Science - USA (2022-05-27)

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adjustedP < 0.05) ( 12 ). Finally, the relative
expression levels of predicted key TFs in
each of the four groups were confirmed by a
quantitative polymerase chain reaction (qPCR)
(fig. S3C).


Classification of CRPC patients using
transcriptomic signatures of the four subtypes
Next, we examined RNA-seq datasets from
366 CRPC patients to assign each patient to
the four subtypes ( 21 ). We derived the sig-

nature genes for each of the four subtypes
as the ones with higher expression in one
group relative to others in organoids and cell
lines, and filtered out genes with low expres-
sion or low variance in CRPC patient samples

Tanget al., Science 376 , eabe1505 (2022) 27 May 2022 5of13


Top 25 highest ranked TFs

Outdegree

low

high

Expr

low

high

Chromatin
accessibility

low

high

Outdegree
Expr

TF rank

ChromatinaccessibilityOutdegree

Expr

TF rank

Chromatinaccessibility

CRPC-AR

CRPC-NE

CRPC-WNT

CRPC-SCL

0

1000

2000

0

1000

2000

Step1. Construct peak-gene links

peak 1 peak 2gene X peak 3
TSS

gene Y
TSS

TF A TF A

Step2. Predict TF binding to peaks

TF B

peak 1 peak 2 peak 3

TF A

Step3. Predict target genes of TF

peak 1 peak 2gene X peak 3
TSS

gene Y
TSS
TF A

Step4. Infer gene regulatory network

TFs
non-TF genes

0

10000

20000

30000

40000

0 102030
genes mapped per peak

Frequency

0

1000

2000

3000

0204060
peaks mapped per gene

Frequency

genes per peak:
mean: 1.4
peaks mapped to
only one gene: 75.2%

peaks per gene:
mean: 8.46
median: 3

D

A

BC

AR
FOXA1

PGR
FOXO3FOXB2FOXK1GATA2FOXO4HOXA13HOXB13FOXJ2HOXC12FO

XN3
NFYBFOXP3FOXL2NFIC
HOXC13FOXC2FOXS1

HSF4
ARID5AHNF1BHOXC10HNF1ATCF7L

2
KL

F^4
SOX4SNAI1TCF7KLF2ZIC1LMO2LEF1TCF4

ID4ZIC

4

TCF7

L1

TWIST1

TCF3SP5KL

F^7 SP9
SOX13
KLF5SP3
RUNX3TGI

F1
HINFP

SP4

NEUROD1

ASCL1TCF12MYOG

MSC
NHLH1ATO H 8NKX24NKX22OLIG2
RFX2EBF1
NHLH2
NEUROG3BHLHE22

RFX3
NEUROG2NEU

ROD2HMX3RFX5HMX2MEO

X2
E2F6
ZBTB18

TAL2
FOS

L1
BAT F
FOSL2JU

NB
TP63JDP2
NFE2L3CEBPBTFAP2C

FOSMAFFNFE2
TEAD3FOSBTFAP2BCEB

PA
NFICATF3
RUN

X2FLI1
ETS2
CEBPDNR

2E1
NFE

2L2
NFKB1

Fig. 3. Identification of the key transcription factors (TFs) of each subtype.(A) Schematic illustrating the construction of sample-specific regulatory networks
using ATAC-seq and RNA-seq data. (B) Distribution of the number of genes linked per peak. (C) Distribution of the number of peaks linked per gene. (D) Rank
order of the top 25 TFs for each of the four subtypes. For each TF, the relative contributions of three metrics to TF rank are shown (Expr, expression). In CRPC-SCL,
FOSL1, BATF, FOSL1, JUNB, JDP2, FOS, MAFF, FOSB, and ATF3 belong to the AP-1 family.


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