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Overview

There are more than 80 autoimmune diseases. These diseases occur when a person’s immune cells mistakenly attack the body’s own tissues. In most cases, the exact origins of these diseases are a mystery; they appear to be triggered by some combination of genetics, environment or even infection. Adding to the puzzle, women are more susceptible to most autoimmune diseases than men.

Autoimmune diseases often feature attacks against certain tissues such as type 1 diabetes (pancreas), multiple sclerosis (brain), atopic dermatitis (skin),  inflammatory bowel disease (intestine), and rheumatoid arthritis (joints).  Others such as lupus have many targets and are considered systemic.

Though there are therapies to lessen many autoimmune disease symptoms, it has been difficult to develop any true cures.

Our Approach

Scientists at La Jolla Institute are investigating what causes immune cells to turn on the body—and how we can intervene.

LJI Professor Hilde Cheroutre, Ph.D., is studying how autoreactive T cells mistakenly learn to recognize “self” in an organ called the thymus. These “educated” autoreactive T cells can actually help the body by regulating immune responses to cancer cells or infected cells. But under the wrong circumstances, a naïve T cell may encounter a self-antigen and spark an autoimmune response. Dr. Cheroutre and her team are working with doctors at Rady Children’s Hospital-San Diego to better understand how this process goes wrong. The team hopes to be able to identify the signs that an infant might be susceptible to autoimmune diseases and perhaps even prevent autoimmunity altogether.

LJI Professor Pandurangan Vijayanand, M.D. Ph.D., is studying genomic data from patients to see which commonly found genetic variants are more prevalent in people with different autoimmune diseases. Dr. Vijayanand and his LJI colleagues have built a database called DICE (Database of Immune Cell Expression, Expression of quantitative trait loci, and Epigenomics), which scientists can use to study the effects of different genetic variants in different immune cells. In 2018, the team published data from 91 healthy donors showing profiles of genetic activity for the 15 most abundant types of immune cells found in human blood. Because autoimmune diseases usually arise from combinations of variants in many different genes, some of which are common and also found in individuals without autoimmune disease, the database gives scientists a guide for comparing variants more often associated with health compared to disease-associated variants.

LJI Associate Professor Sonia Sharma, Ph.D., is studying inflammatory and autoimmune diseases that affect the vascular endothelium, the cells lining the blood vessels. Her laboratory integrates cutting-edge genetics, biochemistry, cell biology, computational and translational approaches to define the key genetic mechanisms regulating cellular innate immunity—and determine how these factors can trigger autoimmune disease. Dr. Sharma was also instrumental in establishing the Institute’s Functional Genomics Center, which she directs.

LJI Professor Michael Croft, Ph.D., studies molecules involved in causing atopic dermatitis, severe asthma and fibrotic diseases caused by chronic inflammation. He has partnered successfully with several companies and his work has led to clinical trials for asthma and atopic dermatitis. 

LJI Professor Matthias von Herrath, M.D., has participated in the Network of Pancreatic Organ Donors to track the immune system in the pancreas of patients with type I and type II diabetes. He is committed to clinical translation of immune-based interventions in autoimmune diseases, with a focus on type 1 diabetes. His experimental research can guide early phase I/II clinical trials and move promising therapies toward phase 3 trials and drug approval. His work spans from fundamental studies to clinical trials, facilitated through his affiliation with NovoNordisk. 

LJI Professor Mitchell Kronenberg, Ph.D., is investigating how surface molecules and intracellular signaling pathways regulate immune cells that reside in the intestine.  These immune cells have a unique challenge because they must co-exist with a highly diverse microbiome. He studies how these cells maintain this peaceful co-existence while responding to pathogens. The loss of tolerance of good bacteria is a key step involved in the pathogenesis of inflammatory bowel diseases (IBD), such as Crohn’s disease and ulcerative colitis.

The lab of LJI Professor Alessandro Sette, Dr. Biol. Sci., is investigating autoimmune diseases from two angles. First, the team is looking at the possible role of autoreactive T cells in causing Parkinson’s disease. Dr. Sette has found that T cells can target misfolded clumps of alpha-synuclein protein in the brain, potentially triggering damage to vulnerable brain cells very early in the disease onset. This research could make it possible to someday detect Parkinson’s disease before the onset of debilitating motor symptoms—and potentially intervene with therapies to slow the disease progression.

Dr. Sette has also teamed up with LJI Professor Bjoern Peters, Ph.D., to build the Immune Epitope Database (IEDB), a publicly available online resource that includes data from researchers around the world. The IEDB is a valuable tool for studying the chemical aspects of what immune cells recognize when they make an immune response, including when they mistakenly target a person’s own organs in different autoimmune diseases.

