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Blood Cell Transcriptome Atlas Enables Study of Immune Disorders

NEW YORK – A team from Sweden, Denmark, and the UK has established an open access, interactive database documenting expression of protein-coding genes across more than a dozen immune cell types and has used this "Blood Atlas" to flag pathways behind inborn errors of immunity and other conditions.

"This newly created resource elucidates the gene expression of individual immune cell populations to allow a better understanding of diseases involving the immune system," first and corresponding author Mathias Uhlen, a researcher affiliated with KTH-Royal Institute of Technology, the Karolinska Institute, and the Technical University of Denmark, and his colleagues wrote.

As they reported online today in Science, the researchers used flow cytometry-based immune cell sorting and deep RNA sequencing in 18 blood immune cell populations and in mixed peripheral blood mononuclear cell populations for the Human Protein Atlas project — an effort that previously yielded a Tissue Atlas, Cell Atlas, and Pathology Atlas.

"Given that blood is the most commonly used material for molecular analyses in clinical labs and in research, characterizing the constituents of blood and updating the Human Protein Atlas with a more fine-grained view of the immune cells in blood will be of importance," the authors explained.

After sorting cell types in whole blood samples from six healthy individuals, the researchers generated RNA sequences spanning known protein-coding genes in 18 immune cell populations from half a dozen blood cell lineages. They considered those immune cell sequences alongside data from the Tissue Atlas, Genotype-Tissue Expression project, and other prior analyses.

The team saw gene expression clusters that roughly corresponded with immune cell origins and relationships, and identified immune-related genes with variable expression patterns from one immune cell population to the next. It also compared the transcriptomes with those in other cell, tissue, or organ types.

More than half of the protein-coding genes had enhanced expression in one or more of the tissues, the researchers found. In contrast, just 737 of the genes appeared to be expressed in a single tissue type, the team reported, while more than 9,600 genes seemed to be expressed across all tissues considered.

When they delved into the sets of genes that had increased expression in specific tissues, the researchers found that blood, in general, shared similarities with lymphoid or bone marrow tissues.

"All 19,670 protein-coding genes in humans have now been analyzed with respect to their tissue specificity," the authors wrote, "and distribution across all major organs, tissues, and blood cells in the human body, and the results are available in the Human Protein Atlas."

Along with more detailed analyses of the types of genes being expressed in the blood and other tissues, the team used the new blood transcriptome atlas to dig into the expression of 224 genes previously linked to primary immunodeficiency.

"A large fraction of these genes is expressed in a large number of cell types," the authors reported, "enforcing the need to take a holistic, body-wide approach to identify genes of importance to human biology and diseases."