T-cells

A T-cell, or T lymphocyte, is a type of white blood cell that plays a central role in cell-mediated immunity. They mature in the thymus and can be distinguished from other lymphocytes, by the presence of a T-cell receptor on the cell surface. There are several subsets of T-cells, such as cytotoxic T-cells, regulatory T-cells, helper T-cells and natural killer T-cells, with functions related to both innate and adaptive immunity.

In the Immune cell section we have 461 cell lineage enriched genes and 166 of these genes has the highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. In addition, 445 genes are cell lineage group enriched and an additional 16 genes are enhanced in this cell lineage. Altogether, 922 genes are elevated and among these 276 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 T-cell lineage as well as in the other 5 cell lineages.

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

Distribution in the six cell lineages
Detected in singleDetected in someDetected in manyDetected in all Total
Specificity
Lineage enriched 18408226 292
Group enriched 0034191 432
Lineage enhanced 16000 16
Total 2000423117 740

Table 2. The genes with the highest level of enriched expression in T-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 T-cell lineage expression to the second highest cell lineage.

Gene Description Cell lineage distribution nTPM Specificity score
FANK1 fibronectin type III and ankyrin repeat domains 1 Detected in single 61.2 612
CTLA4 cytotoxic T-lymphocyte associated protein 4 Detected in single 44.5 445
FOXP3 forkhead box P3 Detected in single 53.3 394
ELOVL4 ELOVL fatty acid elongase 4 Detected in single 23.7 238
PRSS35 serine protease 35 Detected in single 19.5 195
CD248 CD248 molecule Detected in single 21.8 144
NEFL neurofilament light Detected in single 11.2 113
CPA5 carboxypeptidase A5 Detected in single 56.4 102
REG4 regenerating family member 4 Detected in single 24.6 101
TMEM171 transmembrane protein 171 Detected in single 24.1 89
THEMIS thymocyte selection associated Detected in single 58.3 88
PMCH pro-melanin concentrating hormone Detected in single 9.5 85

T-regs

Regulatory T-cells (T-regs) has an important role in maintaining immunological tolerance, by suppressing autoreactive T-cells that have escaped negative regulation and by being involved in ending a T-cell mediated immune reaction.

In the Immune cell section we have 35 T-reg enriched genes and 8 of these genes has the highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. In addition, 222 genes are cell type group enriched and an additional 168 genes are enhanced in this cell type. Altogether, 425 genes are elevated and among these 182 also show highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed.

The T-regs were isolated from PBMCs. Debris and cell aggregates were eliminated based on scatter profiles. The T-reg population was sorted as CD3+/CD4+/CD127low/CD25+/CCR4+ sub-population of lymphocytes (FSClow/SSClow). 4,000 – 7,000 cells were sorted per sample for transcriptomic analysis by mRNA-sequencing. The transcriptome analysis shows that 45 % (n= 9042) of all human proteins (n=20090) are expressed in the T-regs and 222 of these genes show an elevated expression in T-regs 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 T-reg cells as well as in the other 17 cell types.

Table 3. Number of genes in the subdivided categories of elevated expression in T-reg cells.

Distribution in the 18 cell types
Detected in singleDetected in someDetected in manyDetected in all Total
Specificity
Immune cell enriched 151460 35
Group enriched 03416919 222
Immune cell enhanced 2839938 168
Total 438726827 425

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

Gene Description Cell type distribution nTPM Specificity score
FANK1 fibronectin type III and ankyrin repeat domains 1 Detected in some 61.2 16
SEMA3G semaphorin 3G Detected in single 1.4 15
FOXP3 forkhead box P3 Detected in some 53.3 11
HACD1 3-hydroxyacyl-CoA dehydratase 1 Detected in many 55.7 11
ACTG2 actin gamma 2, smooth muscle Detected in single 8.6 11
PMCH pro-melanin concentrating hormone Detected in some 9.5 10
DUSP4 dual specificity phosphatase 4 Detected in single 6.7 9
OGN osteoglycin Detected in single 1.7 9
TRIM16 tripartite motif containing 16 Detected in many 45.1 9
BOLL boule homolog, RNA binding protein Detected in single 1.5 9
RTKN2 rhotekin 2 Detected in some 16.7 8
CEP55 centrosomal protein 55 Detected in single 1.3 8

gdT-cells

Gamma delta T cells (gdT-cells) are a small subset of T cells with a gamma delta T-cell receptor (TCR), instead of the common alpha beta TCR, on the cell surface. gdT-cells seem to be able to recognize whole proteins and not only peptides on the surface of antigen presenting cells, and can also specifically and rapidly respond to phosphoantigens, which is a set of nonpeptidic phosphorylated isoprenoid precursors.