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Office on Women’s Health

Research Projects

Croft
T Cells

T cells are central to almost all immune responses. The CD4 subset is capable of directing B cell responses and

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Cheroutre
The Contribution of Central and/or Peripheral Tolerance in Celiac Disease

Celiac Disease (CD) is an autoimmune-like inflammatory disease induced by aberrant immune responses initiated by MHC class II restricted CD4

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Cheroutre
Mucosal CD4- CD8- T Cells

One large subgroup of specialized T cells is encompassed by the intraepithelial T cells which are located in the epithelium

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Cheroutre
Role of Pre-TCR Signaling in Central Tolerance and Autoimmunity?

Autoimmunity is a self-destructive disease condition mediated mainly by pathogenic selfreactive αβ T cell receptor (TCR) expressing T lymphocytes. Self-tolerance

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Cheroutre
CD4+ Cytotoxic Lymphocytes

MHC class-II restricted CD4+ T cytotoxic cells (CD4 CTL) are among the best examples of extreme measures the immune system

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Cheroutre
T Cell Function

We are now trying to elucidate the regulatory functions displayed by the self-specific agonist selected T cells and their role

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More research projects

Related News

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Labs

Jul 8, 2020
Sharma Lab

Sonia Sharma, Ph.D., and her lab members lead unbiased, genome-scale approaches to unravel innate immunity, the body’s early immune response to microbial pathogens and neoplastic cells.

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Sonia Sharma, Ph.D.
Associate Professor
Center for Autoimmunity and Inflammation, Center for Cancer Immunotherapy
Jul 8, 2020
Rao Lab

Anjana Rao, Ph.D., focuses on understanding how signaling pathways control gene expression, using T cells and other cells of the immune system as models.

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Anjana Rao, Ph.D.
Professor
Center for Autoimmunity and Inflammation, Center for Cancer Immunotherapy
Jul 8, 2020
Ley Lab

Klaus Ley, M.D., and his team study inflammation in health and disease. The lab is focused on mechanisms by which immune cells reach sites of inflammation, as well as investigating atherosclerosis.

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Klaus Ley, M.D.
Professor
Center for Autoimmunity and Inflammation
Jul 8, 2020
Kronenberg Lab

Mitchell Kronenberg, Ph.D., and his team study T cells – white blood cells responsible for recognizing and responding to foreign invaders, such as microbes.

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Mitchell Kronenberg, Ph.D.
President & Chief Scientific Officer
Center for Autoimmunity and Inflammation, Center for Infectious Disease and Vaccine Research
Jul 8, 2020
Kawakami Lab

Toshiaki Kawakami, M.D., Ph.D., and his team study allergic diseases such as asthma, allergic rhinitis, food allergy, and atopic dermatitis.

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Toshiaki Kawakami, M.D., Ph.D.
Professor
Center for Autoimmunity and Inflammation
Jul 8, 2020
Hogan Lab

Patrick Hogan, Ph.D., studies cells at the nano level – seeking to understand how protein-protein interactions on the submicroscopic scale can have gargantuan impacts on human health and disease.

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Patrick Hogan, Ph.D.
Professor
Center for Autoimmunity and Inflammation, Center for Cancer Immunotherapy
Jul 8, 2020
Hedrick Lab

Catherine "Lynn" Hedrick, Ph.D., and her lab members study and target monocytes to aid in the prevention of cancer. The lab also investigates neutrophil heterogeneity in cancer and cardiovascular disease.

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Catherine Hedrick, Ph.D.
Professor
Center for Autoimmunity and Inflammation, Center for Cancer Immunotherapy
Jul 8, 2020
Croft Lab

Michael Croft, Ph.D., and his team focus on a number of molecules that are members of the tumor necrosis factor (TNF) and tumor necrosis factor receptor (TNFR) family.

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Michael Croft, Ph.D.
Director, Scientific Affairs
Professor, Center for Autoimmunity and Inflammation
Jul 8, 2020
Cheroutre Lab

Hilde Cheroutre, Ph.D., and her team study the development, function, and regulation of T lymphocytes, a type of white blood cells.

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Hilde Cheroutre, Ph.D.
Professor
Center for Autoimmunity and Inflammation, Center for Cancer Immunotherapy
Jul 7, 2020
Altman Lab

Amnon Altman, Ph.D., and his team study T lymphocytes—white blood cells formed in the thymus that are essential in the body’s fight against infection and disease.

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Amnon Altman, Ph.D.
Professor
Center for Cancer Immunotherapy
Jul 2, 2020
Sette Lab

Alessandro Sette, Dr. Biol. Sci., defines in chemical terms the specific structures (epitopes) that the immune system recognizes and uses this knowledge to measure and understand immune responses.

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Alessandro Sette, Dr.Biol.Sci.
Professor
Center for Autoimmunity and Inflammation, Center for Infectious Disease and Vaccine Research