Know The Proteome, Know Yourself – Unlocking The Secrets Of Proteins Could Save Lives
From repairing tissues to transporting oxygen in your body, proteins serve many vital functions. Studying the proteome, the complete set of proteins expressed by a living being, can reveal new information about the organism and potentially help prevent or cure diseases.
Seer, a life sciences company, is commercializing a new platform for proteomics, the study of proteomes. Using proprietary engineered nanoparticles, automation instrumentation, consumables, and a software suite, the company can perform deep proteomic analysis at scale in a matter of hours.
Nano Solutions to Big Problems
Today’s Seer platform didn’t wasn’t originally inspired by the proteome. Omid Farokhzad, CEO of Seer, explains that they had developed different nanotechnologies for medical applications. Many of the nanotechnologies were for drug delivery, and some were for vaccines. But one of the issues they had with the nanoparticles occurred when they exposed them to a biological system.
Farokhzad describes how the team would inject nanoparticles into the body to deliver drugs. But the moment the nanoparticles hit the body’s plasma or blood, they would form a layer of biomolecules and proteins on their surface.
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“Initially, we did not like it because we thought it was messing up our pristine nanoparticle that we had designed for therapeutic applications,” says Farokhzad. “It turned out that we could not have been more wrong. The binding of those macromolecules and proteins to the surface of a nanoparticle was very precise and important. The binding happened because of the physical and chemical properties of the nanoparticle.”
Millions of years of evolution in biology have created proteins that are designed to bind with each other. This is how they function, come together, and form units that are the basis of life. Proteins come together because the physical and chemical properties of one protein match the properties of another protein. In the human body, proteins can only come together if they are expressed in the same place and time.
“At Seer, we have solved the place and time problem by putting the proteins in the same 96 well plate in the lab. We control the physical and chemical properties through engineering, machine learning, and data science. By understanding the proteome, we can learn more about the complexity of proteins and how they work together,” says Farokhzad.
In the past, the approach to proteomics was biased or targeted and relied on using a ligand (binding molecule) to find the protein. An average human protein is 470 amino acids long, but an average ligand only binds to five to eight amino acids. A targeted approach means you miss the enormous complexity of the proteome.
Seer’s technology can examine the complete proteome by combining different nanoparticles in a panel at scale and speed. Instead of a targeted approach, it uses an unbiased method by examining each amino acid of the protein.
“We are all born with about 20,000 genes, and all of our cells have the same genes. But biology is complex. As you go from the genome to the proteome, you end up with anywhere between 1 million to 4 million proteins,” says Farokhzad.
Humans make new proteins every day. As we interact with the environment, our proteome changes in response. The proteome is dynamic, so it is important to study all of it to get a full understanding of how proteins work.
What the Future Looks Like
When proteomics and genomics combine, they create the field of proteogenomics, and Farokhzad believes there is enormous potential here. “When we understand the complexity of the genome at the functional level, our lives will change. It will open up new possibilities and markets,” says Farokhzad.
For example, many neurodegenerative changes occur at the protein level in the human body, so studying genes is not enough to understand them fully. Proteogenomics opens up the possibility of learning more about Alzheimer’s, dementia, and multiple sclerosis (MS). In addition, since every person has a different proteome, being able to study individual proteomes will lead to better-personalized medicine and cost savings through the early detection of diseases.
“When vast biological data is going to become available, it is going to create a whole new world. Think of the incredible access to content we have now on the internet. We can catalogue, utilize, and leverage it,” says Farokhzad.
Understanding the proteome can unlock many possibilities in healthcare and other industries. Proteogenomics can take that knowledge to the next level by combining it with the genome and leveraging the data.