In the Immune cell section we have 13 gdT-cell enriched genes and 5 of these genes has the highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. In addition, 140 genes are cell type group enriched and an additional 74 genes are enhanced in this cell type. Altogether, 227 genes are elevated and among these 75 also show highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed.

The gdT-cells were isolated from PBMCs. Debris and cell aggregates were eliminated based on scatter profiles. Monocytes, and B-cells were eliminated by selecting CD14neg/CD19neg/CD3+ sub-population of lymphocytes (FSClow/SSClow). The gdTCR cells were sorted as gdTCR+/TCR Vα7.2neg cells, and 5,000 – 46,000 cells were sorted per sample for transcriptomic analysis by mRNA-sequencing The transcriptome analysis shows that 45 % (n= 9081) of all human proteins (n=20090) are expressed in the gdTCRs and 140 of these genes show an elevated expression in gdT-cells compared to the other 17 cell types (see figure below).

Figure 4. The distribution of all genes across the five specificity categories based on transcript abundance in gdT-cell cells as well as in the other 17 cell types.

Table 5. Number of genes in the subdivided categories of elevated expression in gdT-cell.

Distribution in the 18 cell types
Detected in singleDetected in someDetected in manyDetected in all Total
Specificity
Immune cell enriched 5260 13
Group enriched 01510520 140
Immune cell enhanced 1622297 74
Total 213914027 227

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

Gene Description Cell type distribution nTPM Specificity score
TMEM132C transmembrane protein 132C Detected in single 1.9 19
GSC goosecoid homeobox Detected in single 3.6 8
LIM2 lens intrinsic membrane protein 2 Detected in some 11.3 7
BNC2 basonuclin 2 Detected in single 2.5 5
KIR3DL1 killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1 Detected in single 1.8 4

MAIT T-cells

Mucosal associated invariant T-cells (MAIT T-cells) are involved in innate immunity and the defence against microbial activity and infection, but they also support the adaptive immune response and are thought to have a role in some autoimmune diseases.

In the Immune cell section we have 27 MAIT T-cell enriched genes and 3 of these genes has the highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. In addition, 149 genes are cell type group enriched and an additional 64 genes are enhanced in this cell type. Altogether, 240 genes are elevated and among these 84 also show highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed.

The MAIT T-cells were isolated from PBMCs. Debris and cell aggregates were eliminated by gating based on scatter profiles. Monocytes, and B-cells were eliminated by selecting CD14neg/CD19neg/CD3+ sub-population of lymphocytes (FSClow/SSClow). MAIT T-cells were sorted as gdTCRneg/TCR Vα7.2+/CD161+ cells and 3,800 – 12,000 cells were sorted per sample for transcriptomic analysis by mRNA-sequencing. The transcriptome analysis shows that 45 % (n= 9066) of all human proteins (n=20090) are expressed in the MAIT T-cells and 149 of these genes show an elevated expression in MAIT T-cells compared to the other 17 cell types (see figure below).

Figure 5. The distribution of all genes across the five specificity categories based on transcript abundance in MAIT T-cells as well as in the other 17 cell types.

Table 7. Number of genes in the subdivided categories of elevated expression in MAIT T-cells.

Distribution in the 18 cell types
Detected in singleDetected in someDetected in manyDetected in all Total
Specificity
Immune cell enriched 13950 27
Group enriched 01111820 149
Immune cell enhanced 827263 64
Total 214714923 240

Table 8. The genes with the highest level of enriched expression in MAIT T-cells."nTPM" shows the transcript level as protein-coding transcripts per million. Specificity-score corresponds to the score calculated as the fold change of MAIT T-cell expression to the second highest cell type.

