Schedule for: 22w5139 - Sensing and Signaling in Immune Systems: Mathematics meets Biology

A buffet dinner is served daily between 5:30pm and 7:30pm in Kinnear Center 105, main floor of the Kinnear Building.

If in-person participants wish to gather the day prior, you may use TCPL foyer. No BIRS staff present, however, during the weekends.

Breakfast is served daily between 7 and 9am in the Vistas Dining Room, the top floor of the Sally Borden Building.

A brief introduction to BIRS with important logistical information, technology instruction, and opportunity for participants to ask questions.

Using our human TCR gene amplification and sequencing platform, we tracked the clonal evolution of circulating T follicular helper cells after repeated exposure of naive individuals to sporozoites of the malaria parasite Plasmodium falciparum. Expression cloning of selected Tfh cell TCRs identified TCRs with reactivity against the major sporozoite surface antigen CSP, a leading malaria vaccine target. I will discuss how we integrate this data to instruct malaria vaccine design.

Adaptive immunity relies on specific binding of hyper-variable receptors to diverse molecular targets. The many-to-many mapping between receptors and epitopes determines how the immune system senses threats, but an understanding of its global structure has remained elusive. In my talk I will introduce an analytical framework to quantify statistical structure in high-throughput measurements of such maps. I will discuss how a combination of ideas from population genetics, molecular biophysics, and machine learning is enabling us decipher the probabilistic rules of the degenerate molecular binding code of the immune system.

I will describe and discuss a theory of adaptive immunity in which B cells anticipate the future evolution of viruses. Three distinct phases of naive emerge as a function of the viral evolutionary rate and upfront cost of immunity, depending on whether and how memory is formed. The model predicts cycles where new memories are not made, which can be linked to the phenomenon of "original antigenic sin."

Biological systems, ranging from the brain to the immune system, store memory of molecular interactions to efficiently recognize and respond to stimuli. In this talk, I will discuss how statistics and dynamics of stimuli should determine the optimal memory encoding strategies in biological networks. In particular, I will contrast the compartmentalized memory in the adaptive immune system, which primarily interacts with evolving pathogens, with the distributed memory in the olfactory cortex, which interacts with relatively static odor molecules. Focusing on the adaptive immune system, I will discuss how memory encoding could be understood in light of host-pathogen coevolution

Lunch is served daily between 11:30am and 1:30pm in the Vistas Dining Room, the top floor of the Sally Borden Building.

Meet in the PDC front desk for a guided tour of The Banff Centre campus.

Meet in foyer of TCPL to participate in the BIRS group photo. The photograph will be taken outdoors, so dress appropriately for the weather. Please don't be late, or you might not be in the official group photo!

A buffet dinner is served daily between 5:30pm and 7:30pm in the Vistas Dining Room, the top floor of the Sally Borden Building.

Analyzing T cell repertoires from mice from different stages of development, we tried to charactarize selection on these cells at different maturation stages.

The amount of publicly available scientific data produced as a consequence of the COVID-19 pandemic, far exceeds any previous effort against a specific disease or condition. This unprecedented situation allows for development and application of new research approaches for understanding immune responses to SARS-CoV-2. Here we describe, how TCR repertoire structure can direct the epitope discovery process by pointing towards the most public and immunogenic responses. We performed an integrative meta-analysis of large public single-cell and bulk TCR datasets from SARS-CoV-2 infected individuals to identify strong and public CD4+ responses, with six prominent TCR similarity clusters.

Human T cell analysis requires knowledge of the specificity (antigen target) and cellular functional profile. These analyses are complicated by the vast potential diversity of T cell receptors (estimated at >1061) and variation in presented target antigens determined by HLA. Here I will discuss approaches to deconstruct this complexity, utilizing TCR distance-based analysis and novel methods for integrating TCR sequence and single cell gene expression data. These approaches will be applied to studies of SARS-CoV-2 infection and influenza vaccination to identify diverse T cell differentiation trajectories and clinically relevant associations with protected and susceptible phenotypes.

Two loosely-connected topics: (1) genetic influences on the TCR generation process (mostly published), (2) analysis of convergent TCR selection in single-cell data (work in progress, looking for feedback).

