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 Blood Atlas we have 347 cell lineage enriched genes and 54 of these genes has the highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. In addition, 771 genes are cell lineage group enriched and an additional 21 genes are enhanced in this cell lineage. Altogether, 1139 genes are elevated and among these 219 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 23709713 347
Group enriched 0067299 771
Lineage enhanced 20010 21
Total 2570770112 1139

Table 2. The genes with the highest level of enriched expression in dendritic cell lineage. "pTPM" 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 pTPM Specificity score
TPM2 tropomyosin 2 Detected in single 499.2 727
LRRC26 leucine rich repeat containing 26 Detected in single 142.6 408
ASIP agouti signaling protein Detected in single 163.7 321
TNFRSF21 TNF receptor superfamily member 21 Detected in single 85.3 309
GPM6B glycoprotein M6B Detected in single 95.3 240
KRT5 keratin 5 Detected in single 33.1 197
SCARA5 scavenger receptor class A member 5 Detected in single 25.6 173
NTM neurotrimin Detected in single 21.1 157
SCT secretin Detected in single 136.1 152
SHD Src homology 2 domain containing transforming protein D Detected in single 18.8 148
KCNA5 potassium voltage-gated channel subfamily A member 5 Detected in single 15.3 134
KCNK10 potassium two pore domain channel subfamily K member 10 Detected in single 12.8 123

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 Blood Atlas we have 51 myeloid DC enriched genes and 6 of these genes has the highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. In addition, 324 genes are cell type group enriched and an additional 152 genes are enhanced in this cell type. Altogether, 527 genes are elevated and among these 98 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 52% (n=10173) of all human proteins (n=19,670) are expressed in the myeloid DCs and 324 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
Cell type enriched 321540 51
Group enriched 014415723 324
Cell type enhanced 3275450 152
Total 6423420623 527

Table 4. The genes with the highest level of enriched expression in myeloid DCs. "pTPM" 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 pTPM Specificity score
GPR31 G protein-coupled receptor 31 Detected in single 0.6 28
ODF3L1 outer dense fiber of sperm tails 3 like 1 Detected in single 0.4 25
PRB2 proline rich protein BstNI subfamily 2 Detected in single 0.3 23
CD207 CD207 molecule Detected in single 1.2 18
ARSE arylsulfatase E (chondrodysplasia punctata 1) Detected in single 0.2 17
CLEC14A C-type lectin domain containing 14A Detected in single 0.1 16
MRC1 mannose receptor C-type 1 Detected in single 5.2 15
EBLN1 endogenous Bornavirus like nucleoprotein 1 Detected in single 0.1 14
CRIP3 cysteine rich protein 3 Detected in many 49.1 14
ADGRG6 adhesion G protein-coupled receptor G6 Detected in single 0.9 13
CRABP1 cellular retinoic acid binding protein 1 Detected in single 0.1 13
CD1E CD1e molecule Detected in some 67.6 13

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 Blood Atlas we have 266 plasmacytoid DC enriched genes and 45 of these genes has the highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. In addition, 234 genes are cell type group enriched and an additional 318 genes are enhanced in this cell type. Altogether, 818 genes are elevated and among these 155 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 53% (n=10456) of all human proteins (n=19,670) are expressed in the pDCs and 234 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
Cell type enriched 17651354 266
Group enriched 01289313 234
Cell type enhanced 6512810520 318
Total 24130723337 818

Table 6. The genes with the highest level of enriched expression in plasmacytoid DCs. "pTPM" 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 pTPM Specificity score
TPM2 tropomyosin 2 Detected in single 499.2 727
LRRC26 leucine rich repeat containing 26 Detected in single 142.6 408
ASIP agouti signaling protein Detected in single 163.7 321
GPM6B glycoprotein M6B Detected in single 95.3 222
KRT5 keratin 5 Detected in single 33.1 197
NTM neurotrimin Detected in single 21.1 157
SCT secretin Detected in single 136.1 152
SHD Src homology 2 domain containing transforming protein D Detected in single 18.8 148
KCNA5 potassium voltage-gated channel subfamily A member 5 Detected in single 15.3 134
SCARA5 scavenger receptor class A member 5 Detected in single 25.6 117
MYMX myomixer, myoblast fusion factor Detected in single 12.7 115
EPHA2 EPH receptor A2 Detected in single 11.2 115