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 resource we have 460 cell lineage enriched genes and 171 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 15 genes are enhanced in this cell lineage. Altogether, 920 genes are elevated and among these 275 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 18508125 291
Group enriched 0033893 431
Lineage enhanced 15000 15
Total 2000419118 737

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 61.4 614
CTLA4 cytotoxic T-lymphocyte associated protein 4 Detected in single 42.6 427
FOXP3 forkhead box P3 Detected in single 52.0 360
ELOVL4 ELOVL fatty acid elongase 4 Detected in single 23.8 238
PRSS35 serine protease 35 Detected in single 19.5 196
CD248 CD248 molecule Detected in single 21.9 145
NEFL neurofilament light chain Detected in single 11.2 113
CPA5 carboxypeptidase A5 Detected in single 56.6 101
REG4 regenerating family member 4 Detected in single 24.7 100
TMEM171 transmembrane protein 171 Detected in single 24.1 89
PMCH pro-melanin concentrating hormone Detected in single 9.6 86
THEMIS thymocyte selection associated Detected in single 57.0 83

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 resource we have 36 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, 223 genes are cell type group enriched and an additional 172 genes are enhanced in this cell type. Altogether, 431 genes are elevated and among these 187 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= 9015) of all human proteins (n=20162) are expressed in the T-regs and 223 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 19 cell types
Detected in singleDetected in someDetected in manyDetected in all Total
Specificity
Immune cell enriched 161460 36
Group enriched 03217219 223
Immune cell enhanced 2841958 172
Total 448727327 431

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
ENSG00000290184 novel protein Detected in single 2.0 17
FANK1 fibronectin type III and ankyrin repeat domains 1 Detected in some 61.4 16
SEMA3G semaphorin 3G Detected in single 1.4 15
FOXP3 forkhead box P3 Detected in some 52.0 11
HACD1 3-hydroxyacyl-CoA dehydratase 1 Detected in many 55.9 11
ACTG2 actin gamma 2, smooth muscle Detected in single 8.6 11
PMCH pro-melanin concentrating hormone Detected in some 9.6 10
BOLL boule homolog, RNA binding protein Detected in single 1.5 10
TRIM16 tripartite motif containing 16 Detected in many 44.9 9
OGN osteoglycin Detected in single 1.7 9
DUSP4 dual specificity phosphatase 4 Detected in single 6.8 9
RTKN2 rhotekin 2 Detected in some 16.7 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 resource 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, 141 genes are cell type group enriched and an additional 74 genes are enhanced in this cell type. Altogether, 228 genes are elevated and among these 74 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= 9048) of all human proteins (n=20162) are expressed in the gdTCRs and 141 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 19 cell types
Detected in singleDetected in someDetected in manyDetected in all Total
Specificity
Immune cell enriched 5260 13
Group enriched 01510620 141
Immune cell enhanced 1623287 74
Total 214014027 228

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 1.8 19
GSC goosecoid homeobox Detected in single 3.7 8
LIM2 lens intrinsic membrane protein 2 Detected in some 11.3 7
KIR3DL1 killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1 Detected in single 1.8 5
BNC2 basonuclin 2 Detected in single 2.5 5
TARP TCR gamma alternate reading frame protein Detected in many 1208.2 5

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 resource 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, 154 genes are cell type group enriched and an additional 63 genes are enhanced in this cell type. Altogether, 244 genes are elevated and among these 85 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= 9036) of all human proteins (n=20162) are expressed in the MAIT T-cells and 154 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 19 cell types
Detected in singleDetected in someDetected in manyDetected in all Total
Specificity
Immune cell enriched 14850 27
Group enriched 01112320 154
Immune cell enhanced 825273 63
Total 224415523 244

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
IL23R interleukin 23 receptor Detected in some 24.1 9
TPBG trophoblast glycoprotein Detected in single 1.4 8
SLC4A10 solute carrier family 4 member 10 Detected in some 63.4 8
ITPKA inositol-trisphosphate 3-kinase A Detected in single 1.4 8
ME1 malic enzyme 1 Detected in some 16.0 7
COLQ collagen like tail subunit of asymmetric acetylcholinesterase Detected in some 61.0 6
TSPAN15 tetraspanin 15 Detected in many 19.5 6
CYP27B1 cytochrome P450 family 27 subfamily B member 1 Detected in single 1.2 6
ELOVL4 ELOVL fatty acid elongase 4 Detected in some 23.8 6
ROR2 receptor tyrosine kinase like orphan receptor 2 Detected in single 1.0 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 resource 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, 204 genes are cell type group enriched and an additional 84 genes are enhanced in this cell type. Altogether, 289 genes are elevated and among these 126 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 44 % (n= 8967) of all human proteins (n=20162) are expressed in the naive CD4 T-cells and 204 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 19 cell types
Detected in singleDetected in someDetected in manyDetected in all Total
Specificity
Immune cell enriched 0010 1
Group enriched 02915916 204
Immune cell enhanced 1333353 84
Total 136219519 289

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 87.9 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 resource 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, 221 genes are cell type group enriched and an additional 25 genes are enhanced in this cell type. Altogether, 248 genes are elevated and among these 122 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= 9085) of all human proteins (n=20162) are expressed in the memory CD4 T-cells and 221 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 19 cell types
Detected in singleDetected in someDetected in manyDetected in all Total
Specificity
Immune cell enriched 1100 2
Group enriched 02517818 221
Immune cell enhanced 510100 25
Total 63618818 248

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 chain 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 resource 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, 241 genes are cell type group enriched and an additional 29 genes are enhanced in this cell type. Altogether, 278 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 45 % (n= 9103) of all human proteins (n=20162) are expressed in the naive CD8 T-cells and 241 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 19 cell types
Detected in singleDetected in someDetected in manyDetected in all Total
Specificity
Immune cell enriched 5300 8
Group enriched 03518620 241
Immune cell enhanced 81470 29
Total 135219320 278

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 13
CD248 CD248 molecule Detected in some 21.9 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 2.1 6
REG4 regenerating family member 4 Detected in some 24.7 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 resource 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, 230 genes are cell type group enriched and an additional 18 genes are enhanced in this cell type. Altogether, 248 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 45 % (n= 9116) of all human proteins (n=20162) are expressed in the memory CD8 T-cells and 230 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 19 cell types
Detected in singleDetected in someDetected in manyDetected in all Total
Specificity
Immune cell enriched 0000 0
Group enriched 02118920 230
Immune cell enhanced 1971 18
Total 13019621 248

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