|Advances in flow cytometry could enable researchers to uncover valuable insights about food allergies without allergen exposure.Food allergies affect an estimated 220 million people(Opens in a new window) around the world, the World Health Organization reports. In the United States alone, one in 13 children are living with life-threatening food allergies, according to the non-profit organization Food Allergy Research and Education (FARE(Opens in a new window)). A major milestone in this field was reached in 2024 when the U.S. Food and Drug Administration approved the first biologic to treat food allergies after accidental exposures, Xolair (omalizumab). While there are a handful of other food-allergy treatments in the development pipeline, including combinations of monoclonal antibodies and immune-boosting drugs, innovation in this field remains limited.

Replacing dated and harmful methods
One limitation holding back the development of new therapies for food allergies is that many commonly used research tools are outdated and often impractical. Research has been hindered by several factors, most notably the burdensome process of introducing potential allergens to determine a response. When experimental treatments reach clinical trials, the most commonly used method to test efficacy in patients is the Oral Food Challenge (OFC), which involves exposing patients to gradual amounts of foods to determine if they have reactions.

This method is often inconclusive, or worse, it can cause anaphylaxis in some participants. The mere stress of risking potential reactions during an oral food challenge, coupled with the need to travel to a medical facility for the testing, would likely discourage many people from participating in a research trial. Parents would also be unlikely to agree to intentionally expose their children to potential food allergens. One study(Opens in a new window) found that 23% of children undergoing an oral food challenge experienced multiple systemic reactions, and 15% of those cases require epinephrine.

Meanwhile, one of the most promising methods to advance in vitro food-allergy testing is the basophil activation test (BAT), which uses flow cytometry to measure the activation of basophils, a type of white blood cell, in blood samples that are exposed to allergens. The challenge here is that BAT assays are complex, multistep workflows that require expertise and that rely on fresh blood samples which can be difficult to collect, store and transport.

A recent study demonstrated how new technology could solve these problems for researchers investigating new treatments for food allergies. A team led by the Icahn School of Medicine at

Mount Sinai in New York demonstrated how BAT workflows that combine ready-to-use reagents with automation and artificial intelligence can streamline assays. This emerging technology could make it feasible for researchers around the world to carry out food-allergy studies that they couldn’t before because they lacked the proper equipment or expertise. In the future, the same technology could greatly simplify the diagnosis of food allergies in people.

Streamlining flow cytometry workflows
BAT enables researchers to capture many features unique to individual patients from blood draws, including specific anaphylactic pathways in cells that are activated in response to certain foods. To effectively interrogate the function of these cellular pathways, however, labs need flow cytometry expertise and a constant supply of fresh blood samples. The typical workflow for food-allergy research involves at least 10 manual pipetting steps and one or two centrifugation steps. Logistically this is just not feasible for many labs.

For the recent study(Opens in a new window), researchers at 15 clinical sites in the U.S. collected a total of 241 blood samples from children between the ages of 1 and 3. Instead of having to rush the samples into BAT assays, the researchers at the collection sites mixed the blood with dry reagents that were shipped to them in ready-to-use tubes. To enable the measurement of responses to allergens and medicines used to treat allergic diseases, some of the tubes also contained increasing amounts of dried peanut extract or other reagents enabling the realization of negative and positive controls. Despite different compositions, all tubes could be processed following the exact same approach, significantly simplifying experimental protocols.

The new process employed for this study was built for ease, efficiency and accuracy. Because the reagents were dry and prepacked, the clinical collection sites could work with them at room temperature and then send them back to a centralized processing site without having to worry about preserving their freshness. The 10-step-plus pipetting process that would typically be required was reduced to four steps, with no need for centrifugation. Fewer manual steps translate to fewer opportunities for mistakes, while also reducing the risk that variabilities in manual handling might negatively affect the results.

The researchers compared the data they collected from the streamlined BAT workflow to a double-blind placebo-controlled food challenge study involving peanut exposure. They reported that the BAT data accurately predicted outcomes from the food challenge.

Future opportunities
Streamlining BAT testing could open up new avenues of research into novel approaches to treating food allergies. In this study, the 241 patient samples were divided into two groups — one of which was used to train a machine learning algorithm and the other to test it. A similar process could be used to improve the methods by which food allergies are characterized.

Most food allergy specialists agree that no single biomarker is enough to fully elucidate how allergens touch off dangerous reactions in people. Instead, there are likely many different biomarkers at play — and artificial intelligence could be used to derive insights into those biomarkers that could then be used to define new targets for treatments. The beauty of AI is that it simplifies the task of taking biomarkers that have been identified and studied in a vast array of clinical trials and deriving insights from it that could quickly lead to new treatment ideas.

A broader use of BAT testing could also contribute to the replacement of OFC in clinical trials of new therapies. OFC testing can be a logistical hassle, particularly when the patients are children. Exposing children to foods that are known to be problematic raises ethical concerns, and it can be difficult to ascertain how a child feels after exposure and treatment anyway. A streamlined BAT process could offer the ability to measure all of this with simple blood tests instead.

There’s a sustainability advantage, as well. During the Mount Sinai-led study, there was no need to store blood samples in refrigerators or use dry ice to ship them to the central laboratory that processed them, thanks to the dry reagents, which were formulated to remain stable at room temperature. Without the need for cold storage, it’s easy to imagine how food-allergy research could be greatly expanded to include small, remote clinical research centers, as well as sites that may have limited cold-storage capacity.

In the future, it may be possible to apply new BAT techniques for clinical use, easing the process of identifying and diagnosing patients with food allergies.

As flow cytometry technology continues to improve, so will our ability to uncover new insights and therapeutic targets in food allergies — and to bring innovations to market that will enhance the diagnosis and treatment of patients around the world.