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.

Distribution in the six cell lineages
Detected in singleDetected in someDetected in manyDetected in all Total
Specificity
Lineage enriched 13207230 234
Group enriched 00419171 590
Lineage enhanced 6000 6
Total 1380491201 830

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 117.6 1177
TPM2 tropomyosin 2 Detected in single 398.6 920
ASIP agouti signaling protein Detected in single 134.8 356
KRT5 keratin 5 Detected in single 32.6 326
TNFRSF21 TNF receptor superfamily member 21 Detected in single 69.2 303
GPM6B glycoprotein M6B Detected in single 77.7 268
SCARA5 scavenger receptor class A member 5 Detected in single 21.1 211
SHD Src homology 2 domain containing transforming protein D Detected in single 17.8 178
NTM neurotrimin Detected in single 17.4 175
SCT secretin Detected in single 126.7 138
KCNA5 potassium voltage-gated channel subfamily A member 5 Detected in single 12.2 122
SERPINF1 serpin family F member 1 Detected in all 1454.4 121

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.

Distribution in the 18 cell types
Detected in singleDetected in someDetected in manyDetected in all Total
Specificity
Immune cell enriched 15850 28
Group enriched 08013748 265
Immune cell enhanced 1340292 84
Total 2812817150 377

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
MRC1 mannose receptor C-type 1 Detected in single 4.8 16
CRIP3 cysteine rich protein 3 Detected in many 44.6 16
CD1E CD1e molecule Detected in some 62.5 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 465.9 12
PKIB cAMP-dependent protein kinase inhibitor beta Detected in some 34.8 11
NDRG2 NDRG family member 2 Detected in many 204.4 11
DEPTOR DEP domain containing MTOR interacting protein Detected in some 20.3 11
EHF ETS homologous factor Detected in single 1.7 11
C19orf33 chromosome 19 open reading frame 33 Detected in many 22.2 10
SDS serine dehydratase Detected in some 11.6 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 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.

Distribution in the 18 cell types
Detected in singleDetected in someDetected in manyDetected in all Total
Specificity
Immune cell enriched 10245347 188
Group enriched 0688429 181
Immune cell enhanced 49516926 195
Total 15116418762 564

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 117.6 1177
TPM2 tropomyosin 2 Detected in single 398.6 812
ASIP agouti signaling protein Detected in single 134.8 356
KRT5 keratin 5 Detected in single 32.6 326
GPM6B glycoprotein M6B Detected in single 77.7 220
SHD Src homology 2 domain containing transforming protein D Detected in single 17.8 178
NTM neurotrimin Detected in single 17.4 175
SCT secretin Detected in single 126.7 138
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 10.6 106
EPHA2 EPH receptor A2 Detected in single 9.4 94