Gene Description Cell type distribution nTPM Specificity score
NTN4 netrin 4 Detected in single 1.6 12
PRSS35 serine protease 35 Detected in some 19.5 9
TPBG trophoblast glycoprotein Detected in single 1.4 8
SLC4A10 solute carrier family 4 member 10 Detected in some 63.3 8
ITPKA inositol-trisphosphate 3-kinase A Detected in single 1.4 8
IL23R interleukin 23 receptor Detected in some 21.7 8
ME1 malic enzyme 1 Detected in some 16.0 7
TSPAN15 tetraspanin 15 Detected in many 19.5 6
ELOVL4 ELOVL fatty acid elongase 4 Detected in some 23.7 6
CYP27B1 cytochrome P450 family 27 subfamily B member 1 Detected in single 1.2 6
ROR2 receptor tyrosine kinase like orphan receptor 2 Detected in single 1.0 6
RORC RAR related orphan receptor C Detected in many 50.3 6

Naive CD4 T-cells

NaiveT-cells are located predominantly in lymphoid tissue and are mature T-cells that have not yet encountered its cognate antigen. Upon antigen activation they may further differentiate to memory T-cells.

In the Immune cell section we have 1 naive CD4 T-cell enriched genes and 0 of these genes has the highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. In addition, 203 genes are cell type group enriched and an additional 82 genes are enhanced in this cell type. Altogether, 286 genes are elevated and among these 123 also show highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed.

The naive CD4 T-cells were isolated from PBMCs. Debris and cell aggregates were eliminated based on scatter profiles. The naive CD4 T-cell population was sorted as CD3+/CD4+/CD8neg/CD45RA+ sub-population of lymphocytes (FSClow/SSClow). 10,000 – 77,000 cells were sorted per sample for transcriptomic analysis by mRNA-sequencing. The transcriptome analysis shows that 45 % (n= 9000) of all human proteins (n=20090) are expressed in the naive CD4 T-cells and 203 of these genes show an elevated expression in naive CD4 T-cells compared to the other 17 cell types (see figure below).

Figure 6. The distribution of all genes across the five specificity categories based on transcript abundance in naive CD4 T-cells as well as in the other 17 cell types.

Table 9. Number of genes in the subdivided categories of elevated expression in naive CD4 T-cells.

Distribution in the 18 cell types
Detected in singleDetected in someDetected in manyDetected in all Total
Specificity
Immune cell enriched 0010 1
Group enriched 02815916 203
Immune cell enhanced 1429363 82
Total 145719619 286

Table 10. The genes with the highest level of enriched expression in naive CD4 T-cells. "nTPM" shows the transcript level as protein-coding transcripts per million. Specificity-score corresponds to the score calculated as the fold change of naive CD4 T-cell expression to the second highest cell type.

Gene Description Cell type distribution nTPM Specificity score
FHIT fragile histidine triad diadenosine triphosphatase Detected in many 87.6 4

Memory CD4 T-cells

Memory T-cells provide the immune system with an effective defence against previously encountered pathogens, by having a long lifespan and the ability to quickly expand to large numbers upon re-exposure to their cognate antigen.

In the Immune cell section we have 2 memory CD4 T-cell enriched genes and 0 of these genes has the highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. In addition, 219 genes are cell type group enriched and an additional 23 genes are enhanced in this cell type. Altogether, 244 genes are elevated and among these 119 also show highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed.

The memory CD4 T-cells were isolated from PBMCs. Debris and cell aggregates were eliminated based on scatter profiles. The memory CD4 T-cell population was sorted as CD3+/CD4+/CD8neg/CD45RAneg sub-population of lymphocytes (FSClow/SSClow). 10,000 – 53,000 cells were sorted per sample for transcriptomic analysis by mRNA-sequencing. The transcriptome analysis shows that 45 % (n= 9116) of all human proteins (n=20090) are expressed in the memory CD4 T-cells and 219 of these genes show an elevated expression in memory CD4 T-cells compared to the other 17 cell types (see figure below).

Figure 7. The distribution of all genes across the five specificity categories based on transcript abundance in memory CD4 T-cells as well as in the other 17 cell types.

Table 11. Number of genes in the subdivided categories of elevated expression in memory CD4 T-cells.

Distribution in the 18 cell types
Detected in singleDetected in someDetected in manyDetected in all Total
Specificity
Immune cell enriched 1100 2
Group enriched 02517618 219
Immune cell enhanced 49100 23
Total 53518618 244

Table 12. The genes with the highest level of enriched expression in memory CD4 T-cells."nTPM" shows the transcript level as protein-coding transcripts per million. Specificity-score corresponds to the score calculated as the fold change of memory CD4 T-cell expression to the second highest cell type.

