Center for Autoimmunity and Inflammation

Center for Autoimmunity and Inflammation

The newly established Center for Autoimmunity and Inflammation expands La Jolla Institute’s existing autoimmune and inflammatory disease research and enables our experts to take a deep dive into the complexity of the immune system. LJI researchers work to uncover the causes and commonalities among different autoimmune diseases, such as Type I diabetes, lupus, and inflammatory bowel disease, and other inflammatory diseases such as asthma, atopic dermatitis, and Parkinson’s. Our aim is to develop new treatments that teach the immune system to tolerate the body’s own cells and to not develop overt immune responses.


The majority of auto-immune and immune-related diseases are complex diseases, where a combination of genetic and non-genetic factors plays out against the complexity and diversity of the human immune system. What we don’t know is which genetic risk factors and environmental exposures have to come together and how they interact on the molecular level to push the immune system “over the edge” and into the realm of active autoimmune or inflammatory disease.

LJI is one of the few organizations in the world solely dedicated to research on the immune system. As a result, LJI researchers have wide-ranging expertise in the fundamental mechanisms of self-tolerance, as well as many of the autoimmune or inflammatory diseases that result when self-tolerance breaks down or natural mechanisms to limit the immune response do not work effectively. LJI scientists recently unveiled a publicly available immune atlas, which provides a map of how individual genetic variations affect gene expression in human immune cells. It contains a trove of data that is critical for deciphering how natural genetic variation shapes the immune system’s ability to protect our health. This combination of strengths in fundamental immunology, genomics and data analysis, places LJI researchers in a unique position to unravel the complexities or autoimmune and inflammatory disease.


Ferhat Ay, Ph.D.
Chris Benedict, Ph.D.
Hilde Cheroutre, Ph.D.
Michael Croft, Ph.D.
Catherine “Lynn” Hedrick, Ph.D.
Matthias von Herrath, M.D.
Patrick Hogan, Ph.D.
Toshiaki Kawakami, M.D., Ph.D.
Mitchell Kronenberg, Ph.D.
Klaus Ley, M.D.
Anjana Rao, Ph.D.
Alessandro Sette, Dr. Biol.Sci.
Sonia Sharma, Ph.D.
Pandurangan Vijayanand, M.D. Ph.D.

From The Lab

Oct 30, 2020

Klaus Ley receives $2.3 million to study fundamentals of immune cell activation

New research could shed light on how immune cells can better fight cancers or step back in autoimmune disease
Oct 16, 2020

Diabetes researchers spot dangerous T cells in the pancreas—even in healthy people

Sep 24, 2020

A step toward helping patients breathe deeply

LJI scientists track down a protein that may add to lung damage in asthma and related diseases
Sep 15, 2020

LJI scientists receive $3.5 million to investigate role of immune cells in Parkinson's disease

More than 930,000 Americans are living with Parkinson's disease
Aug 26, 2020

Blocking nerve signals to the pancreas halts type 1 diabetes onset in mice

New LJI discovery could help explain patterns of cell death in many autoimmune diseases