Imagine a rapidly replicating pathogen has just entered your bloodstream. You won’t call your doctor for several days, because you don’t even know you’re infected. Fortunately, you were born with a doctor inside of you. Pulsing through your bloodstream are billions of specialized immune cells, poised to produce hundreds of thousands of protective antibodies.
If we took a sample of your blood, say 500,000 cells, we’d see that about five of them have started producing antibodies that recognize the pathogen to tag it for destruction—all before your brain even knows you’re sick. Those same antibodies could be used to treat someone whose own immune system is struggling to diagnose the problem. But first, we have to find a way to separate the five from the 500,000. That’s a very fine needle in a whole lot of haystack.
In a new study by researchers from the National Institute of Allergy and Infectious Diseases (NIAID) an emerging technique known as single cell immune sequencing was used to find and characterize antibodies capable of stopping the spread of malaria. Now, the company that pioneered the single cell immune sequencing technology is working to replicate this approach for application to SARS-CoV-2, the coronavirus that causes COVID-19.
“By understanding the immune system of patients that have effectively fought the pathogen, we can pinpoint the exact identity of cells that effectively eliminate the SARS-CoV-2 virus out of millions of possibilities,” said Dr. Jian Han, founder of the company, iRepertoire, where the single cell immune sequencing technology was developed.
But pinpointing those cells, called B cells, is no easy task. Over the past ten years, researchers have been increasingly turning to DNA and RNA sequencing to better understand immune cells. Immune sequencing techniques have grown increasingly sophisticated, but most still involve blending up immune cells and sequencing them all in a big batch.
If each B cell is a berry, studying the immune system by traditional approaches is like drinking a fruit smoothie. You can get a general taste, but you can’t really appreciate the individual fruits, and you definitely can’t pick out rare flavors.
The NIAID team was interested in a very particular fruit—one that could block transmission of malaria parasites. Malaria develops after a mosquito carrying the parasite called Plasmodium falciparum bites a person. The antibody that interested the NIAID team is capable of recognizing and neutralizing Plasmodium inside of the mosquitoes. That way, once a person is vaccinated, they would produce the transmission-blocking antibody, and any mosquito that feeds on them would take it in, killing the parasite without harming the mosquito.
“By understanding the immune system of patients that have effectively fought the pathogen, we can pinpoint the exact identity of cells that effectively eliminate the SARS-CoV-2 virus out of millions of possibilities”Dr. Jian Han, founder and CEO of iRepertoire
To understand how the transmission-blocking vaccine might work, the NIAID team needed to identify B cells that recognize the parasite, using samples from malaria vaccine recipients. To do this, they used a Plasmodium protein as bait, the same protein that was used in the vaccine. By pulling out B cells that interact with the Plasmodium protein, the researchers essentially shrank the size of the haystack. At this point, traditional approaches would have required the NIAID team to either sequence the pathogen-recognizing B cells in bulk —the smoothie approach— or grow up individual B cells in cell culture—a lengthy and technically challenging task.
What’s more, each antibody is composed of a “heavy chain” and a “light chain.” These two interconnected parts combine to very specifically interact with pathogens, like two sides of a mold fitted to an asymmetrical object. In bulk immune sequencing, all of the heavy and light chains from a population of B cells are sequenced in one blended batch. That means that all the information about which heavy and light chains go together is lost, effectively producing a collection of half molds with no way to tell which ones go together without a lengthy process of trial and error.
To shortcut the process, the NIAID team collaborated with iRepertoire to sequence each B cell individually. What they found was striking. “For the first time, we saw the same B cell multiple times on a single plate,” said Dr. Byrne Steele, one of the iRepertoire scientists who helped develop the technology. That means that out of just 96 cells analyzed at one time, the same cell kept appearing— a very strong sign that the cell was doing something important.
The NIAID team led by the principal investigator Dr. Patrick E. Duffy and the postdoctoral fellow Dr. Camila H. Coelho went on to demonstrate that the dominant B cell was producing an antibody that was capable of neutralizing multiple life stages of the Plasmodium parasite inside of the mosquito. This is the first time anyone has identified a human antibody against a parasite that initiates transmission in mosquitoes.
The implications of the findings go well beyond malaria. “This work demonstrated that we can capture incredibly rare cell types using this technology,” said Dr. Byrne-Steele. Long before the malaria study results were ready for publication, iRepertoire mobilized to apply a similar approach to COVID-19.
Within just two days of receiving their first COVID-19-positive sample, scientists at iRepertoire identified B cell populations that were expanding in response to the SARS-CoV-2 virus. They’re now in the process of determining whether or not the antibodies produced by these B cells are capable of neutralizing the virus.