factors, hormones, cytokines, inflammation, and
stresses. It controls the expression of many
downstream genes related to cell division,
apoptosis, cell migration, and immunity ( 30 ).
In addition to subtype-specific TF identi-
fication, we also predicted the important TFs
in a sample-specific manner. To do this, we
analyzed all TFs’relative expression and chro-
matin accessibility at their motifs for samples
in CRPC-WNT, CRPC-NE, and CRPC-SCL, and
compared these to the average for CRPC-AR
samples. This analysis demonstrated that the
key TFs identified in a subtype-specific man-
ner agree with the sample-specific results (fig.
S9). We also found significant correlation be-
tween the expression of key TFs and acces-
sibility at their motifs, which suggests that
they likely exhibit pioneering activity (fig. S10,
Tanget al., Science 376 , eabe1505 (2022) 27 May 2022 4of13
A
C
B
D
ATAC-seq group
Group 1
Group 2
Group 3
Group 4
AR expression
AR high
AR low
AR neg
Pathway
UMAP for RNA−seq data GSEA enrichment scores: one vs. others
OncoPrint
MSKPCa2
22Rv
1
LNCaPVCaPPDX09aPDX10aPDX16aPDX16b
MSKPCa19MSKPCa22
PDX34aMSKPCa1
MSKPCa16WCM1078WCM1262
MSKEF1
MSKPCa10MSKPCa14
WCM154
H660
MSKPCa24
PDX01a
MSKPCa11MSKPCa12MSKPCa13MSKPCa15MSKPCa17MSKPCa3MSKPCa8MSKPCa9
WCM155
DU145
PC3
MSKPCa18MSKPCa20
ATAC-seq group
ETS_fusion
20 10 0
23%
66%
23%
46%
20%
11%
6%
6%
14%
14%
14%
6%
14%
20%
9%
9%
17%
3%
9%
11%
9%
14%
14%
29%
3%
AR
TP53
RB1
PTEN
FOXA1
NCOR1
AKT1
PIK3CB
PIK3CA
PIK3R1
BRAF
KRAS
APC
CTNNB1
TCF7L2
MSH2
BRCA2
BRCA1
ATM
ATR
FANCA
CDKN1B
CDKN2A
ZFHX3
SPOP
Alternations
Deep deletion
Amplification
Inframe Mutation (putative driver)
Inframe Mutation (unknown significance)
Missense Mutation (putative driver)
Missense Mutation (unknown significance)
Truncating Mutation (putative driver)
ETS_fusion
Negative
Positive
AR-
associated
pathwPI3K
ay
RASRAF
Wnt
pathw
ay
DNA
damage repair
cyclecell
SPOP
ATAC-seq group
CRPC-AR
CRPC-WNT
CRPC-NE
CRPC-SCL
Lost at RNA level (RNA-seq)
Lost at protein level (WB)
CRPC-AR CRPC-WNT
CRPC-NE CRPC-SCL
−0.5 0.0 0.5 −0.5 0.0 0.5
−0.5 0.0 0.5 −0.5 0.0 0.5
LIM_MAMMARY_
STEM_CELL_UP
BELTRAN_
NEPC_UP
HALLMARK_WNT_BETA_
CATENIN_SIGNALING
TCGA_ANDROGEN_
RESPONSE
Enrichment Score
LIM_MAMMARY_
STEM_CELL_UP
BELTRAN_
NEPC_UP
HALLMARK_WNT_BETA_
CATENIN_SIGNALING
TCGA_ANDROGEN_
RESPONSE
Enrichment
neg_enrich(padj < 0.05)
not_sign(padj > 0.05)
pos_enrich(padj < 0.05)
Pathway
(z-score)
Gene expression
Fig. 2. Transcriptomic and genomic characterization of the four CRPC
subtypes defined by ATAC-seq.(A) Unsupervised UMAP on the mRNA
expression values of the 1000 most variably expressed genes across
all samples. (B)EnrichmentscoresandP values from GSEA indicate that
the four signals are significantly positively enriched in specific subtypes but not
in others. (C) Heatmap shows the relative expression of subtype-specific
marker genes and basal/luminal genes across all samples. The ATAC-seq
group and signature scores of the four representative pathways for each
sample are shown at the top. (D) OncoPrint shows the genomic alterations of
the 35 samples with DNA-sequencing data. MSKPCa8 to 20, 22, and 24
were sequenced with MSK-IMPACT. The SNVs and CNVs for cell lines (LNCaP,
22Rv1, VCaP, H660, DU145, and PC3) were collected from CCLE (Cancer
Cell Line Encyclopedia). Whole-exome sequencing (WES) was performed for
other samples.
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