Research

The Bottini laboratory at UCSD studies intracellular signaling pathways in cell types involved in human autoimmune connective tissue diseases, with particular emphasis on rheumatoid arthritis and systemic sclerosis. The laboratory studies the mechanism of action of signaling molecules encoded by human disease-predisposing genes and also analyzes signal transduction pathways in pathological specimens from patients.
The goal is to dissect relevant intracellular pathways to design new methods for disease activity monitoring and to identify new treatment strategies.

The laboratory specializes in the study of a family of signaling enzymes called protein tyrosine phosphatases, which regulates phosphorylation of proteins on tyrosine residues.

The laboratory strongly emphasizes translational "bed to bench to bedside" research and collaborations with pharmaceutical companies are routinely sought to accelerate translation of laboratory findings into the clinic.

GENETICS OF AUTOIMMUNE DISEASES
WHY we work in this area
Autoimmune diseases are caused by a complex of combination of genetic and environmental factors. For example, genetic studies in the past 15 years have identified almost 100 different relevant genes for rheumatoid arthritis (see this recent review 
http://www.ncbi.nlm.nih.gov/pubmed/24276088). A major problem is that the mechanism of action of most of these genes in human autoimmunity is currently unknown. Understanding the effect of disease-associated genetic variations on gene function is important because it might pave the way to targeting these genes or other components of the pathways to which the genes belong for novel therapies. In addition, genes are partially responsible for the fact that not all therapies work in all patients. Thus studying the function of such genes will enable development of more efficient personalized therapies that are tailored on the specific mechanism that causes disease in each patient.

WHAT we are doing in this area
Two major autoimmunity genes, PTPN22 and PTPN2 encode for enzymes with tyrosine phosphatase activity. Dr. Bottini reported the initial discovery that a single nucleotide substitution in PTPN22 significantly increases the risk of autoimmunity in human carriers
(http://www.ncbi.nlm.nih.gov/pubmed/15004560). Part of the Bottini laboratory is dedicated to understanding the mechanism of action of PTPN22 in autoimmunity. PTPN22 currently ranks as the second most important gene in rheumatoid arthritis, and the third in type 1 diabetes. It also increases the risk of other connective tissues diseases including systemic lupus erythematosus and systemic sclerosis. The laboratory uses a range of approaches from manipulation of PTPN22 expression in human cell lines and cells from human subjects, to modeling of the gene function in mice affected by autoimmune disease.

HOW we support our work in this area

Work on the genetics of autoimmune diseases in the laboratory has been supported by the NIAID, the Rheumatology Research Foundation and the JDRF.

EXAMPLES of PUBLICATIONS from our laboratory in this area

http://www.annualreviews.org/doi/abs/10.1146/annurev-immunol-032713-120249 A recent review on the immunology of PTPN22 in autoimmunity.

http://www.ncbi.nlm.nih.gov/pubmed/23871208 In collaboration with Drs. Erik Peterson at University of Minnesota and Klaus Ley at the La Jolla Institute for Allergy and Immunology, the Bottini laboratory discovered that PTPN22 –which was believed to operate mainly if not exclusively at the level of B and T cells- also plays an important role in signaling in myeloid cells.

http://www.ncbi.nlm.nih.gov/pubmed/20538612 Biochemical work on PTPN22 showed that the phosphatase can be regulated by phosphorylation in a portion of the molecule that affects the activity of the enzyme. The common and autoimmune predisposing variants of the phosphatase are differentially regulated.

http://www.ncbi.nlm.nih.gov/pubmed/18981062 The Bottini laboratory discovered a second mutation in PTPN22, which leads to reduced function and protects humans from systemic lupus erythematosus and rheumatoid arthritis.

http://www.ncbi.nlm.nih.gov/pubmed/16273109 Biochemical work in cell lines and cells from human carriers of the autoimmune-predisposing mutation shows that the common and autoimmune predisposing variants of the phosphatase differentially regulate intracellular signaling in T cells.

KEY COLLABORATORS OUTSIDE UCSD
Michel Tremblay, PhD, McGill University, Montreal, Canada
Tony Tiganis, PhD, Monash University, Victoria, Australia

RHEUMATOID ARTHRITIS

WHY we work in this area

Rheumatoid arthritis (RA) is a common rheumatologic disease where the immune system mistakenly attacks joint tissues causing inflammation (arthritis). If the inflammation is not controlled, with time it leads to damage of the cartilage and bone, resulting in deformities of the joints, chronic pain and functional limitation. Immunological research in the past 15 years has led to the development of several medications able to suppress the hyperactivation of the immune system (so called immunosuppressants), which are now available for patients affected by RA. Although immunosuppressants are in general very effective, a consistent proportion of patients (up to 1/3) do not experience a complete remission of their symptoms, despite trying several of these medications. We cannot combine two immunosuppressant medications to improve control of inflammation because higher suppression of the immune system would increase the risk of infections to unacceptable levels. Therefore our goal is to explore other therapies that can be used in combination with immunosuppressants in hope to benefit patients who do not respond well to immunosuppressants alone.

