Stadtmaueret al.,Science 367 , eaba7365 (2020) 28 February 2020 9of12
IP 10 113
Time (Days)
0.0
0.2
0.4
0.6
0.8
1.0
Cell Proportion
NY-ESO-1 TCR
TRAC Mutations
TRBC Mutations
PDCD1 Mutations
0.0
0.2
0.4
0.6
0.8
1.0
Cell Proportion
IP 113 IP 113
NY-ESO-1 TCR- NY-ESO-1 TCR+
Time (Days)
Wild-type
1 Mutation
2 Mutations
3 Mutations
Infusion Product
(IP)
Post-Infusion
(Day 10)
Post-Infusion
(Day 113)
RIPOR2TECR
GIMAP4UBE2V2
ICAM2SARS
C12orf65RAP1A
CCND3PTPRC
AC133644.2TAGAP
MAT2BTRAT1
FCMRCCR7
ATP5F1ECRIP1
CHCHD2H3F3A
HLACD52−A
S100A4FOS
AL138963.3TCF7
PNRC1HLA−E
SNHG8SYTL3
PABPC1PIK3R1
LEPROTL1PDCD4
SH3BGRL3IL7R
TMSB10CAPG
ENO1B2M
ACTBCFL1
SERF2TXN
DDIT4MIF
PTPRCAPJUNB
PIK3IP1BTG1
CD69TPT1
TSC22D3STK17A
ZFP36L1JUN
PTMAFTH1
CIRBPZFP36
HLAEIF1−B
EEF1A1HLA−C
ABRACLMYL6
CST7FTL
AHNRNPFTP6V0E1
SELPLGIL32
PRDX1TPI1
GAPDHACTR3
RAC2PPIA
S100A11STMN1
TMSB4XARPC5
NDFIP2DYNLL1
(IP) (Day 10) (Day 113)
0
max
UMAP1
(^2) PA
MU
NY-ESO-1 TCR
TCF7
A
B
C
D
E
NYCE T cell Infusion Product (IP)
NY-ESO-1 TCR+
11
6
6
2
0
1
1
PDCD1
TRAC
TRBC
− 2 −10 1 2
Expression
(43 Total Cells; 16 Unedited Cells)
84 104 43 8
Fig. 6. Single-cell RNA sequencing of patient UPN39 CRISPR-Cas9–
engineered NYCE T cells pre- and postinfusion.(A) Venn diagram showing
relative numbers of NY-ESO-1 TCR–positive cells withTRAC,TRBC,and/orPDCD1
mutations in the NYCE T cell infusion product (IP) (day 0). (B) Proportions of
preinfusion (IP, day 0) and postinfusion (days 10 and 113) wild-type T cells with
TRAC,TRBC,orPDCD1mutations or expressing the NY-ESO-1 TCR transgene.
Numbers of cells belonging to each of these categories are listed below the graph.
(C)AnalysisofNY-ESO-1TCR–positive (right) and NY-ESO-1 TCR–negative (left)
cells without mutations (wild type) or with single, double, or triple mutations at day 0
(NYCE T cell infusion product) and day 113 post–NYCE T cell infusion. Numbers of
analyzed cells for each time point are listed above the bars. (D) Uniform manifold
approximation and projection (UMAP) plots of gene expression data. Analysis
was performed on all T cells integrated across time points, but only NY-ESO-1 TCR–
expressing cells, split by time point, are shown (top). The increase inTCF7
expression is indicative of an acquired central memory phenotype (bottom, same
cells). (E) Heatmap showing scaled expression of differentially expressed genes
in NY-ESO-1 TCR–positive T cells across time points. Color scheme is based on
scaled gene expression from–2 (purple) to 2 (yellow).
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