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 resource we have 232 cell lineage enriched genes and 18 of these genes has the highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. In addition, 582 genes are cell lineage group enriched and an additional 5 genes are enhanced in this cell lineage. Altogether, 819 genes are elevated and among these 117 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.

Distribution in the six cell lineages
Detected in singleDetected in someDetected in manyDetected in all Total
Specificity
Lineage enriched 13107328 232
Group enriched 00414168 582
Lineage enhanced 5000 5
Total 1360487196 819

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.

Gene
Description
Cell lineage distribution
nTPM
Specificity score
LRRC26 leucine rich repeat containing 26 Detected in single 117.8 1179
TPM2 tropomyosin 2 Detected in single 399.5 922
ASIP agouti signaling protein Detected in single 125.9 340
KRT5 keratin 5 Detected in single 32.6 327
GPM6B glycoprotein M6B Detected in single 78.2 313
TNFRSF21 TNF receptor superfamily member 21 Detected in single 69.3 302
SCARA5 scavenger receptor class A member 5 Detected in single 21.1 212
PTPRS protein tyrosine phosphatase receptor type S Detected in single 153.7 197
SHD Src homology 2 domain containing transforming protein D Detected in single 17.8 179
NTM neurotrimin Detected in single 17.5 175
SCT secretin Detected in single 126.8 137
KCNA5 potassium voltage-gated channel subfamily A member 5 Detected in single 12.2 122

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 resource 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, 263 genes are cell type group enriched and an additional 82 genes are enhanced in this cell type. Altogether, 373 genes are elevated and among these 64 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=9048) of all human proteins (n=20162) are expressed in the myeloid DCs and 263 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.

Distribution in the 19 cell types
Detected in singleDetected in someDetected in manyDetected in all Total
Specificity
Immune cell enriched 15850 28
Group enriched 08113547 263
Immune cell enhanced 1338301 82
Total 2812717048 373

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.

Gene
Description
Cell type distribution
nTPM
Specificity score
XCR1 X-C motif chemokine receptor 1 Detected in single 2.3 24
MRC1 mannose receptor C-type 1 Detected in single 4.8 16
CRIP3 cysteine rich protein 3 Detected in many 44.7 16
CD1E CD1e molecule Detected in some 62.6 14
HTR7 5-hydroxytryptamine receptor 7 Detected in single 1.4 12
CD207 CD207 molecule Detected in single 1.1 12
CLEC10A C-type lectin domain containing 10A Detected in many 466.5 12
NDRG2 NDRG family member 2 Detected in many 204.5 11
DEPTOR DEP domain containing MTOR interacting protein Detected in some 20.3 11
EHF ETS homologous factor Detected in single 1.7 11
PKIB cAMP-dependent protein kinase inhibitor beta Detected in some 34.9 10
C19orf33 chromosome 19 open reading frame 33 Detected in many 22.3 10

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 resource we have 186 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, 177 genes are cell type group enriched and an additional 198 genes are enhanced in this cell type. Altogether, 561 genes are elevated and among these 71 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=9089) of all human proteins (n=20162) are expressed in the pDCs and 177 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.

Distribution in the 19 cell types
Detected in singleDetected in someDetected in manyDetected in all Total
Specificity
Immune cell enriched 10145337 186
Group enriched 0707829 177
Immune cell enhanced 49557123 198
Total 15017018259 561

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.

Gene
Description
Cell type distribution
nTPM
Specificity score
LRRC26 leucine rich repeat containing 26 Detected in single 117.8 1179
TPM2 tropomyosin 2 Detected in single 399.5 811
ASIP agouti signaling protein Detected in single 125.9 340
KRT5 keratin 5 Detected in single 32.6 327
GPM6B glycoprotein M6B Detected in single 78.2 230
PTPRS protein tyrosine phosphatase receptor type S Detected in single 153.7 197
SHD Src homology 2 domain containing transforming protein D Detected in single 17.8 179
NTM neurotrimin Detected in single 17.5 175
SCT secretin Detected in single 126.8 137
KCNA5 potassium voltage-gated channel subfamily A member 5 Detected in single 12.2 122
SCARA5 scavenger receptor class A member 5 Detected in single 21.1 121
MYMX myomixer, myoblast fusion factor Detected in single 10.6 107