B-cells

B cells, also known as B lymphocytes, are a type of white blood cell of the lymphocyte subtype, that mature in the bone marrow. They express B cell receptors on their surface that allow them to bind specific antigens, and function in the humoral immunity component of the adaptive immune system by secreting antibodies. Additionally, B cells are classical antigen-presenting cells (APCs) and also secrete cytokines.

In the Immune cell section we have 303 cell lineage enriched genes and 156 of these genes has the highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. In addition, 286 genes are cell lineage group enriched and an additional 5 genes are enhanced in this cell lineage. Altogether, 594 genes are elevated and among these 235 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 B-cell lineage as well as in the other five cell lineages.

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

Distribution in the six cell lineages
Detected in singleDetected in someDetected in manyDetected in all Total
Specificity
Lineage enriched 880498 145
Group enriched 0021265 277
Lineage enhanced 5000 5
Total 93026173 427

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

Gene Description Cell lineage distribution nTPM Specificity score
VPREB3 V-set pre-B cell surrogate light chain 3 Detected in many 803.7 732
AC233755.1 immunoglobulin heavy variable 4-38-2-like Detected in single 403.0 447
AC233755.2 Detected in single 34.3 344
COL19A1 collagen type XIX alpha 1 chain Detected in single 31.9 299
IGLL5 immunoglobulin lambda like polypeptide 5 Detected in many 615.5 246
AC141272.1 Detected in single 17.6 176
AC136616.2 Detected in single 21.7 150
WNT16 Wnt family member 16 Detected in single 15.6 146
KLHL14 kelch like family member 14 Detected in single 10.5 106
CPNE5 copine 5 Detected in single 51.6 105
MS4A1 membrane spanning 4-domains A1 Detected in many 627.0 96
CD19 CD19 molecule Detected in many 172.1 89

Naive B-cells

Naive B-cells reside in lymph nodes and are B-cells not yet exposed to an antigen. Upon antigen activation they will differentiate to either plasma cells or memory B-cells.

In the Immune cell section we have 21 naive B-cell 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, 364 genes are cell type group enriched and an additional 113 genes are enhanced in this cell type. Altogether, 498 genes are elevated and among these 206 also show highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed.

The naive B-cells were isolated from PBMCs. Debris and cell aggregates were eliminated based on scatter profiles. Subsequently, monocytes, were eliminated by selecting CD14neg/SSClow sub-population of lymphocytes (FSClow/SSClow). B-cells population was selected as CD19+/CD3neg population. At the final step, population of CD19+/CD27neg naïve B-cells was sorted and 20,000 – 50,000 cells were sorted per sample for transcriptomic analysis by mRNA-sequencing. The transcriptome analysis shows that 46% (n=9186) of all human proteins (n=20090) are expressed in the naive B-cells and 364 of these genes show an elevated expression in naive B-cells 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 naive B-cells-cells as well as in the other 17 cell types.

Table 3. Number of genes in the subdivided categories of elevated expression in naive B-cells.

Distribution in the 18 cell types
Detected in singleDetected in someDetected in manyDetected in all Total
Specificity
Immune cell enriched 13800 21
Group enriched 022811125 364
Immune cell enhanced 2938406 113
Total 4227415131 498

Table 4. The genes with the highest level of enriched expression in naive B-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 B-cell expression to the second highest cell type.

Gene Description Cell type distribution nTPM Specificity score
KCNG1 potassium voltage-gated channel modifier subfamily G member 1 Detected in single 7.1 20
GPR17 G protein-coupled receptor 17 Detected in single 1.9 19
APBB2 amyloid beta precursor protein binding family B member 2 Detected in single 5.6 14
DSP desmoplakin Detected in single 2.0 13
AC136616.3 Detected in single 5.0 11
JSRP1 junctional sarcoplasmic reticulum protein 1 Detected in single 2.6 10
SLC26A4 solute carrier family 26 member 4 Detected in single 1.0 8
TUBB3 tubulin beta 3 class III Detected in single 2.5 8
CCN2 cellular communication network factor 2 Detected in some 8.1 7
AKAP6 A-kinase anchoring protein 6 Detected in single 3.5 6
SLC2A5 solute carrier family 2 member 5 Detected in some 23.3 5
H4C4 H4 clustered histone 4 Detected in single 3.4 4

Memory B-cells

Memory B-cells are formed within germinal centers following primary infection, and are important in generating an accelerated and more robust antibody-mediated immune response in the case of re-infection. They are localized in areas of facilitated antigen encounter and compared to naive B-cells they have higher affinity to the immunizing antigen, a lifespan of decades instead of weeks, and faster and more efficient proliferation and differentiation.

In the Immune cell section we have 26 memory B-cell 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, 366 genes are cell type group enriched and an additional 95 genes are enhanced in this cell type. Altogether, 487 genes are elevated and among these 215 also show highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed.

The memory B-cells were isolated from PBMCs. Debris and cell aggregates were eliminated based on scatter profiles. Subsequently, monocytes were eliminated by selecting CD14neg/SSClow sub-population of lymphocytes (FSClow/SSClow). B-cells population was selected as CD19+/CD3neg population. At the final step, population of CD19+/CD27+ memory B-cells was sorted and 5,000 – 19,000 cells were sorted per sample for transcriptomic analysis by mRNA-sequencing. The transcriptome analysis shows that 46% (n=9222) of all human proteins (n=20090) are expressed in the memory B-cells and 366 of these genes show an elevated expression in memory B-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 memory B-cells as well as in the other 17 cell types.

Table 5. Number of genes in the subdivided categories of elevated expression in memory B-cells.

Distribution in the 18 cell types
Detected in singleDetected in someDetected in manyDetected in all Total
Specificity
Immune cell enriched 20510 26
Group enriched 022611426 366
Immune cell enhanced 1939343 95
Total 3927014929 487

Table 6. The genes with the highest level of enriched expression in memory B-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 B-cells expression to the second highest cell type.

Gene Description Cell type distribution nTPM Specificity score
TAS1R3 taste 1 receptor member 3 Detected in single 1.6 17
ARL14 ADP ribosylation factor like GTPase 14 Detected in single 1.8 15
APOD apolipoprotein D Detected in single 5.0 14
RASSF6 Ras association domain family member 6 Detected in single 2.7 8
IL5 interleukin 5 Detected in single 1.4 8
DKKL1 dickkopf like acrosomal protein 1 Detected in single 1.7 6
H3C7 H3 clustered histone 7 Detected in single 1.8 5
COL4A4 collagen type IV alpha 4 chain Detected in single 4.1 5
SPACA3 sperm acrosome associated 3 Detected in single 1.2 5
PXDC1 PX domain containing 1 Detected in single 1.2 4
SLC16A4 solute carrier family 16 member 4 Detected in single 1.5 4
NPIPB15 nuclear pore complex interacting protein family member B15 Detected in single 1.0 4