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Problem Solvers by Nature: How Digital Proteomics is Using Bioinformatics with the Aim to Unlock the Power of the Human Immune System

By JLABS
Q&A

 

Natalie Castellana, PhD

Natalie Castellana, PhD, CEO of Digital Proteomics, knew from an early age that that the traditional career path for a computer scientist was not for her.

Instead, Dr. Castellana found herself drawn to the idea of applying her expertise to some of the greatest challenges in biology. She began to explore the idea of applying algorithms for protein analysis when she realized that most methods on the market were not utilizing one of the most powerful resources in scientific discovery – the human body’s own adaptive immune system.

Having recently graduated from Johnson & Johnson Innovation – JLABS @ San Diego, Dr. Castellana shares how Digital Proteomics aims to continue pushing the boundaries of bioinformatics to drive the next potential breakthrough in drug discovery. 

Can you tell us where the idea for Digital Proteomics came from?

Digital Proteomics is a biotech company, but my first language was definitely not biology. I graduated with my PhD in Computer Science from the University of California, San Diego and have always been interested in informatics and problem solving.

As I was growing up in the D.C. area, I saw that nearly everyone who graduated with a degree in Computer Science ended up at a big tech company, which did not feel like the right fit for me. I wanted to do something different. One of the things I like to say is that we are “computer scientists with a soul.” 

I began exploring bio-focused research and trying to address those challenges, yet at the time, bioinformatics was a relatively new field that most people had never heard of. One of our co-founders, Pavel Pevzner, was teaching at UCSD at the time and is credited for his early work in advancing bioinformatics algorithms. I enrolled at the University to work directly with him and another co-founder, Vineet Bafna, to deepen my understanding of bioinformatics.

We began collaborating together on algorithms for protein analysis, which is how I also met and connected with our CSO and CTO, fellow alumni of UCSD Stefano Bonissone and Anand Patel. The idea to launch Digital Proteomics as its own spinout company followed directly from the algorithms that were conceived at UCSD. 

Digital Proteomics aims to advance antibody discovery and sequencing. Can you explain your approach for doing so?

The thesis behind our technology was first observed over a hundred years ago. We did not know how to define it at the time, but using antibodies from survivors of disease is a proven method for treating diseases like measles and diphtheria. Infectious diseases are the obvious area where this thesis is true; however, many cancers also have an immune component. 

We focus on the antibody molecule directly, which may sound like a simple concept, yet the landscape of the industry tends to focus on the B cells that produce the antibodies. Despite the fact that antibodies are the active molecule in our immune response, the field of proteomics is not as mature as genomics, so most technologies have leaned heavily on gene sequencing as a proxy for protein expression.

We now know that we are missing out on potentially game-changing methods for drug discovery by ignoring the antibody proteins. That is a key strength of Digital Proteomics as we focus on the significance of analyzing proteins. A decade ago in drug discovery, we had to rely on using mice immune systems to generate new drug hits. Now we are seeing that the more human-like an antibody can be, the greater chance of success it has.

We have larger companies reaching out to us and asking for our guidance on this approach to antibody discovery, and our suggestion is to look to the original pharma company – the human immune response system. Harnessing the power of the human immune response system is our core approach at Digital Proteomics, and we are leveraging algorithms and machine learning to do so.

What are some of Digital Proteomics’ short-term and long-term growth plans?

We believe our technology is ready to go for infectious diseases and oncology. In the next two years, we will continue validating and extending our platforms as well as to have antibodies in preclinical development for several therapeutic areas.

As we continue to broaden our footprint in this space, we are also seeking to actively expand our team, from research and development to sales and marketing. We believe good ideas can come from anyone and anywhere, and we aim to enable a culture at Digital Proteomics that empowers our employees to take a cross-disciplinary approach to help solve the challenges of antibody discovery. 

Having relocated to San Diego initially for academic purposes, how do you think being a member of the region’s innovation ecosystem has led the company to where it is today?

San Diego is remarkably collaborative and a top-tier environment for research. At UCSD, we had resources across a variety of departments and worked closely with their technology transfer office. There is such a great and diverse talent pool coming out of San Diego’s academia, and so many companies in the area are spinouts from these local universities and research institutes.

We were recently awarded $75,000 in funding at the San Diego Angel Conference, which is a program that runs out of the University of San Diego’s School of Business. This is just one example of how the region’s academia continuously seeks to nurture the growth of early-stage companies with promising solutions to drive change.

Our residency at Johnson & Johnson Innovation – JLABS (“JLABS”) was serendipitous as it connected us into the broader ecosystem in San Diego, exposing us to an interesting mash-up of expertise that can inspire ideas you would not expect. It taught us how to fundraise, form partnerships, and think critically about our own science. Everyone at JLABS is eager to share know-how and make introductions to truly support one another. “The rising tide lifts all boats” is the motto I best think captures the spirit here.

You do not have to be an established entrepreneur to get value from JLABS and other institutes in San Diego. Just plug into the ecosystem even as an observer to see who the key players are and how you can apply their learnings to your own goals. There is so much to learn from others, so don’t hold back. 

To learn more about Digital Proteomics, please visit their website at https://www.digitalproteomics.com/.

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