Natural killer cells (NK-cells), are a type of cytotoxic lymphocyte critical to the innate immune system. NK-cells respond to virus-infected cells, and also to tumor formation, and the ability to recognize stressed cells in the absence of antibodies and MHC allows for a much faster immune reaction as well as destruction of cells that cannot be detected and destroyed by other immune cells. In addition, NK-cells secret cytokines that boost the antitumor immunity and they also display memory cell-like features.

In the Immune cell section we have 64 cell lineage 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, 278 genes are cell lineage group enriched and an additional 1 genes are enhanced in this cell lineage. Altogether, 343 genes are elevated and among these 94 also show highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed.

The NK-cells were isolated from PBMCs. Debris and cell aggregates were eliminated based on scatter profiles. Monocytes, T- and B-cells were eliminated by selecting CD14neg/SSClow and CD3neg/CD19neg sub-population of lymphocytes (FSClow/SSClow). At the final step, population of CD56+/SSClow was selected and 2,300 – 5,000 cells were sorted per sample for transcriptomic analysis by mRNA-sequencing. The transcriptome analysis shows that 46% (n=9201) of all human proteins (n=20090) are expressed in the NK-cells and 152 of these genes show an elevated expression in NK-cells compared to the other 17 cell types (see figure below).

Figure 1. The distribution of all genes across the five specificity categories based on transcript abundance in NK-cells as well as in the other 17 cell types.

Table 1. Number of genes in the subdivided categories of elevated expression in NK-cells.

Distribution in the 18 cell types
Detected in singleDetected in someDetected in manyDetected in all Total
Immune cell enriched 48970 64
Group enriched 0488717 152
Immune cell enhanced 2827484 107
Total 768414221 323

Table 2. The genes with the highest level of enriched expression in NK-cells. "nTPM" shows the transcript level as protein-coding transcripts per million. Specificity-score corresponds to the score calculated as the fold change of NK-cell expression to the second highest cell type.

Gene Description Cell type distribution nTPM Specificity score
COX6A2 cytochrome c oxidase subunit 6A2 Detected in single 15.0 150
ZMAT4 zinc finger matrin-type 4 Detected in single 8.6 86
APOC2 apolipoprotein C2 Detected in single 3.2 30
KIR2DL4 killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4 Detected in single 2.8 28
BAALC BAALC binder of MAP3K1 and KLF4 Detected in single 3.7 28
EXOC1L exocyst complex component 1 like Detected in single 1.9 20
NFILZ NFIL3 like basic leucine zipper Detected in single 17.5 20
SERPINE1 serpin family E member 1 Detected in single 9.5 20
RAMP1 receptor activity modifying protein 1 Detected in some 70.1 18
TRIM54 tripartite motif containing 54 Detected in single 3.6 17
LGALS9B galectin 9B Detected in single 12.7 17
PRDM16 PR/SET domain 16 Detected in single 2.4 16