Science - USA (2022-05-27)

and 22Rv1 (Fig. 6C and fig. S19C;P < 0.0001,

two-tailed unpairedt test).

AP-1 and YAP/TAZ are important for

subtype-specific chromatin accessibility

and gene expression in CRPC-SCL and can

be targeted by drugs

Knockdown of FOSL1 and YAP/TAZ shows impact

on chromatin accessibility and gene expression

We performed ATAC-seq and RNA-seq in

MSKPCa3 cells with knockdown ofFOSL1,

YAP, TAZ,andYAP/TAZtogether. We observed

a significant decrease ofchromatin accessibility

at the CRPC-SCL–specific open chromatin sites

as well as at regions bound by FOSL1, TEAD,

YAP, and TAZ from ChIP-seq uponFOSL1, YAP,

andYAP/TAZknockdown (Fig. 6, D and E, and

fig. S20) (P < 0.001, permutation test). The sig-

nal was strongest uponFOSL1and doubleYAP/

TAZknockdown and highlights their impor-

tant role in maintaining the chromatin acces-

sibility landscape for the CRPC-SCL group. In

agreement with the decrease in chromatin ac-

cessibility, we found that CRPC-SCL peaks

are the most enriched among down-regulated

ATAC-seq peaks uponFOSL1, YAP,andYAP/

TAZknockdown (table S13). Moreover, we

found that the TEAD and AP-1 motifs are the

most enriched at the regions where chromatin

accessibility is reduced uponYAP/TAZdouble

knockdown, further confirming the model in

which YAP and TAZ cooperate with AP-1 and

TEAD (fig. S21A). Consistent with ATAC-seq

results, we found down-regulation of YAP/

TAZ targets in RNA-seq data in all knock-

down assays (Fig. 6F and fig. S21B). Double

knockdown ofYAPandTAZshowed stron-

ger inhibition of canonical downstream tar-

gets (CTGF, CYR61, AJUBA,andANKRD1)and

cell cycle–regulating geneCCND1(Fig. 6A and

fig. S19A), which have been reported as YAP/

TAZ targets in various model systems, rela-

tive to individual knockdown ofYAPor TAZ

( 35 , 40 ). Although we also observed enrichment

of CRPC-SCL genes among the down-regulated

genes, their enrichment in the up-regulated

gene set showed that ATAC-seq changes are

likely a more meaningful marker to analyze

lineage plasticity, as also demonstrated by pre-

vious studies (table S14) ( 41 ). Similar chromatin

accessibility and gene expression changes were

observed uponYAP, TAZ,andYAP/TAZknock-

down in DU145 (figs. S21, C and D, and S22).

Positive feedback loop between YAP/TAZ

and FOSL1

We found thatYAP/TAZdouble knockdown

caused robust depletion of FOSL1, the pre-

dicted master TF, at RNA and protein levels

in both MSKPCa3 and DU145 (Fig. 6, A and B,

and fig. S19, A and B). Moreover, in our regulatory

networks for CRPC-SCL samples,FOSL1was

predicted to be a target of FOS/JUN itself as

Tanget al., Science 376 , eabe1505 (2022) 27 May 2022 8of13

Enrichment Score

CRPC-SCL compared to others

Cell competition assay of FOSL1 KO

AP-1

TEAD

YAP/TAZ

DNA

Overlap of ChIP-seq peaks in MSKPCa3

ChIP-seq signals at ATAC-seq peaks

FOSL1

TAZ

TEAD

YAP

ChIP-seq signals

-2.0 2.0Kb

Fold change over

control

FOSL1

-2.0 2.0Kb

TAZ

-2.0 2.0Kb

TEAD1

-2.0 2.0Kb

YAP

-2.0 2.0Kb

AR

CRPC-ARCRPC-WN

TCRPC-NE

-2.0 2.0Kb

distance to peak center

CRPC-SC

L

-2.0 2.0Kb

distance to peak center

-2.0 2.0Kb

distance to peak center

-2.0 2.0Kb

distance to peak center

-2.0 2.0Kb

distance to peak center

CRPC-AR specific ATAC-seq peaks CRPC-WNT specific ATAC-seq peaks

CRPC-NE specific ATAC-seq peaks CRPC-SCL specific ATAC-seq peaks

1.6 2.4 3.2 1.6 2.4 3.2 1.0 1.5 1.0 1.5 1 2 3

1

2

3

4

1

2

3

0.75

1.00

1.25

1.50

1.75

0.8

1.0

1.2

2

4

6

8

(18,858)

(2,520) (7, 9 19) (18,296)

(4,737)

WANG_YAP_TAZ_TARGETS

NES = 2.60

FDR < 0.001

A

D

F

C

B

0.0

0.5

1.0

1.5

relative sgRNA positive cells

p0

p1

p2

p3

** **** ** **

** * *

0.0

0.5

1.0

1.5

relative sgRNA positive cells

p0p1

p2

MSKPCa3 (CRPC-SCL) MSKPCa2 (CRPC-AR)

GAPDH

FOSL1

E

Fold changeover control

FOSL1 TAZ TEAD1 YAP AR

Consensus ChIP-seq peak

s

sgR26

sgFOSL1

#1

sgFOSL

1 #2

sgFOSL

1 #3

sgRPA

3

sgR26

sgFOSL

1 #1

sgFOSL

1 #2

sgFOSL1

#3

sgRPA3

sgR2

6

sgFOSL1

#1

sgFOSL1

#2

sgFOSL1

#3

Fig. 5. AP-1 works together with YAP, TAZ, and TEAD in CRPC-SCL.(A) Percentage of GFP-positive
MSKPCa3 (left) or MSKPCa2 (right) expressing CRISPR guides against FOSL1 or sgR26 (negative control) or
sgRPA3 (positive control). Mean ± SEM,n =2forMSKPCa3,n = 2 for MSKPCa2. P < 0.001, P <0.01,
P < 0.05 [multiple unpairedt test comparing between passages (p1 versus p0, p2 versus p0, p3 versus p0)].
Knockout of FOSL1 was confirmed in MSKPCa3 by Western blot. (B) Schematic showing the cooperation of
AP-1 with YAP/TAZ and TEAD in CRPC-SCL samples. (C) GSEA plot showing enrichment of YAP/TAZ signature in
CRPC-SCL organoids and cell lines compared to other samples. (D) Venn diagram showing the overlaps of FOSL1,
TEAD, YAP, and TAZ ChIP-seq peaks in MSKPCa3. Overlaps with more than 1000 peaks are marked, and those
between YAP/FOSL1 (48 peaks) and YAP/FOSL1/TEAD (4 peaks) are not shown. (E) ChIP-seq signal of FOSL1,
TAZ, TEAD1, and YAP in MSKPCa3, and AR (GSE61852) from LNCaP on the consensus peak set. (F)ChIP-seqsignal
of FOSL1, TAZ, TEAD1, and YAP in MSKPCa3, and AR (GSE61852) from LNCaP on subtype-specific ATAC-seq
peaks. FOSL1, TEAD1, YAP, and TAZ ChIP-seq peaks for MSKPCa3 show stronger signal at CRPC-SCL–specific
ATAC-seq peaks, whereas AR (GSE61852) ChIP-seq peaks have stronger signal in CRPC-AR–specific peaks.

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