and fig. S35), while many astrocyte and microglia
genes are classified as elevated in other tissues. In
fact, several astrocyte signature genes are highly
expressed in liver and/or muscle tissue, whereas
many microglia signature genes are enriched in
lymphoid tissue, bone marrow, and/or blood.
In summary, the global analysis reveals that
most of the putative astrocyte and microglia
signaturegenesarehighlyexpressedinselec-
tive peripheral tissues, often exceeding the ex-
pression levels in the brain.
We superimposed the putative cell type sig-
nature genes on the global tissue expression
landscape using the data from this study (Fig.
7C). Expression of only 180 of the human cere-
bral cortex cell type signature genes (43%) was
classified as brain-elevated with regard to ex-
pression, and 158 genes (38%) were classified
as elevated in expression in nonbrain tissues
and the expression of the remaining genes
(n= 82) classified as low tissue specific. To
further explore this lack of“brain specificity”
of many of the putative brain signature genes,
we analyzed some of these genes further, as
showninFig.7D.Themicrogliasignature
genes arachidonate 5-lipoxygenase (ALOX5)
and integrin subunit beta 2 (ITGB2) both showed
elevated expression in blood (lymphoid tissues),
while other microglia signature genes showed
elevated expression in specific blood cells. For
example, the gene for PYD and CARD domain
containing protein (PYCARD) is expressed by
granulocytes, monocytes, and dendritic cells.
These results confirm the notion of shared
origin and functions between microglia and
immune cells. In contrast, several astrocyte sig-nature genes are classified as genes with ele-
vated expression in liver or muscle tissue. Out
of the 19 genes with liver-elevated expression,
six are transport-related genes, including solute
carrier family 13 member 5 (SLC13A5), detected
in the membrane of hepatocytes and end feet
of astrocytes in brain, and nine genes code for
metabolic enzymes such as aldehyde dehy-
drogenase 1 family member L1 (ALDH1L1),
detected in cytoplasm of hepatocytes and as-
trocytes. Genes classified as having muscle-
elevated expression include several proteins
with structural function, such as syntrophin
alpha 1 (SNTA1), detected both in astrocytes
andskeletalmuscle.Allthreearethusclassified
as showing elevated expression in tissues other
than brain on the tissue level. These results
highlight the shared function of astrocytesSjöstedtet al.,Science 367 , eaay5947 (2020) 6 March 2020 9of16
Basal ganglia CerebellumGFAPADORA2ACRYABTestis Brain HippocampusCACNG3ALDH6A1AIF1RFX2ACSL4ATP1A3520
48356229668358097AKAP17A2072Regional specificityARHGEF33ANK1Heart muscleHeart muscleHeart muscleLymph nodeLymph nodeLymph node1776802710594395Elevat
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Brain llyTissue specificityFig. 6. The regional expression in brain compared with whole-body
expression.Gene classification based on tissue specificity using transcript
expression data in 37 different tissue types enables separation of genes
into brain-elevated, elevated in tissues other than brain, and low tissue
specificity. This is compared to the classification based on regional expression
in the brain. Of 1059 genes, 520 with regionally elevated expression were
also classified as brain-elevated. Genes classified as elevated in tissues other
than the brain are often detected in brain but expressed with low regional
specificity. Rho guanine nucleotide exchange factor 33 (ARHGEF33) is brain-
enriched, including cerebellum-enriched, and here detected in Purkinje cells
(HPA041051). ATPase Na+/K+transporting subunit alpha 3 (ATP1A3) is
group-enriched in brain and heart muscle and detected in all brain regions
with low regional specificity. Immunohistochemistry using HPA056446
displayed the intercalated discs in heart muscle and had a synaptic location
in brain. Crystallin alpha B (CRYAB) is tissue-enhanced in striated muscle,
found in all brain regions with low tissue specificity, and detected in
oligodendrocytes (HPA057100). Regulatory factor X2 (RFX2) is elevated in
testis and detected in all brain regions with low regional specificity, and with a
nuclear localization in testis and neuropil in brain (HPA048969). AIF1 is
enhanced in blood and lymphoid tissues, while also detected in microglia in
all brain regions with low regional specificity (HPA049234). ACSL4 is classified
as low specificity both in tissues as well as brain regions (HPA005552).
ADORA2A is group-enriched in lymphoid tissues and brain, including basal
ganglia–enriched (HPA075997). Calcium voltage-gated channel auxiliary
subunit gamma 3 (CACNG3) is brain-enriched and group-enriched in cerebrum
regions but was not detected in cerebellum, also verified at the protein level
(HPA077238). ANK1 is group-enriched in skeletal muscle and tongue as well as
cerebellum-enhanced in brain, where the protein is selectively associated
with the Purkinje cell membrane (HPA004842). GFAP is brain-enriched and
detected in all brain regions with low regional specificity (HPA056030).
ALDH6A1 is group-enriched in kidney and liver, detected in all brain regions with
low regional specificity, and, as GFAP, localized to astrocytes (HPA029074).
AKAP17A is expressed in all tissue types with low tissue specificity as well as
low regional specificity in the brain; the protein is detected in subsets of
cell nuclei and in brain in glial cells as well as granular cells in cerebellum
(HPA043247). Scale bar, 25mm.RESEARCH | RESEARCH ARTICLE