Science - USA (2022-04-08)

Perezet al.,Science 376 , eabf1970 (2022) 8 April 2022 4 of 13

A

CD4Naive

CD8Naive

CD4EM

CD4Reg

CD8GZMH

CD8GZMK

CD8MAIT

NKBright

NKDim

BNaive

BMem

BPlasma

BAtypical

Progen

B

CD4Naive

CD8Naive

CD4EM

CD4Reg

CD8GZMH

CD8GZMK

CD8MAIT

NKBright

NKDim

BNaive

BMem

BPlasma

BAtypical

Progen

CD4CD8ACD8B

CCR7

IL74

TNFRSF4

CD40LG RTKN2FOXP3PRF1GZMHGZMBGZMKKLRB1GNLYNKG7FCGR3ATCL1ABANK1MZB1FCRL5CD19MS4A1CD79ASOX4

1.0

0.8

0.6

0.4

0.2

0.0

Normalized Expression

CD4Naive CD8Naive CD4EM CD4Reg CD8GZMH

NKBright NKDim BNaive BMem BPlasma Progen

CD8GZMK CD8MAIT

*

*

C

*

BAtypical

60

0

20

0

20

0

50

0

25

0

1

0

10

0

5

0

20

40

20

15

10

5

50

0

20

0

5

0 0

**** * **

ECTLESLEACTLASLEECTLESLEACTLASLEECTLESLEACTLASLEECTLESLEACTLASLEECTLESLEACTLASLEECTLESLEACTLASLEECTLESLEACTLASLE

D

Cytotoxic Exhaustion Type-1 ISG

Cytotoxic

CTL SLE

Exhaustion Type-1 ISG

Signature Expression

* *

CD8GZMH CD8GZMH CD8GZMH

(^01) Density
20
40
(^6010)
8
6
4
2
2.5
2.0
1.5
1.0
0.5
50
30
(^100)
CTL SLE

• CTL SLE
  ISG15RGS1
  EPSTI1CD8AIFI16
  STAT1HBB
  SP110SP100
  EIF2AK2IFI27IFI44
  RNF213IFI44LPATL2
  ISG20LAG3IFI6
  XAF1BST2MX1
  TYROBPMYOM2OAS1
  KLRC1KLRC2GNLY
  KIR2DL3TMSB4XKLRF1
  HSP90AA1CD99B2M
  CCND3PPIAIL32
  HLA-DPB1HLA-DPA1CD3D
  HLA-DRB1PTPRCAPRARRES3
  CALM1FTH1UBC
  IFITM2GSMBMYL6
  ARPC3GSMHLY6E
  PSME2DDIT4HLA-B
  PSME1SRGNPRF1
  HLA-CHLA-AVIM
  HLA-ECD3GHCST
  TMSB10ID2FTL
  S100A4H3F3ANKG7
  S100A11S100A6CD2
  LGALS1CD53CD52
  SH3BGRL3ARPC4CALR
  GAPDHEMP3UBB
  FGFBP2ATP5ECCL5
  ACTG1
  ISG15RGS1EPSTI1CD8AIFI16STAT1HBBSP110SP100EIF2AK2IFI27IFI44IFI44LPATL2RNF213IFI6ISG20LAG3MX1XAF1BST2OAS1MYOM2TYROBPGNLYKLRC1KLRC2KIR2DL3KLRF1TMSB4XCD99B2M
  HSP90AA1
  PPIAIL32CCND3CD3D
  HLA-DPB1HLA-DPA1HLA-DRB1PTPRCAPRARRES3
  UBCCALM1FTH1MYL6IFITM2GSMBGSMHARPC3LY6EPSME2DDIT4HLA-BPSME1PRF1SRGNVIMHLA-CHLA-ACD3GHCSTHLA-E
  TMSB10
  ID2FTL
  H3F3ANKG7S100A4S100A6S100A11CD2CD53LGALS1CD52
  SH3BGRL3
  ARPC4CALREMP3GAPDHUBBATP5EFGFBP2CCL5ACTG1
  Type-1 ISG
  Pseudobulk Coexpression
  Cellular Coexpression
  Cytotoxic markers
  E
  CD8GZMH
  F
  GZMH+: 59%
  GZMK+: 21.3%
  Expanded CD8 TCRs
  UMAP1
  UMAP2
  UMAP1
  UMAP2
  UMAP1
  UMAP2
  G
  CD8 TCRs
  CTL SLE
  Normalized
  Shannon’s Entropy
  1.00
  0.92
  0.94
  0.95
  0.93
  0.96
  0.97
  0.98
  0.99
  H
  Type-1 ISG
  Proportion of
  expanded CD8 TCRs 0
  0.2
  0.4
  CytotoxicExhaustedCD8
  GZMK
  CD8GZMH
  Rest
  Fig. 2. Reduction of naïve CD4+and expansion of cytotoxic CD8+T cells in SLE.
  (A) UMAP of lymphoid cells reclustered into 14 subpopulations: naïve, effector
  memory, and regulatory CD4+T cells (CD4Naïve, CD4EM, CD4Reg); naïve,GZMH+
  cytotoxic,GZMK+cytotoxic, and mucosal-associated invariant CD8+T cells (CD8Naïve,
  CD8GZMH, CD8GZMK, CD8MAIT); CD56brightand CD56dimnatural killer cells (NKBright,
  NKDim); naïve, memory, plasma, and atypical B cells (BNaïve,BMem,BPlasma,BAtypical);
  and CD34+progenitors (Progen). (B) Expression of marker genes (columns) used to
  annotate each subpopulation (rows) colored by normalized expression level.
  (C) Percentage (yaxis) versus case-control status (xaxis) for each lymphoid
  subpopulation separated by ancestry. Subpopulations with significant percentage
  changes between cases and controls are highlighted. Padjusted<0.05(WLS);bluebar
  indicates significant meta-analysis by Fisher’s method. (D) Density plot showing
  average expression of cytotoxic, exhaustion, and type 1 interferon–stimulated gene
  (ISG) signatures in CD8GZMHcells (top) and across individuals (bottom) separated by
  case-control status and ancestry. P<0.05(WLS).(E) Coexpression of top 300
  differentially expressed genes between cases and controls in CD8GZMHcells computed
  across single cells (lower triangular matrix) or across donor-specific pseudobulk
  expression profiles (upper triangular matrix). (F) All (light pink) and expanded (red)
  TCR sequences detected shown on UMAP of all cells (left) andGZMH+cells (right).
  (G) Normalized Shannon’s entropies of CD8+TCR repertoire diversity (yaxis) in cases
  and controls (xaxis). P<0.05(WLS).(H) Percentage of expanded CD8+TCRs
  identified asGZMH+cells expressing cytotoxic, ISG, and exhaustion signatures,
  GZMK+cells (GZMK), and all other cells (Rest). ECTL, European control; ESLE,
  European case; ACTL, Asian control; ASLE, Asian case.
  RESEARCH | RESEARCH ARTICLE