Disease-Specific Research Programs

The UCSF Division of Rheumatology supports a variety of disease-specific research programs across rheumatic diseases and disciplines.

Ankylosing Spondylitis

Dr. Lianne Gensler is the Ankylosing Spondylitis (AS) Clinic Director and performs research in AS and related fields. Currently, she is enrolling patients in 2 observational studies to better understand outcomes in patients with AS. One of these is in collaboration with other investigators to better understand the genetic contributions towards the disease. She is also studying a survey tool to identify patients with AS early, with the hope of reducing the current delay to diagnosis of 5-10 years.

Rheumatoid Arthritis (RA)

Dr. Jonathan Graf is the Director of the Rheumatoid Arthritis (RA) Clinic at San Francisco General Hospital and co-director of the UCSF RA cohort. Dr. Graf’s research interests relate broadly to immune mechanisms in rheumatic disease, spanning from basic laboratory research to studies in humans with RA and other rheumatic disorders. Currently, his research focuses on clinical and translational studies of RA, including studies that look at novel therapeutics, biomarkers, and cardiovascular risk in patients with RA. He is the site lead for the Treatments Against RA and Effect on FDG-PET/CT (The TARGET Trial), a randomized controlled trial comparing effects on vascular imaging with FDG PET/CT between two active comparator treatment arms for rheumatoid arthritis (RA) who are methotrexate inadequate responders and the Strategy to Prevent the Onset of Clinically-Apparent Rheumatoid Arthritis (STOP RA Trial), a randomized double blinded placebo controlled trial of hydroxychloroquine (HCQ) to prevent the onset of rheumatoid arthritis (RA) in asymptomatic patients who are anti-CCP positive.

Drs. Art Weiss, Julie Zikherman, Judy Ashouri, and Renuka Nayak are coordinating a broader basic and translational research program focused on understanding basic pathogenic mechanisms in Rheumatoid Arthritis (see Basic and Translational Science section).

Rheumatic immune-related adverse events (irAE)

Along with the incredible advances in cancer treatment brought about by the advent of so-called ‘checkpoint blockade’ drugs that block PD-1 and CTLA-4 signaling on T cells come a host of unwanted autoimmune manifestations termed immune-related adverse events (irAE). Drs. Mary Nakamura and Mehrdad Matloubian have developed a clinic at Parnassus that specializes in diagnosis and treatment of rheumatic irAE, especially arthritis, that can be either self-limited or chronic. In parallel, they have generated a growing cohort of patients and collaborate with other investigators within and beyond our division to understand the pathogenesis of these disorders. Drs. Judy Ashouri and Lin Shen collaborate to pursue translational studies capitalizing on patient samples.


In collaboration with subspecialists across divisions and departments (including Drs. Laura Koth, Nicholas Arger, and Eric Seeley in pulmonary, Dr. Gelfand in neurology, Dr. Gonzalez in ophthalmology, Drs. Vasanth Vedantham and David Rosenthal in cardiac electrophysiology, the UCSF advanced heart failure clinic), Dr. Zikherman helps care for patients with cardiac sarcoidosis. She also participates in studies of this patient population that seek to define response to steroid-sparing therapy and is involved in efforts to establish a formal cardiac sarcoidosis cohort at UCSF for purposes of both clinical and translational research to advance the diagnosis and treatment of this disorder.

Rheumatology fellow Dr. Julie Fiore is interested in defining basic molecular mechanisms that underpin abnormal monocyte biology in sarcoidosis and other granulomatous diseases and has initiated translational studies to do so under the mentorship of Dr. Joel Ernst in the Division of Experimental Medicine at ZSFGH.


The UCSF Scleroderma Cohort Study is a collaborative effort between leading experts in the departments of Rheumatology (Drs. Andrew Gross and Sarah French), Dermatology (Drs. Haemel and Connolly), and Pulmonology (Drs. Wolters and Golden). The purpose of this study is to develop a prospective cohort of patients with autoimmune cutaneous and rheumatic diseases in order to assess changes in clinical manifestations, disease activity, disease damage, quality of life, and disability over time. With this information, we plan to better understand the pathophysiology of rheumatic diseases and evaluate the effects of current therapies in hopes to one day, develop even better treatments to help patients.

Sjögren’s Syndrome

Dr. Lindsey Criswell contributes to research efforts in Sjögren’s Syndrome through her participation in the NIH-funded Sjögren’s International Collaboration Clinical Alliance (SICCA). In addition to extensive clinical information, a bank of salivary gland tissue, blood and other biospecimens have been obtained from over 3,000 participants and are made available to worldwide investigators. These studies have led to the development of new classification criteria for Sjögren’s Syndrome.

Systemic Lupus Erythematosus (SLE)

Dr. Maria Dall’Era is the Director of the UCSF Lupus Clinic, which cares for over 200 patients with systemic lupus erythematosus from all over Northern California. This work has culminated in the demonstration of effective new approaches to induce and maintain remission in people with life-threatening kidney disease due to SLE. This work is based in large part on pioneering basic research conducted at the Rosalind Russell Center at UCSF by Drs. David Wofsy and David Daikh. Currently, her research focuses on the design and conduct of clinical trials in order to develop safer and more effective medications for the treatment of lupus. Her work also looks at the symptoms, clinical course, treatments, and outcomes of lupus patients in a prospective registry.

Dr. Lindsey Criswell’s lupus research focuses on identifying the genes that contribute to the risk and severity of the disease. Through this work, Dr. Criswell and her collaborators have helped to define biologic pathways that contribute to the development of SLE. Ultimately, this work will inform the development of new treatments and provide better diagnostic and prognostic tools. Drs. Sharon Chung and Cristina Lanata collaborate extensively with Dr. Criswell to use genetic, epigenetic, and transcriptional methods to understand SLE clinical manifestations and disease heterogeneity.

A key focus of Jinoos Yazdany's lupus research program has been examining the quality of health care delivered to patients with lupus. In 2009, with lupus experts from around the United States, she spearheaded the development of the first quality measure set for lupus. Subsequently, she has gone on to apply these measures to understand health care quality for patients with lupus. Her work has highlighted gaps in care for the condition, disparities in quality for vulnerable populations such as the uninsured, and also identified preventable medication errors.

Dr. Jimmie Ye’s lab develops novel computational and genomics tools to characterize gene expression and studies the genetic basis for its effects on disease susceptibility. He has recently utilized multiplexed single droplet RNA sequencing to characterized gene expression in single cells of patients with systemic lupus erythematosus. He is Director of the P30 PREMIER Genomics and Molecular Resources Core, and in that role collaborates with a large number of  faculty  performing  autoimmunity  research  at  UCSF.

Vasculitis (Giant Cell Arteritis, Polyarteritis Nodosa, Granulomatosis with polyangiitis)

Dr. Sharon Chung’s research and clinical program focuses on the study of vasculitis, a group of life-threatening diseases caused by inflammation of the blood vessels. As the director of the UCSF Vasculitis Clinic, she works with other UCSF specialists to provide expert care in diagnosing and treating these rare and intensively complex diseases. Dr. Chung also leads state-of-the-art genetic and epigenetic research studies, and collaborates with national and international research networks, to help identify the biologic mechanisms that lead to vasculitis in order to develop less toxic treatments and more informative diagnostic tests.