. Author manuscript; available in PMC: 2015 Oct 1.

Published in final edited form as: Cancer Immunol Res. 2014 Oct;2(10):937–942. doi: 10.1158/2326-6066.CIR-14-0152

Table 2.

Image analysis-guided molecular profiling of cell subsets in the tumor microenvironment:

SPECIMEN TYPE	METHOD	ANALYSES
Formalin-fixed paraffin embedded tissue (FFPE)	Digital image analysis (brightfield or multiplex immunofluorescence)	quantify intensity, distribution, and colocalization of molecular analytes of interest
FFPE or flash- frozen tissue	Immuno-laser capture microdissection (tissue compartments, or individual cells, or individual structures)	TCR deep sequencing, clonal analysis, epigenetic profiling, mRNA transcriptomes
primary tissue explants	isolate viable T cells	phenotyping, single cell TCR sequencing, functional polarization
primary tissue explants	isolate passage one fibroblasts
endocervical cytobrush specimens	isolate viable T cells from longitudinally obtained specimens: Single cell toolbox: microengraving, imaging	phenotyping, cytokine kinetics, RNAseq, FISH
peripheral blood (PBMC and plasma)	ELISPOT, intracellular cytokine staining, flow cytometry	quantify antigen-specific response
peripheral blood (PBMC and plasma)	ELISPOT, intracellular cytokine staining, flow cytometry	exosome signature