ITI Seed Grants 2011

The Stanford Institute for Immunity, Transplantation and Infection (ITI)

Announcing the Recipients of the 2011 ITI Seed Grants and Young Investigator Awards
funded by

  • The Marion Avery Family Seed Grant Endowment for ITI
  • The Arnold and Mabel Beckman Foundation
  • The Dean's office, Stanford School of Medicine
  • Judith & Leslie Denend Seed Grant for ITI
  • ITI General gift fund
  • The Brennan Family


Single-Cell Analysis of Disease-Specific T Cells in Celiac Sprue

PI:  Chaitan Khosla, Professor, Depts of Chemistry & Chemical Engineering
Co-Investigators: Mark Davis, Professor, M&I and Arnold Han, Gastroenterology & Hepatology Fellow

Celiac sprue is a common, lifelong disease caused by the ingestion of wheat gluten and related cereal proteins. Available evidence strongly implicates a role for T cells in this small bowel disorder, but the biology of these disease-specific T cells is poorly understood. We seek to isolate gluten-specific T cells from healthy controls and celiac patients, and to decode how and why a patient’s T cells respond inappropriately to dietary gluten. To do so, we will use a spectrum of state-of-the-art “omic” technologies. Our findings could not only lead to better clinical tools for managing a serious and widespread disorder, but may also provide fundamentally new insights into the immunobiology of the human gut.

Immune System Dynamics in Early Cardiovascular Aging 

  • Joseph C. Wu, MD, PhD, Associate Professor of Medicine (Co-PI)
  • Mark Davis, PhD, Professor of Microbiology and Immunology (Co-PI)
  • Jose Montoya, MD, Associate Prof of Medicine, Div of Infectious Disease
  • Atul J Butte, MD, PhD, Assistant Prof of Pediatrics-Systems Medicine
  • Shai Shen-Orr, PhD, Research Associate of Mark Davis, and Atul Butte
  • Francois Haddad, MD, Clinical Assistant Prof of Medicine (Cardiology)
  • Ingela Schnittger, MD, Professor of Medicine (Cardiology)

Coronary artery disease is the number one cause of morbidity and mortality in the US and western world. There has been a growing body of research supporting a central role of inflammation and immunity in early cardiovascular aging and atherosclerosis. Using an integrative approach of high resolution immune monitoring data, our Cardiovascular Immunity working group has been working on identification of novel immune phenotypes based on cytokine response profiles.  In this pilot study, we first propose to determine whether cytokine non-response profile is associated with early cardiovascular aging. We then propose to determine the relationship between immune response profile and endothelial progenitor cell (EPC) frequency. Finally in an exploratory analysis, we propose to use an integrative approach to identify novel immune profiles associated with early cardiovascular aging and atherosclerosis.

Defining the Primary Immune Response to Epstein Barr Virus in Transplant Recipients

  • Olivia Martinez, Ph.D. Professor, Dept of Surgery and Program in Immunology
  • William Berquist, M.D. Professor Dept of Pediatrics
  • Carlos Esquivel, M.D., Ph.D. Professor, Dept of Surgery, Chief, Division of Transplantation
  • Sheri Krams, Ph.D. Associate Professor, Dept of Surgery and Program in Immunology
  • Holden Maecker, Ph.D. Director, Human Immune Monitoring Center
  • Jose Montoya, M.D. Associate Professor, Dept of Medicine/Infectious Disease

People who receive organ transplants must take life-long medication to prevent rejection of their graft.  However, these drugs have the unfortunate side-effect of increasing susceptibility to serious infections and cancer.  Epstein Barr virus (EBV) is a common virus that more than 90% of us are infected with that rarely causes illness in healthy people.  Nevertheless, in transplant recipients that are taking immunosuppressive medications, EBV can cause potentially fatal cancer.  Children, in particular, are at increased risk for these cancers since they often acquire the virus for the first time as a result of receiving their graft from someone who is already infected with EBV.  Knowing the specific time of infection with EBV in someone who has never been exposed to the virus before allows us the unique opportunity to study how the human immune system responds to a new infection.  In this project we will obtain blood from transplant recipients who are exposed to EBV through liver transplantation and will analyze the blood cells for a variety of immune tests to gain a new understanding of how the immune system fights infection.  We will also study a particular group of transplant patients who, for unknown reasons, maintain high levels of EBV in their circulation.  We believe that studying the immune system of these patients will teach us which patients are at risk for developing EBV-related cancer and which are not.  In summary, we anticipate that these studies will provide us with important new information on how the immune system responds to infection that will not only help us develop better vaccines but could help us prevent cancer in people who receive life-saving organ transplants. 

