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 resource we have 301 cell lineage enriched genes and 149 of these genes has the highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. In addition, 280 genes are cell lineage group enriched and an additional 6 genes are enhanced in this cell lineage. Altogether, 587 genes are elevated and among these 226 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 860489 143
Group enriched 0020566 271
Lineage enhanced 6000 6
Total 92025375 420

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 807.5 730
ENSG00000275063 Detected in single 404.4 447
ENSG00000277856 Detected in single 34.5 345
COL19A1 collagen type XIX alpha 1 chain Detected in single 32.0 299
IGLL5 immunoglobulin lambda like polypeptide 5 Detected in many 619.6 247
ENSG00000277836 Detected in single 17.7 178
WNT16 Wnt family member 16 Detected in single 15.6 146
KLHL14 kelch like family member 14 Detected in single 10.6 106
MS4A1 membrane spanning 4-domains A1 Detected in many 630.0 96
CPNE5 copine 5 Detected in single 51.7 93
CD19 CD19 molecule Detected in many 172.5 90
STEAP1B STEAP family member 1B Detected in single 8.4 85

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 resource we have 20 naive B-cell 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, 367 genes are cell type group enriched and an additional 114 genes are enhanced in this cell type. Altogether, 501 genes are elevated and among these 205 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 45% (n=9149) of all human proteins (n=20162) are expressed in the naive B-cells and 367 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 19 cell types
Detected in singleDetected in someDetected in manyDetected in all Total
Specificity
Immune cell enriched 11900 20
Group enriched 022811227 367
Immune cell enhanced 2940396 114
Total 4027715133 501

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
GPR17 G protein-coupled receptor 17 Detected in single 1.9 19
KCNG1 potassium voltage-gated channel modifier subfamily G member 1 Detected in single 7.1 18
DSP desmoplakin Detected in single 2.3 16
APBB2 amyloid beta precursor protein binding family B member 2 Detected in single 5.5 16
JSRP1 junctional sarcoplasmic reticulum protein 1 Detected in single 2.7 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 3.4 6
SLC2A5 solute carrier family 2 member 5 Detected in some 23.3 5
H4C4 H4 clustered histone 4 Detected in single 3.5 4
DBNDD1 dysbindin domain containing 1 Detected in some 12.9 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 resource we have 23 memory 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, 367 genes are cell type group enriched and an additional 95 genes are enhanced in this cell type. Altogether, 485 genes are elevated and among these 205 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=9204) of all human proteins (n=20162) are expressed in the memory B-cells and 367 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 19 cell types
Detected in singleDetected in someDetected in manyDetected in all Total
Specificity
Immune cell enriched 17510 23
Group enriched 022611328 367
Immune cell enhanced 2139323 95
Total 3827014631 485

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
SPACA3 sperm acrosome associated 3 Detected in single 1.2 5
SLC16A4 solute carrier family 16 member 4 Detected in single 1.5 4
NTNG1 netrin G1 Detected in single 1.1 4
PCDHGA12 protocadherin gamma subfamily A, 12 Detected in single 1.2 4