The Tana Lab researches health equity in autoimmune hepatitis. We follow a diverse cohort of patients and controls and collaborate with other centers internationally. We use biospecimens and novel technologies to improve understanding of mechanisms.

The Wilson Lab's research is focused on infectious and autoimmune diseases of the central nervous system. Our lab applies metagenomic and immune repertoire sequencing techniques as well as phage display autoantibody and viral antibody discovery technologies to enhance our understanding of the causes and immunopathogenesis of multiple sclerosis as well as autoimmune and infectious causes of meningoencephalitis. To fuel these inquiries, we have a large effort to biobank blood and cerebrospinal fluid samples from over 1,000 patients with a variety of neuroinflammatory diseases.

The McManus lab studies fundamental processes relating to the regulation of gene expression. We take high-throughput approaches, analyzing hundreds of thousands to millions of experiments at once, using unique and complex libraries coupled to deep sequencing. Our systems span from cell culture to in vivo models, focusing on a broad array of disease relevant tissues. From cancer to diabetes, we develop novel technologies to help us better understand how genes are regulated and how they function in cells. We aim to uncover the dark matter of the genome, to help unravel the beautiful genomic complexity of pathways and how genes interact in development and disease.

The Kattah Lab studies how various genes and diverse cell types lead to Inflammatory Bowel Disease (IBD). We have a particular interest in the role of intestinal epithelial cells in IBD. We are using a variety of techniques including multiplex single-cell RNA sequencing, flow cytometry, and culture of intestinal organoids to study patient samples and mouse models of disease.

The Waterfield Lab���������s main focus is to understand the basic mechanisms by which immune tolerance is broken. Specifically, the lab is interested in studying the role of epigenetics in the development of autoimmunity. In order to study the role of epigenetics in the development of autoimmunity, the lab utilizes a variety of novel conditional knockout mouse lines to study the effect of deletion of specific epigenetic prote

The Matloubian Lab's interests broadly lie in mechanisms of immune mediated diseases and approaches for a better understanding of the molecular bases of such processes. Our goal is to provide therapeutic treatment of autoimmune and inflammatory diseases through a better understanding of the involved pathways.

The Rosenblum Lab's central focus is to understand how the immune system is regulated or controlled in peripheral tissues and how this knowledge can be exploited for therapeutic benefit. To this end, we currently have two areas of active investigation: 1) Understanding how regulatory T cells (Tregs) control immune responses outside of lymphoid organs and 2) Understanding the 'alternative' functions of Tregs in peripheral tissues. Because of its complex immunological properties, its accessibility, and potential for clinical translation, the skin is the model peripheral tissue that we primarily focus on. Approximately 50% of our research employs a reductionist approach, utilizing transgenic animal models to ask fundamental questions of how the immune system functions in skin (and other peripheral tissues) at both the cellular and molecular levels. The other half of our work focuses on doing functional immunology with human tissue, human blood and humanized mice.

The Ott Lab is interested in how viruses interact with the host cell. Through these interactions we hope to gain new insight into cellular processes and the viral life cycle. Currently, we focus on three pathogens-the human immunodeficiency virus (HIV-1), Zika virus, and the hepatitis C virus (HCV)-and three cellular processes-lipid droplets, transcriptional elongation, and immune reprogramming. We recently developed several human 3D organoid models in the lab and study how viruses spread in these models using single-cell RNA-Seq. Our research is relevant for efforts to eradicate HIV from patients, to alleviate fatty liver disease in chronic HCV infection, and suppress uncontrolled immune activation in virally infected patients or patients with autoimmunity.

Dr. Kotas's interest is in the mechanisms by which structural cells such as epithelial cells and immune cells communicate to enable effective barrier defense and promote proper functioning of the airway. The focus of her work is on type 2 inflammation, but her overarching interest is in common inflammatory mediators and converging pathways that facilitate homeostasis or produce airway inflammation during various environmental challenges. For example: Can humans define shared inflammatory signals that induce airway mucus overproduction in COPD and asthma? What immune cues can promote barrier integrity in response to both bacteria and allergens? How do tissue parenchymal cells remember and adapt to prior insult? According to Dr. Kotas, answering these questions could enable our understanding of fundamental principles of airway biology and facilitate development of therapies to target common pathological mediators in common airway inflammatory diseases. The Kotas Lab performs basic mechanistic experiments in organoid or air-liquid interface cultures; physiologic measurements, flow cytometry and confocal microscopy in mouse models; and transcriptional profiling of human airway epithelial samples from patients with inflammatory airway diseases such as nasal polyps or asthma. They currently have three major foci of investigation: (1) They are studying how innate memory of type 2 inflammation is encoded through cooperation of innate lymphocytes and tissue parenchymal cells.(2) They are examining how tuft cells adjust type 2 tone in the airway and influence physiologic and inflammatory responses to allergens. (3) They are investigating how prostaglandin E2 promotes mucous metaplasia in the airway epithelium in response to inflammatory injury. Dr. Kotas strongly believes in team science, to the extent that all of these current areas of investigation involve collaboration with other investigators at UCSF. She also has a strong interest in expanding the current ImmunoX pipeline for obtaining human airway biospecimens and leveraging the ImmunoX CoProjects and CoLabs to analyze these using multi-omics approaches.

The Spitzer Lab is working to develop our understanding of how the immune system coordinates its responses across the organism with an emphasis on tumor immunology. We combine methods in experimental immunology and cancer biology with computation to understand the modes in which the immune system can respond to tumors and to rationally initiate curative immune responses against cancer.

The Fassett Lab's research program focuses upon understanding the tissue-centric and systemic neuroimmune biology of IL-31 in inflammatory skin diseases. IL-31 is expressed in a tiny number of immune cells, yet therapeutic blocking of its receptor results in impressive reduction in disease metrics in at least two chronic inflammatory skin conditions: atopic dermatitis and prurigo nodularis. Together, these findings suggest IL-31 is a tightly-regulated, highly-potent protein. Therefore, our current research goals are: A) to elucidate the gene regulation of IL-31; B) to rigorously characterize the rare IL-31-producing lymphocyte and non-lymphocyte populations in chronic skin inflammation; and C) to define disease-relevant contributions of IL-31-producing cells and IL-31-responsive cells in skin and other barrier organs.

Dr. Wabl���������s research focus has been the generation of antibody diversity and the basis of autoimmunity. Specifically, the use of antibodies in tuberculosis therapy has been the main focus as of late. The challenge of antibody therapy exceeds the capacity of one person or a small academic lab, but can be explored in a larger setting. View Dr. Wabl�

The Krummel Lab focusses on understanding patterns of immune cell-cell interactions and how these generate ���������the immune system���������. Our studies of the immune synapse have shown how T cells regulate their motility, how they signal through synapses while moving, how they communicate with each other during arrest, and how they ���������search��������� a new tissue. These are all fundamental findings and provide a lens through which we understand T cell function. Over the past four years, we have developed novel methods and computational platforms to understand immunological processes in space and in time within normal and diseased organs. We were the first to live-image events in progressive tumors in which incoming tumor-specific T cells are captured by a population of myeloid cells. I am tremendously excited that we have begun to develop a pipeline of next-generation protein immuno-therapeutics using imaging to �����te, observation of the immune system in the homeostatic, infected/injured, allergic or metastatic lung. As with primary tumors, this latter focus has allowed us to dismiss many hypothetical immune scenarios and intensely study those that define the biology in situ. These studies define how the immune system is organizing over space and time and guides novel therapeutic solutions.