Transplantation Methods for Intestinal Stem Cells

  • C. Andrew Bonham, MD, Associate Prof of Surgery
  • Calvin Kuo, MD, PhD, Associate Prof of Medicine
  • Sheri Krams, PhD, Associate Professor, Dept of Surgery/Transplant Div
  • Karl Sylvester, MD, FACS, FAAP, Associate Prof of Surgery and Pediatrics

The roughly 8 meters of intestine in the adult human are essential for numerous processes including absorption of food and providing a barrier against infection. Numerous conditions affect the intestine, including inflammatory bowel diseases and cancer, and there are also congenital syndromes and trauma that can result in “short-gut” syndromes resulting in severe deficiencies of physiologic intestinal function and effective intestinal failure. Currently, such intestinal failure is treated using total parenteral nutrition, in which all nutrition is provided intravenously, or intestinal transplantation, which over the last two decades has become an accepted treatment for patients suffering the complications of short bowel syndrome. Outcomes have improved with better immunosuppressive therapy, but rejection remains a significant problem, and represents the leading cause of graft loss.           

The intestine has tremendous regenerative potential, whereby intestinal stem cells (ISC) resident in proliferative crypt regions give rise to progenitors capable of multilineage differentiation.   These ISC can repopulate the epithelium of the entire 8-meter length of the adult human intestine every 5-7 days, helping to maintain the integrity of the mucosal barrier and effecting tissue repair upon injury.
Despite the clear clinical potential of ISCs, it is notable that transplantation of intestinal stem cells is not a current therapeutic option for human disease, much less the successful correction of a disease phenotype by ISC transplantation.  The current proposal addresses this unmet need by attempting the successful transplantation of intestinal stem cells in animal models and to investigate whether current immunosuppressive drugs used in human intestinal transplantation might have untoward effects on intestinal stem cells.

Allogeneic Graft-versus-Lymphoma Effects in Cutaneous T Cell NHL

  • PI: Wen Kai Weng, MD, PhD, Assistant Prof, BMT
  • Co-Investigator: Youn Kim, MD, Dept of Dermatology
  • Co-Investigator:Richard Hoppe, MD, Radiation Oncology
  • Co-Investigator:Christopher Contag, PhD, Dept of Pediatrics, and M&I

Mycosis fungoides and Sezary syndrome is a malignancy of T lymphocytes, accounting for the majority of skin lymphoma in North America. Patients with this kind of skin lymphoma usually suffer from life-long skin symptoms and require therapies frequently throughout their life. When diseases progress, combination of chemotherapy and biological therapies have to be used with mixed results. Though some patients have slow growing disease, those with advanced disease only survive 1-3 years after diagnosis. To this date, there is no cure for this disease. During the last decade, it has been shown that lymphoma cells are sensitive to a variety of therapies using immune system such as allogeneic blood stem cell transplantation using blood stem cells from a donor. In this case, the donor blood stem cells will provide a new immune system in the patient that can eradicate the lymphoma cells (i.e. graft versus lymphoma effects). However, the significant toxicity associated with traditional allogeneic transplantation prohibits its broad application. Recently, we developed a novel way to perform allogeneic transplantation with significantly less toxicity by using a non-myeloablative regimen. We utilize a low dose radiation to the lymph node and an anti-T lymphocyte antibody to prepare patients before infusion of donor blood stem cells. This novel approach has shown great promise by eliminating most of the toxicities but preserving the anti-tumor effect. To provide a new option for these patients with difficult skin lymphoma patients, we propose a clinical trial using this non-toxic way to perform allogeneic transplantation. Our goal is to test the tumor response and long-term disease control with this novel therapeutic approach. We will also study the status of immune system after the transplantation and the migration of immune cells to the tumor sites. Finally, we will apply state-of-art technologies (high throughput sequencing, miniature handheld confocal microscopy) to monitor disease status after transplant.The knowledge generated from this project can provide valuable information on how the immune cells interact with lymphoma cells in the context of allogeneic transplant and to develop new tools to better monitor minimal disease status after definite therapy, which will lead to better decision-making on further intervention.

