Arunachalamet al.,Science 369 , 1210–1220 (2020) 4 September 2020 6of11
Top BTMs enriched in DEGs COVID-19 (n=7)
vs healthy (n=5) for each cluster
A
C
D
FGH
E
B
1
10
100
1000
10000
0204060
Days post symptom onset
Concentration (fg/ml)
Severity
Healthy
Moderate
Severe
ICU
Proportion variance explained
0.0
0.2
0.4
0.6
0.8
1.0
Age
Severity
Time
Gender
resid
Days symptomsSeverityTAP1IFITM1IFIT2S TAT 1IFIT1IFIT3DDX60IFIH1DDX58OASLPMLRSAD2SP100HESX1HERC5USP18EIF2AK2PLSCR1AS1OIRF7SERPING1PARP9MX2IFI27APOBEC3AOAS3SIGLEC1ATF3C1QBBCL2A1IFNGR2MGST1HLX
Days post
symptom onset
20
5
Severity
Moderate
Severe
ICU
−3
−2
−1
0
1
2
3
z-score
antigen processing and presentation (M200)
enriched in antigen presentation (I) (M71)
reg. of antigen presentation and immune response (M5.0)
Monocyte surface signature (S4)
TLR and inflammatory signaling (M16)
immune activ ric cluster (M37.0)
enriched in antigen presentation (II) (M95.0)
enriched in T cells (I) (M7.0)
cell cycle and transcription (M4.0)
antiviral IFN signature (M75)
enriched in activated dendritic cells (II) (M165)
type I interferon response (M127)
innate antiviral response (M150)
0
10
20
Log of
1/P val
% Path
is DEG
0.3
0.6
0.9
A
IFN signaling
Antigen presentation
Cor: 0.85
5
10
15
20
0.0 2.5 5.0 7.5 10.0
Log of Concentration, fg/ml
33 gene ISG Score
new_id
cov 1
cov 2
cov 3
cov 4
cov 5
cov 6
cov 7
hd2
hd3
hd4
hd5
IFN-α ELISA of plasma
CITE-seq vs IFN-α ELISA Bulk RNA-seq of total PBMCs Bulk RNA-seq of total PBMCs
ATF3IFITM1PARP9PLSCR1PMLMX2IFIH1DDX58HLXOAS3SIGLEC1OASLC1QBIFIT1IFIT3RSAD2SP100DDX60IFI27STAT1APOBEC3AMGST1IFNGR2BCL2A1SERPING1IFIT2HERC5EIF2AK2OAS1HESX1USP18IRF7TAP1 celltypegroup
0.51.0
subjectexp peraverage
Exp r. z−score
−2
−1
0
1
2
group
COVID−19
Healt hy
celltype
C10−PDC
C11−C MONO
C16−C MONO
C3−C MONO
C5−CDC2
CITE-seq of COVID-19 (n=7) and healthy (n=5) subjects
CITE-seq of COVID-19 (n=7) and healthy (n=5) subjects
Experiment layout CITE-seq of COVID-19 (n=7) and healthy (n=5) subjects
Mixing ~1:2 and
CITE-seq
Total PBMCs
Frozen
PBMCs
Magnetic enrichment
Subjects of dendritic cells
7 COVID-19 infected
5 healthy control
RESEARCH | RESEARCH ARTICLE