Skip to main content

Table 3 Emerging techniques to identify spatial structure of the tumor immune microenvironment (TIME)

From: Spatial architecture of the immune microenvironment orchestrates tumor immunity and therapeutic response

Category

Name

Level

Sample preparation

Labels

Visualization

Comments

Refs.

Non-specific technique

H&E staining

Nonspecific structure

FFPE

Hematoxylin and eosin

Visible light

Low-cost; high flux helped by deep learning: poordiscrimination of cell subtypes

[22,23,24,25]

Probe-based in situ imaging

IHC

Peptide and protein

FFPE

Antibody-reporter (usually florescent protein)

Fluorescence, insoluble pigment, etc.

Limited detectable targets simultaneously

[26]

FISH

DNA

FFPE

Oligonucleotides-florescent reporter

Fluorescence

Limited detectable targets simultaneously

[27]

CODEX

Peptide and protein

Fresh-frozen

Antibody-oligonucleotides

Fluorescence

Extended detectible targets simultaneously

[28]

CODEX-FFPE

Peptide and protein

FFPE

Antibody-oligonucleotides

Fluorescence

Extended detectible targets simultaneously

[10]

seqFISH, seqFISH + , corFISH

mRNA (sub-transcriptome)

Live section

Oligonucleotides-florescent reporter

Fluorescence

 > 10,000 detectible genes simultaneously; subcellular resolution ratio

[29,30,31]

MIBI, MIBI-TOF

Peptide and protein

FFPE, immobilized cell suspension

Antibodies-isotypes

Secondary ion beam

Extended detectible targets simultaneously

[19, 32, 33]

IMC

Protein, etc.

FFPE

Antibodies-high mass tag

Ion beam

Subcellular resolution ratio; probes are not necessarily needed

[34, 35]

Spatial transcriptome

Microarray-based spatial transcriptomics

Transcriptome

Live section, FFPE

Spatial transcriptome

Pathology + Computational analysis

Restricted cellular resolution

[36]

Microarray-based spatial transcriptomics + sc-RNAseq

Transcriptome

Live section + single-cell suspension

Spatial transcriptome

Computational matching

Mapping is based on region-cluster matching by multimodal intersection analysis

[37]

ZipSeq

Transcriptome

Live section

Antibody/lignoceric-oligonucleotides-zipcode

Computational matching

Exquisite design in advance is required for accuracy

[38]

Spatial proteome

MALDI MSI

Proteome

Fresh frozen, FFPE

Ion imaging

Label-free; de novo investigation

[39, 40]

  1. H&E, hematoxylin and eosin; FFPE, formalin-fixed and paraffin-embedded; IHC, immunohistochemistry; FISH, fluorescence in situ hybridization; DNA, deoxyribonucleic acid; CODEX, co-detection by indexing; MIBI, multiplexed ion beam imaging; MIBI-TOF, multiplexed ion beam imaging by time of flight; IMC, imaging mass cytometry; sc-RNAseq, single-cell RNA sequencing; MALDI MSI, matrix-assisted laser desorption/ionization mass spectrometric imaging