Telomere Protection in Progenitor Cells and Lymphocytes during Aging and Autoimmune Disease 

  • PI: Cornelia Weyand, MD, PhD, Professor, Division of Rheumatology
  • Co-PI: Gil Chu, MD, PhD, Professor, Depts of Medicine & Biochemistry

To protect the host from infections and malignancies, the immune system is under constant demand to replenish immune cells. With advancing age and under conditions of chronic inflammatory disease, the protective capacity of the immune system dwindles, likely due to impaired regeneration.

Telomeres are the natural ends of chromosomes and function to protect the DNA. They also serve as the cell’s internal clock as cellular growth is associated with the progressive loss of telomeric sequences. We have previously described that immune cells in patients with rheumatoid arthritis (RA) loose telomeres at an accelerated speed and age prematurely. The current project will examine the structure and length of telomeres in immune precursor cells and mature lymphocytes in patients with RA and in healthy individuals that are young, middle-aged or elderly. The ultimate goal is to understand whether the molecular events that lead to telomeric loss in RA are similar as those underlying telomeric shortening during the normal aging process. 

The studies will focus on the shelterin complex, a protein complex that caps telomeres and protects them from erosion and will examine how shelterin proteins interact with enzymes, e.g. telomerase, that can repair and elongate telomeres. Techniques will include quantitative measurements of shelterin proteins during distinct life stages of immune cells and structural analysis of the different telomeric ends on the same chromosome. Better understanding of telomere biology will ultimately help to develop strategies aimed at slowing the aging process of the immune system.

Monitoring B-cell Populations in Sensitized Kidney Transplant Patients

  • PI: Julie M. Yabu, MD, Nephrology
  • Co-Investigator: Holden T. Maecker, PhD, Director, Human Immune Monitoring Center
  • Co-Investigator: Stephen Quake, PhD, Prof Bioengineering and Applied Physics
  • Co-Investigator: Dolly Tyan, PhD, Prof, Pathology

The long-term objective of this research is to improve the health of sensitized patients with end-stage kidney disease by increasing the number of transplants and improving graft survival.  Desensitization strategies that utilize intravenous immunoglobulin (IVIG) and rituximab to decrease HLA antibodies have allowed successful transplantation of highly sensitized patients.  Despite early success, the incidence of antibody-mediated rejection and graft loss remains high in sensitized kidney transplant patients.  Current monitoring of desensitization therapies is hindered by lack of in-depth immune monitoring strategies.  In order to improve outcomes of sensitized kidney transplant recipients, there is a critical need for comprehensive immune monitoring to identify patients at risk for rejection and need for early intervention.  The central hypothesis is that sensitized kidney transplant patients have clonal expansion of plasma and memory B-cells that produce HLA antibodies and HLA antibodies that fix complement predict higher incidence of rejection.  The overall objective of this application is to determine the longitudinal changes in B-cell populations, injurious cytokines, signaling networks, and presence of HLA complement (C1q)-fixing antibodies in sensitized transplant patients.  I plan to test my central hypothesis and accomplish the overall objective of this application by pursuing the following specific aims:  1) Determine the B-cell signature in sensitized patients that predicts HLA antibody production, antibody-mediated rejection, and transplant glomerulopathy; 2) Determine the genomic immune repertoire of B-cells in patients undergoing desensitization to monitor effectiveness of therapy and ability to predict antibody-mediated rejection; and 3) Determine if formation of complement-fixing donor specific antibodies in sensitized patients after kidney transplantation is predictive of graft injury.  Our interdisciplinary team will bring together the expertise of Dr. Stephen Quake (expert in sequencing and microfluidic techniques), Dr. Holden Maecker (Director, Stanford Human Immune Monitoring Core [HIMC]), Dr. Dolly Tyan (developer of C1q assay), and Dr. Julie Yabu (transplant nephrologist).

