Cell Circuits and Immunology Core

    Overview

    The major goal of the Cell Circuits and Immunology Core is to provide expertise in design, implementation, and analysis for immunological assays to members of the CSIBD by equipping the community with cost-effective access to crucial instruments, reagents, protocols, training, and education. The Core is centered on modern approaches to the study of the human immune system and their application to the study of IBD and related disorders.

    Core Personnel

    Andrew D. Luster, MD, PhD
    Co-Director

    Shiv Pillai, MD, PhD
    Co-Director

    Shannon Bromley, PhD
    Manager

    Kathy Devaney
    Research Technologist

    James Moon, PhD
    Consultant

    Objectives

    1. Provide CSIBD members with access to immunological resources that would otherwise be cost-prohibitive to individual researchers
    2. Offer CSIBD investigators access to cutting-edge immunological techniques that are at the forefront of immunology research
    3. Promote the development of junior investigators and foster collaborations by providing a connection point between investigators of varying research approaches

    Services

    Education and Training Services

    A central goal of this core is to provide instruction for investigators in modern immunologic methods. The co-directors and the manager of the Cell Circuits and Immunology Core have extensive experience in modern immunologic techniques and a longstanding commitment to teaching. Three levels of supervision are offered: consultation, short-term supervision of investigators in a specific technique, and long-term guidance on project development.

    In each of the several areas of expertise described above, consultation is provided to CSIBD investigators with laboratories actively using these techniques. However, many investigator-Core interactions involve more intensive training to permit a CSIBD investigator to apply several of these techniques to a specific research project. This expectation follows from the complex multi-step nature of these techniques and the requirement for specific modifications for most applications. For these interactions, a CSIBD investigator, or a member of their laboratory, spends the necessary time to learn and modify the technique under the direct guidance of Core personnel.

    A cornerstone of the educational activities of the Core is the Immunology Program Seminar, Grand Rounds, and Work-in-Progress Series. These series brings world-renowned immunology experts to visit the greater MGH community and present work on a wide variety of topics in basic and clinical immunology. Grand Rounds meetings in particular feature talks from clinicians, translational scientists, and basic research investigators on a clinically-relevant topic each month. Work-In-Progress meetings are designed to provide opportunities, especially for trainees, to present recent results and challenges as well as to receive feedback and suggestions on ongoing projects.

    Routine Immunology Services

    • Flow cytometry for both basic flow cytometry using up to 21 color parameters with the Cytoflex LX as well as more complex flow cytometric analysis using up to 33 color parameters on the Astrios sorter.
    • Cell sorting and leukocyte isolation using high-speed cell sorting.
    • Dendrimer-based in situ hybridization and immunofluorescence on both FFPE and frozen sections to identify and monitor activity of disease-associated clones at sites of inflammation. For in situ hybridization, DNA probes provided by Affymetrix allow sensitive detection of RNA in tissues.
    • Phosphoproteomics to analyze signaling pathways and protein expression in activated T and B cells.

    Specialized Immunology Services

    • Next-generation sequencing to identify clonal expansion of T and B cells in the blood and tissues.
    • Single-cell cloning of activated B cells to match Ig H and L chain sequences and create disease-related human monoclonal antibodies to monitor cells and expression patterns during disease flares as well as progression and response to therapies.
    • MHC class II tetramers to identify, purify, and characterize disease-causing antigen-specific T cells. The extracellular domains of MHC class II alpha and beta chains can be enzymatically biotinylated using the BirA ligase and then tetramerized using fluorochrome-conjugated streptavidin.
    • Antigen multimers to identify, purify, and characterize disease-causing antigen-specific B cells; these are also created by enzymatic biotinylation of antigen and tetramerization using streptavidin.
    • Novel pathway-based computational approaches and CRISPR on primary immune cells to aid the discovery of biologically relevant genetic variants that may represent therapeutic targets in disease-specific activated B, T, and myeloid cells. Perturb-Seq combines pooled CRISPR screens with massively parallel scRNA-seq to provide a scalable approach for parallel screening.
    • Suite  of general molecular immunology tools to address the challenge of finding the genetic variants that are directly responsible for observed genotype-phenotype associations in health and disease.
    • GPCR-seq, a multiplexed screening platform to identify agonists for orphan GPCRs from in-house natural product libraries including microbiome metabolites, microbial fractions, organic volatiles, food additives, and more traditional commercial pharmaceutical libraries.
    • Toolbox of base editors, including a suite of more than 10 editors that achieved high efficiencies and accuracy with flexibility in editing, which can be used for phenotyping coding variants at scale in primary immune cells and high-fidelity cell models.
    • Single-cell and spatial methods, including single-cell and single-nucleus RNA-sequencing, high-definition spatial transcriptomics (HDST), spatial technology platforms (Visium, Xenium, CosMx), and multiplexed error-robust FISH (MERFISH).