Adaptive Biotechnologies: AI can ‘translate’ immune system

By Jenni Spinner

- Last updated on GMT

(Blue Planet Studio/iStock via Getty Images Plus)
(Blue Planet Studio/iStock via Getty Images Plus)

Related tags Immune system Artificial intelligence preclinical Microsoft

The company is putting artificial intelligence to work in the hopes of coming up with more precise, effective tests and therapies for a range of diseases.

Increasingly, life-sciences companies are harnessing the power of advanced computer technology in the pursuit of faster, more effective development of therapies. One such firm is Adaptive Biotechnologies, whose researchers are using various technologies to analyze and translate the human immune system.

Outsourcing-Pharma (OSP) recently spoke with Adaptive Biotechnologies cofounder and chief scientific officer Harlan Robins, to learn how Adaptive uses immunosequencing technology in an effort to move immune-driven medicine forward.

OSP: Please tell us about Adaptive—what you do, how you got started, who your key clientele is, and what sets you apart from competitors.

HR: We believe that the immune system is nature’s most finely tuned diagnostic and therapeutic – it contains all the history about any disease you’ve ever had, as well as information about diseases you have presently.

At Adaptive Biotechnologies, we believe that if we can read and translate the language contained within the cells of our immune system – and see how they detect and fight disease – we can use this information to create more precise and effective diagnostics and therapeutics.

Over the last decade, we’ve built an immune medicine platform that applies high throughput genetic sequencing to the immune system to decode characteristics of immune cells, including how they see and attack disease. After realizing the potential of this technology to be used across a multitude of diseases, I called my brother, Chad, who was working in finance at the time, and we decided to go into business together and create Adaptive Biotechnologies.  

What sets Adaptive apart is the speed, scale and precision by which we can sequence immune cells.

For example, we recently partnered with Amgen to develop potential antibody therapies for COVID-19. The trick to doing that is finding the strongest antibodies within the blood of COVID-19 survivors that can be packaged into a therapeutic to treat others at risk for or currently fighting the virus.

Using our immune medicine platform, we’re able to identify and screen more receptors at a much faster rate than other companies, increasing our chances of finding the “Michael Jordan” of antibodies – called neutralizing antibodies – that can defeat this virus all on their own. It’s like being able to scout every high school basketball player in the US all at the same time to find the “MVP” or “Dream Team” (Michael Jordan, Scotty Pippin and LeBron James) of antibodies.

Once we find the best candidates, we will deliver to Amgen to leverage their world-class manufacturing capabilities and develop a therapeutic.

OSP: How do you harness technology to translate the human immune system?

HR: The immune system is astonishingly brilliant in its ability to precisely detect and treat disease. We are using our immune medicine platform to decode this activity so we can understand every disease a person is fighting or has fought.

By reading the diverse genetic code of a patient’s immune system and understanding exactly how it detects and treats disease, we can use that information to inform more accurate diagnostics and therapeutics.

OSP: How does combining immunosequencing with other advanced technology like AI and ML work?

HR: Two and a half years ago, Adaptive partnered with Microsoft to take on a first-of-its-kind endeavor – to map the trillions of T cell receptors (TCRs) in our immune systems with the millions of disease-causing antigens to create a massive “TCR Antigen Map” showing how the immune system detects and fights disease. Our hope is that one day, through an immune system “x-ray” or new test, we will be able to tell every disease a patient is fighting or has fought.

Every time we detect a new “signal” or a signature immune response to a disease, the map grows. Currently, we are mapping the immune system’s response to COVID-19 and Lyme disease.

OSP: Could you give an example of how a pharma company might use such analysis in creating and developing therapies/vaccines/etc.?

In January 2019, Adaptive announced a partnership with Genentech to develop personalized cellular therapies for cancer patients. Through this partnership, Adaptive is identifying optimal T cell receptors (TCRs) that target each patient’s neoantigens most effectively; Genentech will then take those TCRs and engineer and manufacture a personalized cellular medicine to deliver to each patient.

OSP: Could you please explain how your diagnostic tool interprets patient immune systems, and how it might be used to diagnose or predict diseases?

HR: clonoSEQ is the only FDA-cleared test to monitor minimal residual disease (MRD) in patients with multiple myeloma (MM) and B-cell acute lymphoblastic leukemia (ALL) using DNA from bone marrow samples. MRD refers to the remaining number of cancer cells that are present in a patient’s body during and after treatment, which may eventually lead to recurrence of the disease.

MRD testing is performed as a series of tests throughout a patient’s cancer journey to monitor for remission, detect relapse, determine response to treatment and inform care. Controlled trials have shown that even the smallest amounts of residual disease can significantly predict a patient’s long-term clinical outcomes.

OSP: What’s ahead for your company? Do you have any specific projects you’re working on, or technological areas you’re exploring?

Harlan Robins, cofounder/chief scientific officer, Adaptive Biotechnologies

HR: Since our platform was specifically built to map population-wide immune responses to many diseases, we were able to immediately apply our technology to the race for COVID-19 solutions.

Currently, we are pursuing two separate but synergistic applications of our immune medicine platform to combat COVID-19.

First, we extended our existing partnership with Microsoft to decode the immune system’s response to COVID-19 and potentially develop a more sensitive diagnostic that can detect disease in those who have mild symptoms or are asymptomatic, determine how severe a patient’s symptoms will be, or tell who has been previously infected even if antibodies are not present. We believe having a more accurate picture of a patient’s COVID-19 “status” will go a long way in helping to reopen society.

To develop this novel diagnostic, we recently launched ImmuneRACE, a virtual clinical study that is seeking 1,000 blood samples from those who are actively fighting, have recently recovered from or have been exposed to someone diagnosed with COVID-19. The de-identified data from the study will also be made freely available to academic researchers, public health officials and biopharma industry around the world to help accelerate solutions to the pandemic.

Secondly, we announced a partnership expansion with Amgen to leverage our platform’s drug discovery capabilities to develop potential antibody therapies for COVID-19. As part of this collaboration, Adaptive will screen the blood of recovered COVID-19 patients to identify the strongest antibodies that Amgen can package into a therapeutic to help prevent and treat COVID-19.

We believe our immune medicine platform puts us in a position to uniquely contribute to solving this global crisis.

OSP: What else would you like to add?

HR: Our ImmuneRACE study is still enrolling. If you are currently fighting, have recently recovered or have been exposed to COVID-19, your immune system holds important clues about how to detect and fight this disease; by capturing these important lessons learned, we can potentially develop new diagnostics and therapeutics that leverage the power of our bodies’ natural immune response.

Through our partnership with Microsoft, we’re using our platform and technology to map immune responses to infectious disease, autoimmune disorders and cancer with the goal of developing a diagnostic that could potentially more easily diagnose difficult diseases like Lyme and earlier. Currently serology testing is used to detect Lyme disease, which can lead to false negatives and false positives.

Similar to our work with Microsoft on COVID-19, Adaptive is launching a Lyme study with the goal of developing a diagnostic test based the T cell response to the disease. T cells expand immediately in response to exposure to a pathogen. Measuring this response may allow for accurate detection almost immediately after the tick bite or the first sign of symptoms, and accurate detection in later weeks when the disease has presumably been treated and the presence of expanded Lyme-specific T cells should diminish.

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