"The 'helper' and 'killer' phenotypes of T cells were first linked to the mutually exclusive expression of CD4 and CD8 surface molecules in the 1970s. At the time, however, it was unclear whether CD4/CD8 were simply markers for these cells or in fact directly involved with signaling. Impressive advancements over the next few decades revealed how CD4/CD8 interact with invariant regions of MHC class II/MHC class I molecules, respectively, and bind to the Src-family kinase Lck, thus enabling the single molecule sensitivity of TCR. However, these coreceptor proteins are dispensable when sufficient pMHC is present, and their interactions with MHC molecules are exceptionally weak, with CD8 binding relatively better than CD4 at binding to respective MHC. How can this be reconciled with the well-established roles for CD4 and CD8 in amplifying signaling from the TCR and helping developing T cell discriminate the type of pMHC that engages their TCR? Through the use of fluorescence microscopy and correlation spectroscopy, we show that CD4 and Lck diffuse together at the surface of live cells, in contrast to recent models in which only a fraction of CD4 have bound Lck. When combined with mutagenesis, our correlation measurements reveal the role of the amphipathic helix of CD4 in stabilizing the interaction with Lck. Experiments with functionalized lipid bilayers and engineered Jurkat T cells also indicate that the CD4-Lck interaction is unaffected by signaling through the TCR, but brightness analysis reveals systematic formation of a dimer of dimers (CD4-Lck)2. Experiments in which CD4 and CD8 are co-expressed with Lck, as in double positive thymocytes, reveal a complex hierarchy of interactions where CD4 has a stronger interaction with Lck than CD8, but conditions can be established where occupancy by Lck is similar. Our results are important for refining current models of coreceptor function and, in turn, how T cell signaling is amplified and antigen discrimination is achieved."

Cross-wired pathways where multiple ligands bind the same receptor or activate an overlapping set of downstream regulators, are ubiquitous in signaling in various systems - from the immune system to development. Yet, cells are able to produce distinct responses to distinct ligands of combinations thereof. I will discuss several theoretical approaches to the cross-talk problem and examine their applications on the example of the Type I Interferon signaling.

Immune cells must respond appropriately to diverse pathogens or immune stimuli. Four signaling pathways function combinatorially and dynamically to transmit information about the immune threat to nuclear immune response genes. I will present our work on understanding the nature of this signaling code and its capacity and fidelity to transmit information.

T cells use their T cell receptors (TCRs) to discriminate between lower-affinity self and higher-affinity non-self peptides presented on major histocompatibility complex (pMHC) antigens. Although the discriminatory power of the TCR is widely believed to be near-perfect, technical difficulties have hampered efforts to precisely quantify it. Here, we accurately measure TCR discrimination finding that although enhanced compared with conventional cell-surface receptors, it is imperfect: primary human T cells can respond to ultra-low affinity ligands. Our findings explain why self pMHC frequently induce autoimmune diseases and anti-tumour responses, and suggest ways to modify TCR discrimination.

Cells within tissues and organisms rely on sensing local gradient cues which are irregular, conflicting, and changing over time and space. We propose that computations with transiently stable states enable cellular sensing and responsiveness to non-stationary signals. We furthermore generalise this principle to describe how specific and generalization in the signal processing emerge on the level of biochemical networks in single cells.

Kinetic proofreading is known to be critical in the specificity of T-cells to their cognate antigens, but there is still a large degree of uncertainty around the biochemical steps in T-cell activation that are responsible for this proofreading. To address this question, I measured the responses of T cell receptor proximal signaling components to pMHC stimulation, using a designed protein scaffold that allows for quantitative control of pMHC spacing and number, then built a computational model based on these results. My results suggest that a delay in signaling condensate nucleation may constitute a major kinetic proofreading step for T cell antigen recognition.

Natural Killer (NK) cells sense cognate ligands expressed on healthy and diseased target cells with a diverse array of activating and inhibitory receptors. We use mechanistic spatially resolved models combined with data from microscopy experiments to elucidate interplay between spatial clustering of NK cell receptors and early time signaling kinetics.

Upon initial pathogen encounter, naive T cells differentiate into effector cells and memory cells, which persist confer protective immunity to a subsequent challenge. Using long-term quantitative imaging in an ex vivo system, we directly visualized pathways for memory cell formation at the clonal lineage level. We find that memory cells can form via two distinct pathways, one involving direct differentiation of naive cells, and another involving the de-differentiation of effector cells. These findings unify two long-standing models in the field for how memory cells form, and could explain how these cells acquire heterogeneous functional attributes during differentiation.

High-throughput single-cell methods have uncovered substantial heterogeneity in the pool of hematopoietic stem and progenitor cells (HSPCs), but how much instruction is inherited by offspring from their heterogeneous ancestors remains unanswered. Using a method that enables simultaneous determination of common ancestor, division number, and differentiation status of a large collection of single cells, our data revealed that murine and human cells that derived from a common ancestor had significant similarities in their division progression and differentiation outcomes.

