The Leukocyte-specific proteome

Blood & immune cells develop from hematopoietic stem cells (HSCs), which are multipotent cells with the ability to self-renew that can differentiate into all types of blood cells included in the lymphoid and the myeloid lineage. These cells reside in the medullary region of the bone marrow. Mature blood cells and immune cells circulate in the blood, and certain immune cells also reside within different tissues, e.g. liver and placenta. The immune cells within the brain are here divided into two main groups, the central nervous system macrophages (microglia and barrier-associated marcophages) and leukocytes.

Leukocytes is the name for white blood cells, and includes; granulocytes (neutrophils, eosinophils, and basophils), monocytes (macrophages), and lymphocytes (T cells and B cells). All Leukocytes can be found circulating the blood of the brain, while it is mainly T- cells that infiltrate the brain parenchyma, suggested memory T-cells (Smolders J et al. (2018)). B-cells and plasma (a type of B-cell) cells are rarely, but can occationally be found in the brain parenchyma (Jain RW et al. (2022)).


Learn more about the different immune cell and their expression profiles compared to eachother here, explored in detail using flowcytometric sorted immune cells and RNAsequencing, or explore the tissue specific immune cells and their expression profile compared to cell types throughout peripheral tissues.

This page focuses on the snRNAseq analysis of cell types within the brain, and gene expression in brain immune cells compared to other cells and clusters of the brain.

Transcriptome analysis shows that 68% (n=13765) of all human proteins (n=20162) are detected in blood & immune cells and 1039 of these genes show an elevated expression in any blood & immune cells compared to other brain cell types.


The blood & immune cell transcriptome

The snRNA-seq-based blood & immune cell transcriptome can be analyzed with regard to specificity, illustrating the number of genes with elevated expression in blood & immune cell type compared to other brain cell types (Table 1). Genes with an elevated expression are divided into three subcategories:

  • Cell type enriched: At least four-fold higher mRNA level in a certain cell type compared to any other cell type within the brain.
  • Group enriched: At least four-fold higher average mRNA level in a group of 2-10 cell types compared to any other cell type within the brain.
  • Cell type enhanced: At least four-fold higher mRNA level in a cell certain cell type compared to the average level in all other cell types within the brain.

Table 1. Number of genes in the subdivided specificity categories of elevated expression in the analyzed blood & immune cell types.
Cell type
Tissue origin
Cell type enriched
Group enriched
Cell type enhanced
Total elevated
Leukocyte Amygdala, Basal ganglia, Cerebellum, Cerebral cortex, Hippocampus, Hypothalamus, Medulla oblongata, Midbrain, Pons, Spinal cord, Thalamus 267 304 468 1039

Expression profile of different cell markers

The snRNA-seq-based analysis of brain cell types highlights genes with elevated expression in immune cells compared to other brain cell types. The immune cells were found in a couple different superclusters (such as miscellaneous) in Siletti K et al. (2023). Here, we separated the immune cells from the neuron clusters, based on the cell identity provided, enabling a cell type comparison to the other brain cell types and superclusters.

Utilizing the immune cell expression profiles we are able to explore the specific subtypes of leukocytes thought the brain dataset.

T-cell markers expressed in brain leukocytes

TRBV28 and TRAV17 are both T-cell enriched and show specific expression in T-cells in peripheral tissues, when comparing different immune cells. Both genes are expressed by the population of leukocytes in the brain, with a differences in the regional expression level.
THEMIS and PDCD1 are also T-cell related proteins, with an enriched expression in brain leukocytes, and found in all brain regions. PDCD1 show highest expression in memory T-cells and show a higher expression in spinal cord compare to the other brain regions. THEMIS show high expression in Naive T-cells, as well as a subset of neuronal cells. The immunohistochemical images are showing the detection in immune-related tissue types.


THEMIS - cerebral cortex
02004006008001,0001,200nTPM
THEMIS - Cerebral cortex

THEMIS - thymus


PDCD1 - spinal cord
0102030405060nTPM
PDCD1 - Spinal cord

PDCD1 - tonsil

B-cell markers expressed in brain leukocytes

FCRL1 is a B-cell specific marker, while FCRL2 and FCRL5 show expression in both B-cells and plasma cells, based on periperal tissue cell type expression profiles. All three genes show some variation across the brain regions. CXCR5 and MS4A1 are both specific for B-cells, and when exploring the protein location using immunohistochemistry and images available in the Tissue Atlas resource, both targets seems to be related to the vasculature. This suggests that at least a number of cells represented in this dataset are perivascular lymphocytes, B-cells located within the perivascular space. And interestingly, CXCR5 is not found among the spinal cord leukocytes.


CXCR5 - cerebellum
0246810nTPM
CXCR5 - Cerebellum

CXCR5


MS4A1 - cerebellum
010203040506070nTPM
MS4A1 - Cerebellum

MS4A1

NK-cell markers expressed in brain leukocytes

There are limited number of genes classified as NK-cell elevated, and many genes with high expression in NK-cells also show expression in T-cells. NCR1 is an example of NK-enriched expression in both the peripheral tissue comparison, as well as the immune cells comparison, and the brain leukocytes include this gene expression through out the different brain regions.

Dendritic cell markers expressed in brain leukocytes

Out of the three genes classified as dendritic cell enriched, that is overlapping with dendritic cell enriched in peripheral tissue types, TTC24 is the only gene with an elevated expression in leukocytes of the brain. However, TTC24 also show expression in subsets of neuronal cells. PTCRA show expression in brain leukocytes, but even higher expression levels in microglia/macrophages, additionally, the leukocyte expression is only detected in Amygdala and Cerebellar leukocytes. LILRA4 show no expression in brain leukocytes, only in microglia/macrophages.

Background

Single nuclei RNAseq data

Siletti K et al. (2023) published single nuclei RNA sequencing result, based on over 3 million cells from multiple brain regions, in Science magazine and created an interactive portal (The Human Brain Cell Atlas v1.0 ) available for single cell exploration across human gene expression in healthy brain cells. The Human Protein Atlas aims to generate a comprehensive resource representing the human body and its complexity, and with a need for better representation of the different cell types of the human brain, we imported the expression profiles and grouped them based on our cell type- strategy (providing bar charts of pooled data for each cell type cluster and calculating the average normalized protein-coding transcripts per million). We based the cell type clusters on the 31 superclusters, as well as the provided assigned cell types, and the data is shown as 34 different "supercluster cell types". The expression profile of the different clusters are shown for each of the 11 different brain regions. More details, related to number of M reads and number of cells per brain region/UMAP can be found here. The published cerebral cortex data is represented by a larger number of cells and we only included a random selection of 500 thousand cells. In total, expression data for 2526725 brain cells is displayed in the Brain single nuclei resource, for browsing the gene expression and provide easy comparison to cell type expression in peripheral tissues.

Relevant publications

Uhlén M et al., Tissue-based map of the human proteome. Science (2015)
PubMed: 25613900 DOI: 10.1126/science.1260419

Fagerberg L et al., Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. Mol Cell Proteomics. (2014)
PubMed: 24309898 DOI: 10.1074/mcp.M113.035600

Sjöstedt E et al., An atlas of the protein-coding genes in the human, pig, and mouse brain. Science. (2020)
PubMed: 32139519 DOI: 10.1126/science.aay5947

Siletti K et al., Transcriptomic diversity of cell types across the adult human brain. Science. (2023)
PubMed: 37824663 DOI: 10.1126/science.add7046