Processed CODEX multiplexed imaging data of cellular microenvironment around T cell stimulating hydrogels

Our research used CODEX (Co-Detection by Indexing) multiplexed imaging to
gain insights into the cellular microenvironment surrounding T cell
stimulating hydrogels. These hydrogels were engineered with signals that
could locally expand antigen-specific T cells for use in tumor
immunotherapy. CODEX imaging involves an iterative process of annealing
and stripping fluorophore-labeled oligonucleotide barcodes, complementing
the barcodes attached to over 40 antibodies used for tissue staining.
Subsequently, images underwent standard CODEX image processing (tile
stitching, drift compensation, cycle concatenation, background
subtraction, deconvolution, and determination of best focal plane), single
cell segmentation, and column marker z-normalization by tissue. Our
datasets comprise individual cells as rows, each characterized by 40+
antibody fluorescence values quantified from various markers evaluated for
each study. These markers correspond to the antibodies targeting specific
proteins within the tissue, quantified at the single-cell level. The
values represent per-cell/area-averaged fluorescent intensities,
z-normalized along each column. Each cell is mapped with its cell type,
defined by x and y coordinates representing pixel locations in the
original image.  We then used this data to investigate how
different proportions of the cell types change over time in response to
the stimulating hydrogel injection with antigen-specific T cells. These
data could be used to understand the cellular interactions, composition,
and structure of T cell stimulating biomaterials for antigen-specific
immunotherapy and with adoptive T cell transfer. These datasets offer
valuable insights for researchers interested in engineering T cell
stimulating microenvironments, immune responses, and therapeutic
interventions such as T cell therapies. We investigate the dynamic
interplay between immune responses, antigen-specific T cell interactions,
and hydrogel environment in a murine melanoma model. We injected
antigen-specific T cells with microparticle T cell stimulating hydrogels
into mice subcutaneously. Injection sites were take out at different time
points day=0 (just after injection), day=3, and day=9 (n=3-6 per time
point). Our 51-plex CODEX antibody panel characterizes immune cell types,
T cell phenotypes, and stromal cell types, resulting in a rich dataset of
241,685 cells across 51 marker channels.