Gene regulatory network models have been extremely valuable to explain early embryo development in several organisms, but have not been as successfully predictive of developmental process trajectories in systems like mammalian hematopoiesis to date. One aspect of the problem is that real-life transcription factors (TFs) in this system do not behave according to simple, prokaryote-based assumptions that expression level directly predicts occupancy, and that occupancy directly predicts function. This talk will discuss in-depth analyses of the roles of TF-site affinity, TF dose, partner factor interactions and epigenetic states of sites in constraining TF action across the mouse genome, and the way these features shift radically during the transition from multipotency to T-cell lineage commitment.

Extracellular cues in mammalian cells are fundamentally combinatorial. Here we decipher the logic with which seemingly equivalent or contradictory signals within the TGFb superfamily combine together to control cellular behavior.

Cytokines regulate cellular functions essential for normal physiology and the host response. My laboratory studies how cytokines regulate immune cell fate decisions. The objective is to gain key insights into the molecular mechanisms that underlie cytokine functional diversity. Fundamental to our program is the use of protein engineering to manipulate cytokine immuno-modulatory activities with the ultimate goal to inform new therapies for immunomodulation. I will be presenting new work describing how comparable signalling outputs triggered by different cytokines ultimately lead to diverse functional responses.

Protein diffusion plays a ubiquitous role in signalling pathways. I will discuss several examples of signaling protein diffusion, as observed with fluorescence methods, showing that it is rarely a simple process. As our understanding of the organization of the cellular environment progresses, so does our understanding of protein diffusion in cells, and how it may limit the speed and precision of signaling.

In this talk I will make use of some ``traditional'' algebraic methods (based on the concept of a Gröbner basis) to study cytokine receptor-ligand systems at steady state. In particular, I will focus on the definition of a signalling function, its amplitude and its EC50. I illustrate our results making use of the IL-7 receptor system.

Influenza viruses infect millions of individuals each year and understanding how the virus spreads within the lung, how efficacious host immune control is, and how different factors influence disease severity is important. I’ll discuss an integrative model-experiment exchange used to establish dynamical connections between the virus, host responses, lung pathology, and severity.

I will present our work and view on the role of physical dynamics during immune-environment interaction in cellular information acquisition and shaping of the selection pressure. In particular, I will discuss how active force usage might influence the diversity and adaptability of immune response.

We discuss systems immunology interrogation of the before, during, and after of COVID-19 with a top-down perspective and approach. We next highlight the development of machine learning models of intracellular and intercellular interactions and dynamics.

Allogeneic hematopoietic stem cell transplantation is a potentially curative treatment for hematologic malignancies. Donor T cells help eliminate recipient leukemia cells (graft-vs-leukemia effect), but also target normal tissues of the recipient, causing graft-vs-host disease (GVHD). How T cells maintain GVHD in the face of ongoing alloantigen exposure is an open question. Our joint work with Warren Shlomchik and colleagues on their mouse model of GVHD indicates that the disease is maintained locally by T cells in target tissues rather than fed continuously by secondary lymphoid organs. In my talk, I will discuss how clonal tracing led us to hypothesize that GVHD maintenance is driven by a small population of tissue-resident progenitor T cells, and how single-cell transcriptome analysis suggested a molecular phenotype for these progenitors that allowed testing the GVHD progenitor hypothesis experimentally.

Inspired by Waddington’s illustration of an epigenetic landscape, cell-fate transitions have been envisioned as bifurcating dynamical systems. Single-cell RNA sequencing (scRNA-seq) is making it possible to interrogate cell fate-transitions at whole-genome scales with molecular-scale precision. However, it remains unclear how to bridge the disparate scales of the dynamics of whole transcriptomes to the molecules that define the collective fate-transitions. We bridge these scales by showing that bifurcations in transcriptional states can be analytically pinpointed and their genetic bases revealed, directly from data. We demonstrate the power of our conceptual framework and analytical scheme in the context of a recent scRNA-seq based investigation of hematopoietic stem cells to neutrophils. Our work provides a rigorous and model-independent mathematical framework for detecting and categorizing transitions in cell-fate directly from sequencing data.

We present an experimental/theoretical pipeline to build a quantitative model of antigen discrimination by T cells. We find that the multiplexed dynamics of cytokine production/consumption by T cells ex vivo can be compressed into a 1D model using tools from machine learning. This model highlights two modalities of T cell activation that enforce adaptive kinetic proofreading of of antigen-TCR interaction, and that encode antigen discrimination. We discuss practical applications of rigorous antigen quantification across varied immunological settings (collaboration with Paul François's group)

5-day workshop participants are welcome to use BIRS facilities (TCPL ) until 3 pm on Friday, although participants are still required to checkout of the guest rooms by 11AM.