WHAT we are doing in this area

We turned our attention to a cell type that is present locally in the joint lining, called the synoviocyte. The synoviocyte is sensitive to the activation of cells of the immune system in the joints and in rheumatoid arthritis plays a disease-promoting role by boosting inflammation, directly damaging the cartilage, and indirectly stimulating the cells that damage the bone. Inhibition of synoviocyte activity is believed to result in decreased inflammation and joint damage but it does not result in general suppression of the immune system. Thus anti-synoviocyte therapies could be combined with currently available immunosuppressive therapies to improve control of disease activity in subjects who do not respond well to the immunosuppressant alone. We study biochemical signaling pathways inside synoviocytes trying to identify pathways that are abnormal in RA and/or can be targeted to reduce the activation of synoviocytes in RA. We found that synoviocytes express several molecules with tyrosine phosphatase activity and we are now focused on studying these molecules and assessing whether they can be targeted for therapies of RA.

HOW we support our work in this area

The work on synoviocytes in the Bottini laboratory has been supported by a grant from the NIAMS, a grant from the Department of Defense, a grant from the Harrington Discovery Institute, and contracts from industry.

EXAMPLES of PUBLICATIONS from our laboratory in this area

https://www.ncbi.nlm.nih.gov/pubmed/27275015 We describe how abnormal epigenetic regulation of the PTPN11 gene –encoding the tyrosine phosphatase SHP-2- promotes aggressive FLS behavior in RA, and demonstrate that targeting SHP-2 or the SHP-2 pathway could be a therapeutic strategy for RA.

https://www.ncbi.nlm.nih.gov/pubmed/26414708 We found that through regulation of Src and FAK phosphorylation, the receptor tyrosine phosphatase RPTPα mediates proinflammatory and proinvasive signaling in RA FLS, and that this phosphatase promotes disease in an FLS-dependent model of RA.

https://www.ncbi.nlm.nih.gov/pubmed/25378349 Here we report that through regulation of SRC phosphorylation, the receptor tyrosine phosphatase RPTPκ promotes the pathogenic action of RA FLS, mediating cross-activation of growth factor and inflammatory cytokine signaling by TGFβ in RA FLS.

https://www.ncbi.nlm.nih.gov/pubmed/25995222 In this publication, we demonstrate that in FLS, the receptor tyrosine phosphatase RPTPσ is regulated by components of the extracellular matrix. We also show that this process -called the “proteoglycan switch”- can be targeted for RA therapy.

http://www.ncbi.nlm.nih.gov/pubmed/23335101 Our first survey of tyrosine phosphatase expression in synoviocytes from RA patients led to the identification of a phosphatase that could be targeted for reducing the aggressiveness of these cells in RA.

http://www.ncbi.nlm.nih.gov/pubmed/23147896 A recent review that summarizes the features of synoviocytes and why they are important in RA.

KEY COLLABORATORS OUTSIDE UCSD
Costantino Pitzalis, MD, William Harvey Research Institute, London, UK

SYSTEMIC SCLEROSIS

WHY we work in this area

Systemic sclerosis (SSc) is an autoimmune disease that leads to scarring of the skin and internal organs, resulting in significant limitations in quality of life and often reduced life expectancy in patients. SSc is an orphan disease, and a major problem is that -with the possible exception of heavy immunosuppression- no medication so far has been able to arrest the progression of skin or internal organ scarring. Although the disease is caused by immune system hyperactivation, progression of disease is associated with dysfunction of small blood vessels which ultimately triggers activation of local cells in the skin or internal organs –called fibroblasts. Fibroblasts are normally responsible for wound healing however in systemic sclerosis they become abnormally hyperactive and produce increased amounts of tissue matrix which leads to inappropriate scarring. Most patients are diagnosed at a stage of disease when activation of fibroblasts is prominent and there are scarred (called “fibrotic”) areas of the skin. In that stage steroids and conventional immunosuppression or approaches targeted to the blood vessels are ineffective at slowing down the scarring. Thus several groups have turned their attention to the fibroblast as the key cell whose anomalies need to be normalized by pharmacological intervention if we want to modify disease course in SSc.

WHAT we are doing in this area

We study biochemical signaling pathways inside skin fibroblasts trying to identify pathways that are abnormal in SSc and/or can be targeted to reduce the abnormal tendency of SSc fibroblast that causes scarring. In preliminary experiments we found that synoviocytes express several molecules with tyrosine phosphatase activity and we are now focused on studying these molecules and assessing whether they can be targeted for therapies of SSc. The laboratory recently recruited a new group of patients with SSc and healthy control subjects and study their skin fibroblasts. 

HOW we support our work in this area

The work on dermal fibroblasts in the Bottini laboratory has been supported by a grant from the NIAMS and contracts from industry.

KEY COLLABORATORS OUTSIDE UCSD

Sergio Jimenez, MD, Thomas Jefferson University, Philadephia, PA
Shervin Assassi, MD, University of Texas at Houston, Houston, TX
Francesco Boin, MD, University of California San Francisco, San Francisco, CA
Zhong-Yin Zhang, PhD, Indiana University, Indianapolis, IN