Gene Description Cell type distribution nTPM Specificity score
ADAM23 ADAM metallopeptidase domain 23 Detected in single 2.1 16
NEFL neurofilament light Detected in some 11.2 5

Naive CD8 T-cells

NaiveT-cells are located predominantly in lymphoid tissue and are mature T-cells that have not yet encountered its cognate antigen. Upon antigen activation they may further differentiate to memory T-cells.

In the Immune cell section we have 8 naive CD8 T-cell enriched genes and 0 of these genes has the highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. In addition, 238 genes are cell type group enriched and an additional 29 genes are enhanced in this cell type. Altogether, 275 genes are elevated and among these 121 also show highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed.

The naive CD8 T-cells were isolated from PBMCs. Debris and cell aggregates were eliminated based on scatter profiles. The naive CD8 T-cell population was sorted as CD3+/CD4neg/CD8+/CD45RA+ sub-population of lymphocytes (FSClow/SSClow). 10,000 – 77,000 cells were sorted per sample for transcriptomic analysis by mRNA-sequencing. The transcriptome analysis shows that 46 % (n= 9142) of all human proteins (n=20090) are expressed in the naive CD8 T-cells and 238 of these genes show an elevated expression in naive CD8 T-cells compared to the other 17 cell types (see figure below).

Figure 8. The distribution of all genes across the five specificity categories based on transcript abundance in naive CD8 T-cells as well as in the other 17 cell types.

Table 13. Number of genes in the subdivided categories of elevated expression in naive CD8 T-cells.

Distribution in the 18 cell types
Detected in singleDetected in someDetected in manyDetected in all Total
Specificity
Immune cell enriched 5300 8
Group enriched 03518320 238
Immune cell enhanced 81560 29
Total 135318920 275

Table 14. The genes with the highest level of enriched expression in naive CD8 T-cells. "nTPM" shows the transcript level as protein-coding transcripts per million. Specificity-score corresponds to the score calculated as the fold change of naive CD8 T-cell expression to the second highest cell type.

Gene Description Cell type distribution nTPM Specificity score
CFAP97D2 CFAP97 domain containing 2 Detected in single 4.0 12
CD248 CD248 molecule Detected in some 21.8 7
MXRA8 matrix remodeling associated 8 Detected in single 6.4 7
ZCCHC12 zinc finger CCHC-type containing 12 Detected in single 1.2 6
NRCAM neuronal cell adhesion molecule Detected in single 2.0 6
REG4 regenerating family member 4 Detected in some 24.6 6
SFRP5 secreted frizzled related protein 5 Detected in single 3.6 4
MT3 metallothionein 3 Detected in some 5.0 4

Memory CD8 T-cells

Memory T-cells provide the immune system with an effective defence against previously encountered pathogens, by having a long lifespan and the ability to quickly expand to large numbers upon re-exposure to their cognate antigen.

In the Immune cell section we have 0 memory CD8 T-cell enriched genes and 0 of these genes has the highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. In addition, 227 genes are cell type group enriched and an additional 18 genes are enhanced in this cell type. Altogether, 245 genes are elevated and among these 126 also show highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed.

The memory CD8 T-cells were isolated from PBMCs. Debris and cell aggregates were eliminated based on scatter profiles. The memory CD8 T-cell population was sorted as CD3+/CD4neg/ CD8+/CD45RAneg sub-population of lymphocytes (FSClow/SSClow). 7,000 – 21,000 cells were sorted per sample for transcriptomic analysis by mRNA-sequencing. The transcriptome analysis shows that 46 % (n= 9155) of all human proteins (n=20090) are expressed in the memory CD8 T-cells and 227 of these genes show an elevated expression in memory CD8 T-cells compared to the other 17 cell types (see figure below).

Figure . The distribution of all genes across the five specificity categories based on transcript abundance in memory CD8 T-cells as well as in the other 17 cell types.

Table 15. Number of genes in the subdivided categories of elevated expression in memory CD8 T-cells.

Distribution in the 18 cell types
Detected in singleDetected in someDetected in manyDetected in all Total
Specificity
Immune cell enriched 0000 0
Group enriched 02118620 227
Immune cell enhanced 1881 18
Total 12919421 245

Table 16. The genes with the highest level of enriched expression in memory CD8 T-cells. "nTPM" shows the transcript level as protein-coding transcripts per million. Specificity-score corresponds to the score calculated as the fold change ofmemory CD8 T-cell expression to the second highest cell type.

Gene Description Cell type distribution nTPM Specificity score