Immune Secrets of the Lymph Node Revealed by Spatial Genomics



In this webinar, we will discuss a study performed on lymph node tissue sections taken from five patients using complementary spatial biology platforms: the GeoMx® Digital Spatial Profiler (DSP) and the CosMx™ Spatial Molecular Imager (SMI). With GeoMx DSP, we profiled the whole transcriptome within key structures of the lymph node, including the germinal center, mantle zones, medulla, and paracortex. With CosMx SMI, we analyzed lymph node samples with clear germinal center zonation, capturing data on 1000 transcripts and 63 proteins across serial sections.’

Integrated results from GeoMx DSP and CosMx SMI showed that 643 pathways were enriched in dark and light zones of the germinal center or at their interface, as well as 139 key ligand-receptor interactions driving such pathways. For example, we found co-stimulation of CD28 was enriched within the light zone, and CosMx confirmed that CD86 ligands within light zone B cells were significantly co-localized with the CD28 receptors of the TfH cells of the germinal center. These findings shed light on interactions that happen at key immunological interfaces, which can be used to better understand the immune infiltrate in tumors and identify mechanisms of tumor immune evasion.

Learning Objectives

  • Explain the differences between spatial profiling and imaging with respect to spatial multi-omic analysis of tissue sections.
  • Describe the different functional roles of the germinal center, mantle zones, medulla, and paracortex within the lymph node.
  • Conceive a spatial multi-omic experiment to answer a question from your own field of study that could take advantage of the complementarity of spatial profiling and imaging.


Jason Reeves

Associate Director of Computational Biology

NanoString Technologies

Dr. Jason Reeves, Ph.D. is the Associate Director of Computational Biology at NanoString Technologies. His team is responsible for developing analytical solutions for NanoString’s technology access program and data analysis services supporting academic and industry partnerships across oncology, rare and infectious disease, and neurobiology.