Transcriptional Signatures for Diagnosis of Different Spectra of Mycobacterium Tuberculosis Infection and Characterization of the Immune Response During Latency or Active Disease

Anne O’Garra, Ph.D.

Medical Research Council: National Institute for Medical Research

Funded in December, 2006: $600000 for 3 years
LAY SUMMARY . ABSTRACT . BIOGRAPHY . HYPOTHESIS . SELECTED PUBLICATIONS .

LAY SUMMARY

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Determining Innate Immune Factors that Distinguish Latent TB Infection from Active Disease

This consortium will seek to identify immune factors in people with tuberculosis (TB) that determine whether the bacterial infection is latent (inactive) or active and how these immune factors are modified in TB treatment. Researchers also will seek to identify biomarkers that can be used to diagnose TB and monitor disease progression and immune responses to treatment.

TB is caused by the Mycotuberculosis bacterium. Active TB is second only to HIV as the most fatal infectious disease worldwide. A vast number of additional people have clinically silent, or latent, infection. About ten percent of people with the inactive form will develop active disease, usually within about two years after infection, and scientists do no yet understand the factors involved in this transformation from inactive to active disease. While the nature of the processes involved is not clear, evidence indicates that innate immunity (the body's first line of defense) plays a key role. Understanding immune responses to TB will aid in developing an effective vaccine and therapies that can stimulate the body's immune attacks against the bacteria, while minimizing side effects that occur in currently available drugs.

The MRC National Institute for Medical Research (UK) researchers will undertake studies to understand the immunological factors involved in latent and active TB infection, and those responsible for the conversion from latent to active TB, which may improve diagnosis and treatment. They will study 200 people, including those with active TB, latent TB, and healthy controls. Through blood samples from people in these three groups, they will determine whether there is a clear signature of immunological changes that denote, and are responsible for, latent compared to active TB in blood and lung cells.

The Baylor investigators, meanwhile, will undertake gene array studies to search for biomarkers that might be able to identify specific clusters of genes found in large numbers of people with latent disease and compare these to gene clusters found in those with active disease and healthy volunteers. Through these two related approaches, the Baylor researchers may be able to identify genes, and the MRC researchers may be able to identify specific products of the genes, that act on the immune system to prevent latent infection from becoming active disease.

Significance: The findings of genes and their products that may help to identify why some people infected with TB never develop active infection while others do, may lead eventually to TB vaccine candidates and to development of effective drugs that target the specific factors involved, while minimizing side effects.

ABSTRACT

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Transcriptional Signatures for Diagnosis of Different Spectra of Mycobacterium tuberculosis Infection and Characterization of the Immune Response During Latency or Active Disease

Tuberculosis (TB) is a major and increasing cause of morbidity and mortality worldwide caused by infection with the pathogen Mycobacterium tuberculosis (MTb). The diagnosis of pulmonary TB (PTB) is difficult, can take weeks or may require invasive procedures. Some individuals showing reactivity to MTb antigens, suggesting infection, but without evidence of active disease, are termed latent TB. We cannot yet predict those that will develop active disease. Although deficiencies of individual components of the immune response have been shown to reduce protection against MTb, the contribution of these in individuals without such deficiencies has not been quantified, and it remains unknown why some infected individuals develop TB disease while the majority remain healthy, albeit with latent disease. Blood constitutes an accessible source of clinically relevant information, and a comprehensive molecular phenotype of blood cells can be obtained by generating microarray gene expression profiles.

We postulate that whole blood from patients with TB will carry transcriptional signatures and provide a new perspective on mechanisms of immunopathogenesis and constitute a source of clinically relevant diagnostic and prognostic markers. We also aim to identify factors in the global host response to MTb determining latency and active disease, how these factors are modified in active PTB by chemotherapy, and to identify biomarkers for the diagnosis of TB and monitoring of disease progression/response to treatment. This study will be conducted by a multidisciplinary team composed of clinicians and immunologists from St. Mary’s Hospital and NIMR, London, together with immunologists and bioinformaticians at the BIIR, Dallas.

INVESTIGATOR BIOGRAPHIES

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Anne O’Garra, Ph.D.

Anne O'Garra is the Head of Division of Immunoregulation at the National Institute for Medical Research (NIMR), Mill Hill, London. Dr. O'Garra set up the Division of Immunoregulation in 2001, with the aim to bridge the gap between basic immunology and infectious disease by bringing together knowledge obtained from the study of the immune response to infectious microorganisms in experimental models and clinical disease. The research of the Division is based upon close collaboration with the existing Divisions of Molecular Immunology, Immune Cell Biology, and Parasitology, Virology and Mycobacterial Research at NIMR. Over the next few years the Division will be recruiting additional independent investigators to expand the research. Dr. O'Garra continues the study of the role of cytokines and immune modulators in immune responses, now with a strong emphasis on the immune response to Mycobacterium tuberculosis (MTb), in both experimental mouse models and human disease.

