The core macrophage enriched transcriptome

Resident macrophages are found in almost all tissues, and are responsible for monitoring tissues for potential pathogens or other harmful molecules. Upon activation they can phagocytose pathogens, as well as debris from dead or dying cells, and can present antigens from phagocytosed material towards the adaptive immune system by displaying on MHC class II proteins. They can also aid during wound healing and tissue repair.

In this section we detail the predicted core macrophage transcriptome, highlighting genes classified as having predicted specificity in macrophages in multiple tissue types. Such genes could be useful general markers for macrophages across tissue beds, and are likely critical for macrophage specific functions. These genes are sub-divided into 3 categories, based on the number of tissues in which they were independently classified as macrophage enriched.

Macrophages were profiled in 19 of the tissues featured in the Tissue Cell section.

• 32 genes predicted as enriched in macrophages in 75-100 % tissues
• 44 genes predicted as enriched in macrophages in 50-75 % tissues
• 105 genes predicted as enriched in macrophages in 25-50 % tissues

Protein expression of genes enriched in macrophages across tissue types

An example of a protein with enriched expression in macrophages across multiple tissue types is CD163 Molecule (CD163), a transmembrane scavenger receptor with a role in the regulation of tissue regeneration, clearance of cell-free hemoglobin and capture of bacteria.

CD163 - Adipose subcutaneous
CD163
CD163 - Colon
CD163
CD163 - Liver
CD163
CD163 - Lung
CD163
CD163 - Prostate
CD163

Another example of a protein with enriched expression in macrophages across multiple tissue types is Macrophage Scavenger Receptor 1 (MSR1), a multifunctional phagocytic receptor that participates in many pathophysiological events, such as host defense, endotoxemia, endocytosis, and bone metabolism.

MSR1 - Adipose subcutaneous
MSR1
MSR1 - Colon
MSR1
MSR1 - Lung
MSR1

Genes with predicted specificity in macrophages in individual tissues

A summary table of all genes with predicted high enrichment in macrophages in profiled tissues is provided below. Identified genes are subdivided into 3 categories in each tissue, based on the difference between the enrichment score in macrophages, compared to the other cell types profiled (see Methods Summary page for details):

• Predicted specificity: ´Very high´ - Differential score vs. other profiled cell types within the tissue >0.35
• Predicted specificity: ´High´ - Differential score vs. other profiled cell types within the tissue >0.25
• Predicted specificity: ´Moderate´ - Differential score vs. other profiled cell types within the tissue >0.15

Table 1: Genes predicted to be enriched in macrophages by tissue type