Inflammation

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Inflammation

Investigating chronic immune dysfunction

Understanding inflammatory immune responses to improve patient lives

Our body’s barrier surfaces – including the intestines, skin, and lungs – have a surface area larger than a pickleball court. These surfaces mediate the interactions between the immune system and billions of harmless microbes, pathogens, foods and other substances. The Inflammation program at the Allen Institute for Immunology seeks to decipher the normal and pathologic mechanisms that govern chronic immune dysfunction at barrier surfaces and to uncover new opportunities to reverse or prevent these debilitating conditions. This collaborative team of basic, clinical, and translational scientists, computational biologists, and computing engineers is using integrated omics tools to study immune responses in the barrier and barrier-related tissues. This is combined with a simultaneous investigation of immune events occurring in peripheral blood to generate a systems-level understanding of inflammatory diseases over time.

This piece of large intestine, biopsied from a pediatric IBD patient, has been processed to reveal cellular and molecular features we can use to understand disease activity. These include epithelial cells (green), muscle (dark blue), T cells (lavender and purple), B cells (yellow), monocytes and macrophages (cyan), and cells that are actively dividing (red).

Project: Advancing research in inflammatory diseases

This team primarily focuses on the gut, where they investigate inflammatory bowel disease (IBD). By studying samples from patients with untreated, treated, and treatment-resistant IBD, alongside conditions where gut disease is prominent, the team aims to reveal new insights into how these diseases develop and progress. Research is geared towards IBD, which includes Crohn’s disease and ulcerative colitis, and does not include irritable bowel syndrome (IBS).

Through collaborations with researchers, clinicians, and pharmaceutical companies, this group is committed to accelerating discoveries that could lead to innovative treatments. Their research brings hope to patients whose lives are deeply affected by these chronic conditions, ultimately aiming to improve outcomes and quality of life. Together, these efforts contribute to a broader mission of understanding and addressing immune dysfunction at the body’s barrier surfaces.

Data heat map from long covid research by the Allen Institute for Immunology — Heatmap data showing heightened inflammatory signatures in patients with long-COVID.

Project: Exploring the lingering effects of viral infections including Long COVID

Post-infectious inflammation, particularly following viral infections, typically resolves within a few weeks. However, for some individuals, inflammation can persist for months, leading to extended periods of symptoms and health complications. Researchers at the Allen Institute are deeply engaged in studying the lingering effects of post-infectious inflammation, with a focus on Cytomegalovirus (CMV) and COVID-19 and their long-term impacts.

In their investigation of long COVID, Allen Institute scientists have been profiling the immune systems of patients who continue to experience symptoms months after infection, as well as those who have fully recovered from mild COVID cases. Their work has uncovered a distinct set of molecules linked to inflammation that is present in only a subset of patients with long COVID. These inflammatory markers were not observed in patients who fully recovered, shedding light on potential pathways that contribute to prolonged symptoms. These insights open new opportunities for understanding the underlying mechanisms of post-infectious inflammation and developing targeted therapies to address long COVID and other similar conditions.