Engineering and Development of Interleukin-2 Superkines with Improved Therapeutic Utility

  • PI: Chris Garcia, PhD, Professor, Molecular and Cellular Physiology, and Structural Biology
  • Collaborators: Profs Negrin, Steinman, Fathman

Cytokines are secreted growth factors that hold promise for treatment of immune disease, but most of them have limited clinical utility due to a combination of inefficient activation of the desired responder cell types, and/or undesired activation of cells that lead to toxicity. My lab has initiated a program on the immune cytokines to synergize our expertise in structure and protein engineering with the translational immunology strengths of Stanford. For our ITI seed grant, we are tailoring activities of the critical immune cytokine Interleukin-2 towards particular cell subsets to achieve enhanced clinical utility against a range of diseases in Immunity, Transplantation and Infection. We call these designer cytokines “superkines” and we are developing and testing an exciting new molecule we have engineered, a version of Interleukin-2, termed “super-2”, that has over 2-logs higher affinity for one of its receptors, IL-2Rb, than wild type IL-2, and is extremely potent T cells. We have carried out a variety of functional tests of super-2 agonists, including T cell and NK cell signaling with Prof Garry Fathman, and assessing effectiveness in enhancing antibody dependent cellular cytotoxicity (ADCC) with Prof. Ron Levy. In vivo we are evaluating super-2 toxicity and anti-tumor properties with Prof. Onur Boyman (U. Zurich). We are collaborating with Dr. Rafi Ahmed (Emory) to test super-2 in an LCMV chronic viral infection model. For our super-2 based antagonists, in vivo experiments are ongoing in GVHD (Prof. Rob Negrin), diabetes (Prof. Fathman) and EAE (Prof. Larry Steinman) models. So far we have demonstrated that super-2 is less toxic than wild-type IL-2, and more potent at activating T cells and NK cells, and that we can tailor its effects on specific cell subsets by ‘dialing up or down’ its ability to engage one of its receptors.  Thus, super-2 is a tunable platform for both agonism and antagonism in a spectrum of immune diseases, and we are eager to expand our efforts to both engineer improved versions as well as acquire more in vivo data. Since IL-2 is already clinically validated for several diseases, demonstration of improved super-2 efficacy in mouse models could result in testing in humans in a very short time frame.

Identification of host factors that contribute to defective inflammasome activation in monocytes from patients with systemic juvenile idiopathic arthritis

  • Co-PI: Denise Monack, PhD, Assistant Professor, M&I
    Co-PI: Elizabeth Mellins, MD, Professor, Pediatrics

Systemic juvenile idiopathic arthritis (sJIA) is a chronic rheumatic condition of childhood characterized by remitting fever, transient rash, and relapsing arthritis. Although sJIA represents only 10-20% of the total cases of chronic inflammatory arthritis of children (JIA), it accounts for more than 2/3 of JIA mortality. This high mortality rate is due to its association with a life-threatening complication called macrophage activation syndrome (MAS) and to the need for immunosuppressive therapies, which can lead to fatal infections.  The cause of SJIA is unknown, but recent evidence strongly suggests that a driving force is excessive activity of an endogenous inflammatory mediator called IL-1. This conclusion is based on the efficacy of anti-IL-1 therapy in a large subset of sJIA patients, especially if this treatment approach is instituted early. We are interested in elucidating the basis of uncontrolled IL-1 activity in sJIA. The Mellins laboratory has been studying the immune cells found in the blood of children with sJIA and found evidence for abnormal regulation of IL-1 secretion in these cells. The Monack laboratory has been studying the basic cellular mechanisms that control IL-1 secretion in immune cells. While certain aspects of IL-1 control have been uncovered, such as the importance of a subcellular structure known as the “inflammasome”, it is clear that more molecular events remain to be discovered.  Using modern genetic and biochemical approaches, our two laboratories will work together to identify the molecular steps involved in production and secretion of active IL-1 from immune cells. We then will go on to determine at which step(s) the immune cells from sJIA patients are abnormal.  This project will contribute important new knowledge on the fundamental processes involved in inflammation and will shed light on the mechanism of disease in a chronic, sometimes fatal illness of children, sJIA. The project also has the potential to identify approaches to treatments for sJIA and other inflammatory diseases where IL-1 plays a pathogenic role.

