Session A55: Quantitative Immunology

Signaling reactions on membrane surfaces: breaking the law of averages

Most intracellular signal transduction reactions take place on the membrane surface. The membrane provides much more than just a surface environment on which signaling molecules are concentrated. There is a growing realization that multiple physical and chemical mechanisms allow the membrane to actively participate in the signaling reactions. Using a combination of single molecule imaging and spectroscopic techniques, my research seeks to directly resolve the actual mechanics of signaling reactions on membrane surfaces both in reconstituted systems and in living cells. These observations are revealing new insights into cellular signaling processes as well as some unexpected functional behaviors of proteins on the membrane surface.   

Physics of building an immunological synapse

The adaptive immune response depends upon interaction of T cell antigen receptor (TCR) and peptide-MHC complexes in the nanometer scale (15 nm) gap between the T cell and antigen presenting cells. This immunological synapse is built on a foundation of cell adhesion molecules (CAMs). Short CAM pairs (15 nm) and long CAM pairs ($\sim$30 nm) work in parallel to form immunological synapses under control of antigen receptor signaling. The engaged antigen receptor recruits tyrosine kinases to initiate formation of multicomponent signaling complexes that also incorporate F-actin foci. The physical process by which ligand binding to the TCR ligand in the context of the immunological synapse triggers the kinase cascade is not clear. Self-assembly of CAMs to form terraced junctions- with 15 nm and larger spacing between membranes in different positions, may contribute to triggering. We demonstrated segregation of the short and long CAMs in a model synapse in 1998, which was complementary to results from Kupfer demonstrating a bull's eye organization of TCR in the center surrounded by a ring of long CAMs- described as supramolecular activation clusters (SMACs), but corresponding to the predicted terraces. We can directly observe tyrosine kinase recruitment to the TCR complex and the dependence of this recruitment on the strength of interaction of TCR and peptide-MHC. Experimental manipulation of CAM length can predictably alter the effective 2D affinity, lateral mobility and the organization of other associated elements in a size dependent manner. We have developed a general model and will discuss supporting experimental data and implications for immunological synapse assembly in this talk and a related poster.\\ \\In collaboration with Christopher Peel, David Depoil and Omer Dushek Kennedy Institute of Rheumatology, The University of Oxford, Oxford, UK and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, NY, USA   

Lineage-tracking of stem cell differentiation: a neutral model of hematopoiesis in rhesus macaque

How a potentially diverse population of hematopoietic stem cells (HSCs) differentiates and proliferates to supply more than $10^{11}$ mature blood cells every day in humans remains a key biological question. We investigated this process by quantitatively analyzing the {\it clonal} structure of peripheral blood that is generated by a population of transplanted lentivirus-marked HSCs in myeloablated rhesus macaques. Each transplanted HSC generates a clonal lineage of cells in the peripheral blood that is then detected and quantified through deep sequencing of the viral vector integration sites (VIS) common within each lineage. This approach allowed us to observe, over a period of 4-12 years, hundreds of distinct clonal lineages. Surprisingly, while the distinct clone sizes varied by three orders of magnitude, we found that collectively, they form a steady-state clone size-distribution with a distinctive shape. Our concise model shows that slow HSC differentiation followed by fast progenitor growth is responsible for the observed broad clone size-distribution. Although all cells are assumed to be statistically identical, analogous to a neutral theory for the different clone lineages, our mathematical approach captures the intrinsic variability in the times to HSC differentiation after transplantation. Steady-state solutions of our model show that the predicted clone size-distribution is sensitive to only two combinations of parameters. By fitting the measured clone size-distributions to our mechanistic model, we estimate both the effective HSC differentiation rate and the number of active HSCs.   

Specificity, cross-talk and adaptation in Interferon signaling

Innate immune system is the first line of defense of higher organisms against pathogens. It coordinates the behavior of millions of cells of multiple types, achieved through numerous signaling molecules. This talk focuses on the signaling specificity of a major class of signaling molecules - Type I Interferons - which are also used therapeutically in the treatment of a number of diseases, such as Hepatitis C, multiple sclerosis and some cancers. Puzzlingly, different Interferons act through the same cell surface receptor but have different effects on the target cells. They also exhibit a strange pattern of temporal cross-talk resulting in a serious clinical problem - loss of response to Interferon therapy. We combined mathematical modeling with quantitative experiments to develop a quantitative model of specificity and adaptation in the Interferon signaling pathway. The model resolves several outstanding experimental puzzles and directly affects the clinical use of Type I Interferons in treatment of viral hepatitis and other diseases.   

Within-host co-evolution of chronic viruses and the adaptive immune system

We normally think of evolution occurring in a population of organisms, in response to their external environment. Rapid evolution of cellular populations also occurs within our bodies, as the adaptive immune system works to eliminate infection. Some pathogens, such as HIV, are able to persist in a host for extended periods of time, during which they also evolve to evade the immune response. In this talk I will introduce an analytical framework for the rapid co-evolution of B-cell and viral populations, based on the molecular interactions between them. Since the co-evolution of antibodies and viruses is perpetually out of equilibrium, I will show how to quantify the amount of adaptation in each of the two populations by analysis of their co-evolutionary history. I will discuss the consequences of competition between lineages of antibodies, and characterize the fate of a given lineage dependent on the state of the antibody and viral populations. In particular, I will discuss the conditions for emergence of highly potent broadly neutralizing antibodies, which are now recognized as critical for designing an effective vaccine against HIV.