🔒Protein Power: Quantum-Si works to uncover secrets of human immunity

Studying genes has unlocked key knowledge about how our bodies work, and life sciences company Quantum-Si now aims to bring a new level of understanding about proteins’ impact on our health.

Serial entrepreneur Jonathan Rothberg launched Quantum-Si in 2013 at his 4Catalyzer medical device incubator in Guilford.

In recent months, the company has been rapidly expanding. In January, it announced it would be moving its headquarters to New Haven. It signed a 10-year lease for 65,000 square feet of office and R&D space at Winchester Works, 115 Munson St.

Quantum-Si expects to be at its new headquarters the first half of this year. Last fall, the company also opened a new 25,586-square-foot product development and operations facility in San Diego.

Quantum-Si went public in June 2021, when it merged with New York-based HighCape Capital Acquisition Corp., a special-purpose acquisition company, or SPAC. The $1.46 billion deal pumped more than $500 million into the combined company.

Quantum-Si is focused on the field of proteomics, or the study of proteins. It is developing a suite of technologies, including software and medical instruments that use a semiconductor chip to enable single-molecule protein sequencing. The technology, Quantum-Si says, can be used to advance drug discovery and for diagnostics, potentially leading to new ways to diagnose and treat disease.

In November, Quantum-Si acquired Majelac Technologies LLC, a Pennsylvania company that provides semiconductor packaging and integrated circuit assembly services. The acquisition brings chip assembly and packaging, key for Quantum-Si’s operations, in-house, helping the company as it scales up its operations.

New Haven Biz recently sat down with Quantum-Si’s Chief Executive Officer John Stark, who joined in 2020, to talk about the company’s recent and continued expansion, and what the future holds.

What prompted you to join Quantum-Si?

Protein is really the fundamental building block of life. As we advance through genomics, there has been this tremendous scale of understanding. For proteins, it has really lagged.

About six or seven years ago, we started really focusing on proteomics, the understanding of protein diversity. It has become so critical in so many areas, such as understanding our immune system behavior.

Over the course of the last five to six years, my focus has been renewed not only on proteomics, but understanding single molecule, single cell.

By sequencing the proteome … we have a huge opportunity in front of us. Not only from the business side, but more importantly our impact on medicine.

What does the company’s technology do?

What we are doing is isolating proteins directly from humans, whether it is tissue, blood or a clinical specimen. We are able for the first time to characterize those proteins, not at the fully-assembled level, but the individual building blocks, the backbone that makes up those proteins, which is at the amino acid level.

To put it in a nutshell, what we are enabling now is the exploration of 95% of the biology that occurs in the cell that is really uncharted, and the opportunity for the development of future therapeutics based on the information we discover.

How is it different from what is available now?

We are looking at individual molecules of protein. Typically, groups have looked at whole sample types. Technologies like this allow you to look at a single cell. This allows you to look at specific components of that protein structure, which now gives you insight.

This team has designed a benchtop system (that is cheaper, more efficient and takes up less room than what is currently available in the market).

Instrumentation that has quantified proteins previously has typically filled rooms, cost millions of dollars and was very complicated. This team has not only revolutionized the way to look at greater depths of protein levels and greater sensitivity, but has actually put this on a benchtop instrument that will enable the masses.

How can the technology be used to advance drug discovery and for diagnostics?

I would say over 90% of drugs target a protein. Essentially right now about 85% of what we call the proteome isn’t related to a therapeutic and is undrugged.

So there is a huge opportunity to explore new potential therapeutics and targets to treat various conditions. We will be the engine that discovers those proteins as well as the protein levels that drug companies will essentially use to create new therapeutics.

Would your customers be drug companies, research facilities, universities, hospitals?

All of the above, starting first with mainly the research and pharmaceutical areas. Yale would be a key customer, Jackson Labs, there are a number of them across the Connecticut landscape.

This will progress to drug companies looking to develop new markers and targets for therapeutics. Eventually I can see this fast-tracking right into clinical use.

When will Quantum-Si be moving to New Haven?

As fast as possible. We have officially signed the lease. We began renovations. We are going to be moving in over time.

I would say by the midyear point, we will have pretty much moved out of the Guilford area and into the new highly-advanced New Haven site.

What appealed about the Winchester Works site?

First, it is downtown New Haven right next to Yale and the scientific innovation center. It is just an ideal location not only for current employees, who are super excited about being downtown, but the ability to recruit top talent.

Second, the Winchester site (formerly the Winchester Repeating Arms Co. factory) is a historic icon in town. With the renovations that have been made, it is going to be an absolute world-class facility.

We will basically be tripling our square footage, as well as renovating the center, to take advantage of having up to about 200 employees who go to work at that facility every single day.

You also have a new location in San Diego. What will workers be focused on at that location versus here in New Haven?

New Haven will represent our headquarters, the mothership. It will be the center of excellence for instrumentation development, as well as the home for executives.

You will have all areas and disciplines existing at both sites. San Diego is another hotbed for biotech. These are really two just tremendous locations for us to exist and to recruit talent.

Do you anticipate additional expansion?

After we take a breath. We are basically going from 20,000 square feet to close to 100,000 square feet (between New Haven and San Diego) in a matter of six months. We are witnessing massive expansion.

We have gone from 70 employees before going public to about 200 employees. We are going to continue to expand. We see more of a global expansion, rather than just local.

For the most part we will basically triple the employee base locally in Connecticut. We are committed to staying here for the long term.

Why go public?

The ability to raise over $500 million has equipped us to go through not only this massive expansion, but to really grow and expand and develop world-class products for the next five years.

How has the talent recruitment process been going?

We have probably about 15 different disciplines across our R&D organization, from more traditional biologists and chemists to computational biologists and biophysicists.

To do something like this, not only do you have to go out and raise $500 million, but you have to attract world-class talent. It has been pretty amazing — our ability to recruit here locally, and garner this type of talent, especially from Yale. We have a lot of people coming from Boston, Cambridge and New York.

What’s the status of the company’s commercial launch?

In 2021, we actually started placing our first systems, so we have external customers as we speak. We are going through a period right now of just ensuring quality supply chain, product support, finalization of protocols.

Right now, we are in the process of manufacturing 500 instruments.

Where do you see the company in five years and in 10 years?

Making an impact on general health. We are set for this explosion in discovery. We witnessed this in genomics. Proteins are set for the same expansion, except bigger.

(Proteins) tell you exactly what is going on in a given patient: What stage of disease? Is that therapeutic having the benefit desired?

When you look at a company like Pfizer, a large portion of their investment and drug development portfolio is focused on adjusting and harnessing our immune system to attack disease. That requires technologies like this to really identify what is going on and changing in (a patient’s) immune system.

We are going to be understanding biology that has never been looked at before.

What types of ailments will this help target?

Any disease. It will be about understanding our immune system, which covers all diseases, the trillions of cells that basically attack foreign invaders, viruses that come into us.

It is going to have an impact across the board. I think the biggest impacts will be in neurological disease.

What proteins really tell you is what is happening right now (in a patient). So it is going to become incredibly useful information to have immediate types of treatments. It also starts to detect the early onset of disease, which is the Holy Grail.

People will say, “I am going to have my immune system monitored.”