Cell Circuits and Immunology Core


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

Shiv Pillai, MD, PhD

Shannon Bromley, PhD

Kathy Devaney
Research Technologist

James Moon, PhD


  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


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 his or her 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 MGH Immunology Seminar Series. This series takes place every week in a conference room adjacent to the Center for Immunology and Inflammatory Diseases (CIID; located at MGH East, Charlestown Navy Yard [CNY]-149) and is coordinated by the Core in conjunction with the Harvard Medical School Immunology series such that speakers give a seminar at Harvard Medical School on Wednesday and then give a seminar at MGH on Thursday.

Routine Immunology Tools

  • Flow cytometry for both basic flow cytometry using up to twenty-one color parameters with the Cytoflex LX as well as more complex flow cytometric analysis using up to thirty-three color parameters on the Astrios sorter.
  • Cell sorting and leukocyte isolation using high-speed cell sorting.
  • Multiplex and ELISA cytokine assays including flow cytometer-based cytokine bead arrays and Luminex multiplex cytokine arrays.
  • 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 and Luminex bead assays to analyze signaling pathways and protein expression in activated T and B cells in depth.

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.
  • High-Definition Spatial Transcriptomics (HDST) and multiplexed error-robust FISH (MERFISH), techniques developed by CSIBD members to facilitate spatial resolution of the transcriptome. HDST captures RNA from tissue on a dense spatially barcoded bead array, allowing for high-resolution spatial analysis, while MERFISH is an imaging method that simultaneously measures copy number and spatial distribution measurements of hundreds to thousands of RNA species in single cells.
  • 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 aid in the identification of causal variants underlying genetic signatures linked to IBD.