The role of astrocytes in modulating brain immune responses

  • Co-PI: Marion Buckwalter, MD, PhD, Assistant Prof, Neurology and Nuerological Sciences, and Neurosurgery
  • Co-PI: John C. Boothroyd, PhD, Professor, M&I

For the brain limiting inflammation during infections is paramount. First, the brain has limited regenerative capabilities, and second, the skull limits the amount of swelling that can occur before compression leads to direct brain damage. But limited immune responses may predispose to chronic brain infections. We are focused on the role astrocytes play in modulating the immune response to infections of the brain. In particular, the central goal of this proposal is to develop molecular insights into this process. Astrocytes are unique to the nervous system and recently have been shown to serve as components of the innate immune system. They also interact with neural networks and form the blood brain barrier. They are thus uniquely positioned to limit and coordinate immune responses during brain infections. One such infection is that caused by Toxoplasma gondii, an obligate intracellular pathogen that establishes a chronic, life-long but usually latent brain infection after ingestion by a susceptible host. It is this latent infection, for which there are no treatments, that ultimately allows a recrudescence of the infection in immunosuppressed patients such as AIDS patients or organ transplant patients. We plan to study the role of astrocytic TGFbeta signaling in modulating immune responses to Toxoplasma. We will test the hypothesis that astrocytic TGFb signaling suppresses the immune response during both acute and chronic phases of toxoplasmic encephalitis. At the conclusion of these experiments we will know if blunting of immune responses by astrocytic TGFb signaling affects both initial brain colonization by Toxoplasma and the degree of chronic infection. We will also determine how translational profiles of astrocytes change during Toxoplasma infection. A better understanding of how the brain limits and controls both the infection and the immune response in immunocompetent hosts may ultimately lead to ways to cure patients of Toxoplasma, as well as shedding light on the basic immune functions of astrocytes.

Identifying inflammatory drivers of chronic fatigue via daily immune and symptom sampling

  • PI: Jarred Younger, PhD, Assistant Professor, Dept of Anesthesia
  • Co-PI: Jennifer Frankovich, MD, Instructor, Dept of Pediatric Rheumatology
  • Co-PI: Rachel Manber, PhD, Professor, Dept of Psychiatry and Behavioral Science

Chronic fatigue syndrome (CFS) is a condition that affects over 4 million people in the United States. Individuals with CFS suffer from severe tiredness that drastically interferes with their daily activities, and is not helped by bed rest. While no specific cause of CFS has been identified, we suspect that the immune system plays an important role. We previously found (in a small group of individuals) that 5 immune markers in the blood were associated with fatigue. The immune markers were elevated on days when participants reported severe fatigue, and suppressed on days when participants reported less fatigue. As a result of that pilot work, we have identified a small set of immune factors that may be responsible for the symptoms of CFS. In this new study, we will run a larger number of CFS participants to verify that specific immune system markers are associated with severe daily fatigue. We will track 10 individuals with CFS for 25 consecutive days. Each day, the participants will come to our laboratory for a blood draw. They will also provide daily reports of their fatigue severity via a handheld computer. We will then analyze the blood to find immune markers that are associated with fatigue severity. If we are able to identify a set of immune markers that predict fatigue, it will help us in 2 ways. First, the information will help us to develop a blood test for properly diagnosing CFS. And second, the information will give us new targets for developing better CFS treatments. The data we collect from this grant will allow us to apply for larger grant funding, with the ultimate goal of developing a treatment for CFS that is effective, safe, inexpensive, and easy-tolerate.


An Inducible System for Macrophage Alternative Activation

  • Justin Odegaard, MD, PhD, Rising Fellow, Dept of Pathology

Macrophages are a type of blood cell involved in a large number of processes from fighting infections to wound healing to normal growth and development.  In addition, we are discovering that these cells are key players in a number of chronic disease states including diabetes, obesity, and cancer.  Despite their demonstrable importance, our knowledge of how and what macrophages do is still remarkably limited, in large part due to the lack of tools with which to selectively control these cells.  I propose to construct a system in which macrophage behavior may be selectively, specifically, and reversibly controlled within a mouse model through the administration of otherwise biologically inert small molecules.  This system will provide an unprecedented level of control over macrophage function and will allow us to examine the still obscure functions of this critical cell in human health and disease.

