The core fibroblast enriched transcriptomeGenes with predicted specificity in fibroblasts in individual tissues

Tissue cell type methods

The core fibroblast enriched transcriptome

Fibroblasts are spindle-shaped mesenchymal cells found in the interstitial spaces. They are the primary source of extracellular matrix proteins, which provide a tissue scaffold and play a key role in cell phenotype determination and function. Fibroblasts have an important role in wound healing, migrating to sites of damage following tissue injury, where they deposit new collagen and facilitate the healing process. Fibroblasts can be activated by a variety of biological signals that promote proliferation and cellular differentiation, for example into myofibroblasts which have increased matrix production.

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

Fibroblasts were profiled in 18 of the tissues featured in the Tissue Cell section.

• 7 genes predicted as enriched in fibroblasts in 75-100 % tissues
• 42 genes predicted as enriched in fibroblasts in 50-75 % tissues
• 187 genes predicted as enriched in fibroblasts in 25-50 % tissues

Protein expression of genes enriched in fibroblasts across tissue types

An example of a protein with enriched expression in fibroblasts across multiple tissue types is Microfibril Associated Protein 4 (MFAP4), an extracellular matrix protein that belongs to the fibrinogen-related protein superfamily. This protein is thought to be involved in cell adhesion, intercellular interactions and the assembly and/or maintenance of elastic fibers.

MFAP4 - Colon
MFAP4
MFAP4 - Breast
MFAP4
MFAP4 - Kidney
MFAP4
MFAP4 - Lung
MFAP4
MFAP4 - Prostate
MFAP4
MFAP4 - Skin
MFAP4
MFAP4 - Stomach
MFAP4

Another example of a protein with enriched expression in fibroblasts across multiple tissue types is Cadherin 11 (CDH11), a type II classical cadherin with a role in calcium-dependent cell-cell adhesion.

CDH11 - Kidney
CDH11
CDH11 - Lung
CDH11
CDH11 - Skeletal muscle
CDH11
CDH11 - Thyroid gland
CDH11

Genes with predicted specificity in fibroblasts in individual tissues

A summary table of all genes with predicted high enrichment in fibroblasts 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 fibroblasts, 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 fibroblasts by tissue type