discovery-stage animal models to manufacturing the viruses for human clinical trials to ultimately assisting in sample collection and data analysis in active clinical trials.

As a result of working more closely with physicians on a day-to-day basis as part of my role with the clinical trials, I developed a deep respect for the work they do but also realized that becoming a physician was not the path for me. After deciding not to pursue an MD, it left me at a crossroads on my career journey. I had never felt drawn to pursue a PhD, believing the time commitment was not worth the return. I realized my true passion was at the intersection of business and science, enabling great science to happen by layering a business perspective, onto a science background to know what is meaningful. Majoring in biochem and being pre-med, I had never taken a business class before. To build up my expertise on the business side, I enrolled at NYU Stern and received my MBA specializing in entrepreneurship, innovation, and finance. During my MBA I also had my first taste of the venture world during that time consulted for Lux Capital.

Near the end of my MBA, Lux was spinning out Kallyope, a biotech company backed of course by Lux, but also TCG and Polaris, and I was privileged to join as one of the early employees. Over my eight years at Kallyope, I saw the company grow to about 150 people and had a hand in leading many of the business functions. My time at Kallyope cemented my belief in my passion is the early stage of company building; taking an idea, shaping it, and building a team around it.

Knowing I wanted to jump back to early biotech, I reached out to my network of founders and investors in NYC. Through that outreach, I had the privilege to meet my scientific co-founders Rahul Satija, Harm Vessels, and Yuhan Hao. They were beginning to pitch an exciting scientific idea that we eventually made Neptune. Together, we turned it into a business and raised our seed round in March 2023. Today we are a 12-person team, and I serve as COO and CFO.

Hanna: Would you share sort of an overview of Neptune and the gaps you're addressing?

Ben: Neptune Bio was founded around the belief that most simple diseases have been addressed. However, complex diseases such as neurological, cardiovascular, metabolic, or inflammatory conditions arise from multiple factors. To treat these complex diseases, we need to develop multiplexed therapies that are able to engage multiple targets at once. Neptune’s mission is to develop these therapies. However, to successfully do that, you need to understand how targets are interacting in complex environments, either in synergy or antagonizing. Before Neptune was founded, it was not possible to do this at the scale and scope. Our proprietary platform enables the generation of this data.

The technology that Neptune Bio was founded on is Carpool-Seq, created by my co-founder Harm. Carpool-Seq is a proprietary Cas-13 based system, where we can perturb up to 10 different genes in combination in a single cell environment. We utilize single cell sequencing to understand how those combinations of perturbations affected the entire genetic transcriptome of the cell. Currently, we are working in the cardiovascular and metabolic spaces across a broad pipeline to create and discover multiplex therapies to treat complex disease.

Hanna: What sort of role does technology play in your approach?

Ben: Technology, of course, can mean many things. I think of technology impacting Neptune in two areas; internal and external. We have obviously seen a rise in the sophistication of single cell sequencing. Neptune is not inventing new ways to sequence cells, 10x and Illumina are improving speed and cost, which helps us generate richer datasets. Internally, we our building our platform around Carpool-Seq and developing novel methods to expand its scale. In an ideal world, we would screen 20,000 by 20,000 gene pair combinations in an unbiased way. Right now, that would be prohibitively expensive, but we are developing strategies to make larger-scale, unbiased experiments feasible.

Hanna: How is Neptune changing how therapies are developed or delivered?

Ben: A lot of people in biotech talk about AI, and it applicability to discovering novel targets. My view is that AI is only as valuable as the data you feed it. In biology, the scale of available data is nowhere near what you would find in fields like language processing. That is why generating high-quality, proprietary data is crucial. AI can help us process it, but the real breakthroughs come from building better and proprietary datasets through our platform.

We are also very focused on translational success and minimizing development risk. In preclinical work, the field is well aware that cells in a dish or animal models do not always translate to humans. At Neptune, we are constantly designing our experimental pipelines so that the readouts we measure in vitro are the same ones we will measure in patients. That consistency we believe will increase our odds of success.

Hanna: What has been the most challenging and rewarding part of your journey so far?

Ben: They are two sides of the same coin, building something from nothing. It is incredibly hard but also the most rewarding. At Neptune, our entire team always has to wear many hats and keep all the moving pieces together.

On top of that, investor appetite in biotech has shifted. Ten years ago, you could raise a Series A on a big vision alone. Today, investors expect much more, often human data. Convincing people that what we are doing is worth backing can be tough, but it is also exciting when they buy into the vision.

Hanna: Looking ahead, what are you most excited about for Neptune?

Ben: Near term, I am excited to validate some of our novel targets in complex in vivo models. That will be an important milestone, showing that our approach works beyond discovery. Longer term, the goal is to advance programs toward the clinic. Ultimately, the most meaningful moment will be when our drug is tested in a human for the first time.

Hanna: What’s the best piece of advice you’ve received about company building?

Ben: In startups, and especially in biotech, it is all about the people. You need to work with people you trust, who are smart, and who you enjoy working with. On small teams, one bad apple can sink the company.

Transparency is also key. Biotech takes time; cells and animals grow at fixed rates. Setting the right expectations with investors, partners, and your team is essential. You do not want to overpromise and underdeliver. You want to promise thoughtfully and then deliver.