Evaluation of Pattern Recognition Receptor Responses as a Biomarker of Human Immune Health

  • William E. O’Gorman, PhD, Postdoctoral Researcher, M&I

Although the immune system is of preeminent importance in protecting humans from disease, there are very few (if any) assays utilized by physicians to assess immune health during a routine physical examination. In contrast, basic immunologists have developed an extensive toolbox of analytical techniques that are commonly used to evaluate immune function in mice. Clinical immunology is typically focused on individuals that have rather severe immune disorders, not on evaluating the qualities of a normal immune system. Thus the fundamental characteristics of a healthy human immune system in homeostasis are largely unknown. A comprehensive understanding of these characteristics will facilitate the unambiguous identification of otherwise cryptic immune irregularities. Cellular immune irregularities in healthy individuals may indicate a predisposition to defective immunity. The fundamental goal of this research proposal is to determine whether simple functional assays conducted on human blood are at all correlative to general immune health. We define a healthy immune system as being protective against infection, responsive to vaccination, and resistant to autoimmunity. We will initially focus on analyzing healthy individuals in order to develop a comprehensive understanding of the variation that can occur in cellular immune responses in the absence of overt disease. This research plan focuses on one set of important immune receptors expressed by innate immune cells: pattern receptors (PRRs). PRRs have evolved to recognize essential molecular motifs present within both commensal and pathogenic microbes. In addition, accumulating evidence suggests that PRRs play a role in the initiation and maintenance of autoimmunity. PRRs must therefore be highly sensitive in order to recognize clandestine pathogens but oversensitivity may cause a predisposition to autoimmunity. We will implement new technologies in immune phenotyping to quantify where healthy individuals fall in the spectrum of PRR responsiveness. Experimental vaccination of human subjects and PRR response profiling of lupus patients will then be used to directly investigate the relationship between PRR sensitivity and immune health.  The greatest promise of this research is the identification of meaningful immune metrics that can be used to inform clinical practice.

Conditionally Viable Parasites for Use as Vaccines: Towards the Development of a Malaria Vaccine Candidate

  • Rishi Rakhit, PhD, CIHR Post-Doctoral Fellow, Dept of Chemical and Systems Biology

Parasite infections are a leading cause of morbidity and mortality in both humans and animals across the globe.  Despite intensive study, both drug treatments and vaccination approaches have met with limited success in controlling or eradicating these highly prevalent conditions. We are attempting to produce genetically altered parasites for use as vaccines for these organisms. We will use a combination of chemistry and biology to produce malaria strains that cannot live inside the body, but should produce an immune response so that the vaccinated individual would be protected from future infections. Our approach in some ways mimics a previous strategy that has been shown to be effective in protecting vaccinated individuals from malaria, but should be easier to produce, quality control and scale up for public health applications.

Plasmacyoid dendritic cells and IgA mediated protection against intestinal rotavirus infection

  • Katharina Lahl, PhD, Post-Doctoral Fellow, Dept of Pathology

Antibodies are a necessary component of the immune system to defend against pathogens such as bacteria and viruses. IgA, a specialized subtype of antibody, is highly abundant at mucosal surfaces, such as the intestine, and ensures effective immune defense. The intestinal surface is exposed to many microbes and pathogen-recognizing IgA effectively prevents pathogen entry at this site of high exposure. Using a mouse model of rotavirus infection, I plan to delineate mechanisms that lead to effective, virus specific IgA production in the intestine. In preliminary experiments, I was able to show a role for a main virus-recognizing immunologic cell in this process. These cells, called plasmacytoid dendritic cells,induce IgA-producing B cells. Directly targeting plasmacytoid dendritic cells during vaccination may lead to more suitable and efficient immune responses at the mucosal surface. In this project we use the rotavirus infectious model, but our model of IgA induction within the intestine in response to foreign stimuli likely extends to other infectious agents, such as influenza or HIV.