Dr. O'Garra obtained her Ph.D. at the NIMR in microbiology in 1983. She then changed fields and division and stayed on at the Institute as a Postdoctoral Fellow in immunology, where she conducted her research on the cytokine interleukin-5 (IL-5) and showed that, as well as inducing differentiation of eosinophils, this factor enhanced B lymphocyte function. In 1987 she left England for Palo Alto, California, to work for the DNAX Research Institute (now Schering Plough Biopharma), where by 2000 she had become a principal staff scientist in the Department of Immunobiology.

At DNAX Dr. O'Garra worked for several years to define the function of the cytokines IL-10 and IL-12. She first elucidated that interleukin 10 (IL-10) has broad immunosuppressive functions, inhibiting antigen presentation by dendritic cells and macrophages and their production of inflammatory cytokines. She elucidated fundamental mechanisms regulating the activation of CD4+ T-helper (Th) cell subsets with distinct effector functions, discovering that: IL-12 induced T-helper 1 (Th1) cells secreting IFN, essential for eradication of intracellular pathogens; the key antigen presenting cell, the dendritic cell, produced IL-12, under tight control of IL-10. Her work is now aiming to translate findings in basic immunregulation to human disease to open up new avenues for improved adjuvants and vaccines for prevention or therapeutic intervention in infectious diseases.

Research in the Division of Immunoregulation is concerned with the precise mechanisms of pathogenesis and immune control of infectious disease. Emphasis is given to those bacterial and viral infections, which represent a major threat to human health worldwide and against which vaccines are unavailable or inefficient. We aim to understand how the immune response to infection is regulated at the molecular and cellular level, to identify factors that sway the complex interaction between the infectious microorganisms and the immune system and allow infections to overcome our immune defences, and to use this knowledge to induce or enhance protective immunity against infection. The goal of our research, which includes studies not only on the immunopathogenesis in tuberculosis, but also in influenza, retroviral infection, and listeria, is to lay the basis for improved diagnostic methods and vaccination and therapeutic strategies for the prevention or treatment of infectious diseases.

Damien Chaussabel, Ph.D., is an Assistant Investigator at the Baylor Institute for Immunology Research (BIIR) in Dallas, where he also leads the Genomic Microarray Core facility. Dr. Chaussabel was recruited to BIIR in 2004 to establish genomics and microarray-based projects. He earned his Ph.D. in Immunology from the University of Brussels in 1999. During this time, he studied Chagas Disease, which infects an estimated 16 to 18 million people worldwide, mostly in Central and South America. Dr. Chaussabel helped to develop an experimental model of Chagas Disease.

From 2000-2004, Dr. Chaussabel was a Postdoctoral Fellow at the National Institute of Allergy and Infectious Diseases in Bethesda, Maryland. He joined the Baylor Institute for Immunology Research in 2004 as an Assistant Investigator.

Dr. Chaussabel is using microarray technology to identify disease markers in patients with cancer and autoimmune and infectious diseases, as well as in transplant recipients. He is also developing novel microarray data mining strategies to better utilize the large volume of data that is being collected in his research and that of his collaborators. The immune system responds differently to many types of challenges. Microarrays can measure responses to different challenges, even those that are closely-related. For example, Dr. Chaussabel's group is able to distinguish between viral-based respiratory infections caused by influenza and respiratory syncytial virus. They also see unique immune responses to different types of bacterial infections, such as E. coli and Staphylococcus.

HYPOTHESIS

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Methods:
Three cohorts of patients will be recruited: (1) Potentially active PTB based on clinical diagnosis, subsequently confirmed MTb culture positive; (2) latent TB; (3) healthy volunteer controls. We will establish transcriptional signatures of patients with PTB and latent TB in comparison to healthy donors. Parallel immune phenotyping and immune reactivity studies will also be performed, which will support the interpretation of the microarray data and provide insight into mechanisms of disease pathogenesis.

Longitudinal samples from patients with confirmed active PTB will be analysed. These patients will receive antibiotic therapy for six months, and their signature will then be compared to the baseline obtained from patients with latent TB, allowing comparison of the chemotherapy cured TB with latent TB.

We have now generated preliminary data from samples collected at St Mary’s and shipped to BIIR for microarray analysis, showing the feasibility of the study. Most strikingly, a potent increase in expression of interferon (IFN) inducible genes was observed in a PTB patient. This potent increase in IFN inducible genes clearly demonstrates an expected detectable immune response to MTb infection and the feasibility of obtaining a meaningful transcriptional signature.

SELECTED PUBLICATIONS

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Chaussabel D., Quinn C., Shen J., Patel P., Glaser C., Baldwin N., Stichweh D., Blankenship D., Li L., Munagala I., Bennett L., Allantaz F., Mejias A., Ardura M., Kaizer E., Monnet L., Allman W., Randall H., Johnson D., Lanier A., Punaro M., Wittkowski K.M., White P., Fay J., Klintmalm G., Ramilo O., Palucka A.K., Banchereau J., and Pascual V.   A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus.  Immunity. 2008 Jul;29(1):150-64.

Allantaz F., Chaussabel D., Banchereau J., and Pascual V.  Microarray-based identification of novel biomarkers in IL-1-mediated diseases. Curr Opin Immunol. 2007 Dec;19(6):623-32.