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Single nuclei brain methods
The Leukocyte-specific proteomeBlood & 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 67% (n=13603) of all human proteins (n=20162) are detected in blood and immune cells and 1039 of these genes show an elevated expression in any blood and immune cells compared to other brain cell types. The blood and immune cell transcriptomeThe snRNA-seq-based blood and immune cell transcriptome can be analyzed with regard to specificity, illustrating the number of genes with elevated expression in blood and immune cell type compared to other brain cell types (Table 1). Genes with an elevated expression are divided into three subcategories:
Expression profile of different cell markersThe 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 leukocytesTRBV28 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.
B-cell markers expressed in brain leukocytesFCRL1 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.
BackgroundSingle nuclei RNAseq dataSiletti 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) |
The Human Protein Atlas project is funded
