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 samplesTanget al., Science 376 , eabe1505 (2022) 27 May 2022 5of13
Top 25 highest ranked TFsOutdegreelowhighExprlowhighChromatin
accessibilitylowhighOutdegree
ExprTF rankChromatinaccessibilityOutdegreeExprTF rankChromatinaccessibilityCRPC-ARCRPC-NECRPC-WNTCRPC-SCL010002000010002000Step1. Construct peak-gene linkspeak 1 peak 2gene X peak 3
TSSgene Y
TSSTF A TF AStep2. Predict TF binding to peaksTF Bpeak 1 peak 2 peak 3TF AStep3. Predict target genes of TFpeak 1 peak 2gene X peak 3
TSSgene Y
TSS
TF AStep4. Infer gene regulatory networkTFs
non-TF genes0100002000030000400000 102030
genes mapped per peakFrequency01000200030000204060
peaks mapped per geneFrequencygenes per peak:
mean: 1.4
peaks mapped to
only one gene: 75.2%peaks per gene:
mean: 8.46
median: 3DABCAR
FOXA1PGR
FOXO3FOXB2FOXK1GATA2FOXO4HOXA13HOXB13FOXJ2HOXC12FOXN3
NFYBFOXP3FOXL2NFIC
HOXC13FOXC2FOXS1HSF4
ARID5AHNF1BHOXC10HNF1ATCF7L2
KLF^4
SOX4SNAI1TCF7KLF2ZIC1LMO2LEF1TCF4ID4ZIC4TCF7L1TWIST1TCF3SP5KLF^7 SP9
SOX13
KLF5SP3
RUNX3TGIF1
HINFPSP4NEUROD1ASCL1TCF12MYOGMSC
NHLH1ATO H 8NKX24NKX22OLIG2
RFX2EBF1
NHLH2
NEUROG3BHLHE22RFX3
NEUROG2NEUROD2HMX3RFX5HMX2MEOX2
E2F6
ZBTB18TAL2
FOSL1
BAT F
FOSL2JUNB
TP63JDP2
NFE2L3CEBPBTFAP2CFOSMAFFNFE2
TEAD3FOSBTFAP2BCEBPA
NFICATF3
RUNX2FLI1
ETS2
CEBPDNR2E1
NFE2L2
NFKB1Fig. 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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