Dendritic cells

Dendritic cells (DCs) are antigen-presenting cells (APC) that act as messengers between the innate and the adaptive immune systems. They are present in tissues that are in contact with the external environment, but also in an immature state in the blood, and upon activation they migrate to the lymph nodes to interact with T-cells and B-cells.

In the Immune cell section we have 234 cell lineage enriched genes and 19 of these genes has the highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. In addition, 590 genes are cell lineage group enriched and an additional 6 genes are enhanced in this cell lineage. Altogether, 830 genes are elevated and among these 123 also show highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed.

Figure 1. The distribution of all genes across the five specificity categories based on transcript abundance in dendritic cell lineage as well as in the other 5 cell lineages.

Table 1. Number of genes in the subdivided categories of elevated expression in dendritic cell lineage.

Table 2. The genes with the highest level of enriched expression in dendritic cell lineage. "nTPM" shows the transcript level as protein-coding transcripts per million. Specificity-score corresponds to the score calculated as the fold change of dendritic cell lineage expression to the second highest cell type.

Myeloid DCs

Myeloid dendritic cells (mDCs) are antigen-presenting cells, which capture and process antigens that will be displayed on their surface and subsequently presented to T-cells.

In the Immune cell section we have 28 myeloid DC enriched genes and 4 of these genes has the highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. In addition, 265 genes are cell type group enriched and an additional 84 genes are enhanced in this cell type. Altogether, 377 genes are elevated and among these 67 also show highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed.

The myeloid DCs were isolated from PBMCs. Debris and cell aggregates were eliminated by gating based on scatter profile. The NK-, T- and B-cells were eliminated by selecting CD3neg/CD19neg/CD20neg/CD56neg population. The mDCs were sorted as CD11c+/CD16neg/HLA-Dr+/CD14low sub-population. Between approx. 5,000 – 15,000 cells were sorted per sample for transcriptomic analysis by mRNA-sequencing. The transcriptome analysis shows that 45% (n=9090) of all human proteins (n=20090) are expressed in the myeloid DCs and 265 of these genes show an elevated expression in myeloid DCs compared to the other 17 cell types (see figure below).

Figure 2. The distribution of all genes across the five specificity categories based on transcript abundance in myeloid DCs as well as in the other 17 cell types.

Table 3. Number of genes in the subdivided categories of elevated expression in myeloid DCs.

Table 4. The genes with the highest level of enriched expression in myeloid DCs. "nTPM" shows the transcript level as protein-coding transcripts per million. Specificity-score corresponds to the score calculated as the fold change of myeloid DC expression to the second highest cell type.

Plasmacytoid DCs

Plasmacytoid dendritic cells (pDCs) leaves the bone marrow to mature in the lymphoid organs and in peripheral blood, and they function in the immune system by secreting large quantities of type 1 interferons in response to viral infections .

In the Immune cell section we have 188 plasmacytoid DC enriched genes and 12 of these genes has the highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. In addition, 181 genes are cell type group enriched and an additional 195 genes are enhanced in this cell type. Altogether, 564 genes are elevated and among these 77 also show highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed.

The plasmacytoid DCs were isolated from PBMCs. Debris and cell aggregates were eliminated by gating based on scatter profile. The NK, T- and B-cells were eliminated by selecting CD3neg/CD19neg/CD20neg/CD56neg population. The pDCs were sorted as HLA-Dr+/CD123+/CD11cneg/ CD14neg/ sub-population. 3,500 – 12,600 cells were sorted per sample for transcriptomic analysis by mRNA-sequencing. The transcriptome analysis shows that 45% (n=9126) of all human proteins (n=20090) are expressed in the pDCs and 181 of these genes show an elevated expression in pDCs compared to the other 17 cell types (see figure below).

Figure 3. The distribution of all genes across the five specificity categories based on transcript abundance in plasmacytoid DCs as well as in the other 17 cell types.

Table 5. Number of genes in the subdivided categories of elevated expression in plasmacytoid DCs.

Table 6. The genes with the highest level of enriched expression in plasmacytoid DCs. "nTPM" shows the transcript level as protein-coding transcripts per million. Specificity-score corresponds to the score calculated as the fold change of plasmacytoid DC expression to the second highest cell type.