Science - USA (2022-05-27)

(tables S5 and S9). A template was constructed
for each subtype by combining the top signa-
ture genes. To assign the CRPC patient sam-
ples to a subtype, we used the nearest template

prediction (NTP) algorithm ( 31 , 32 ), which in-

volves computing the cosine distance (d)be-

tween each patient’s RNA-seq data and each of

the four templates and estimating the statistical

significance by random resampling (Fig. 4A). We

applied the method to two cohorts of CRPC

patients with polyA-enriched RNA-seq data,

including 266 published SU2C patients ( 21 )

Tanget al., Science 376 , eabe1505 (2022) 27 May 2022 6of13

CRPC-WNT: 6.80%

CRPC-SCL: 30.10%

SU2C patient composition

CRPC-AR: 45.12%

WCM patient composition

random resampled

set of genes

(1000 iterations)

compute

cosine distance d

N1+N2+N3+N4

N1

N2

N3

N4

RNA-seq data

of a patient

Templates derived using

signature genes

padj < 0.05

radius: cosine distance d

smaller

(more similar)

larger(less similar)

padj >= 0.05

Group1Group2Group3Group4

Expression of

signature genes

Signature genes

derived from

organoids & cell lines

Group1

(N1)

Group2

(N2)

Group3

(N3)

Group4

(N4)

Molecular subtypes

CRPC-AR

CRPC-WNT

CRPC-NE

CRPC-SCL

NE_score

low

high

Pathology

Adenocarcinoma

Small cell/

Adenocarcinoma with NE features

Inadequate for diagnosis/

Not available

AR_score

Gene expression (z-score)

low

high

0

2

4

Squamous

SU2C patients

Molecular classification of patients

WCM patients

CRPC-AR: 50.49%

CRPC-NE: 12.62%

CRPC-WNT: 4.88%

CRPC-NE: 28.05% CRPC-SCL: 21.95%

A

B

C D

E +

+

+ +

+

0.00

0.25

0.50

0.75

1.00

0102030

+

+

AR amplification and mutation WNT pathway mutation RB1 deep deletion

Fig. 4. Classification of CRPC patients using transcriptomic signatures for the four subtypes.(A) Schematic illustrating the assignment of each patient to one
of the four groups using nearest template prediction. (B) Heatmaps showing relative expression of signature genes in SU2C and WCM patients. Top annotations
indicate the AR score, NE score, pathology classification, and molecular subtypes of each patient. (C) Patient compositions for SU2C and WCM cohorts. (D)AR
amplification and mutation, WNT pathway component mutations, and RB1 deep deletion are enriched in CRPC-AR, CRPC-WNT, and CRPC-NE SU2C patients,
respectively (two-sided Fisher’s exact test). (E) CRPC-SCL patients exhibit shorter time on ARSI treatment relative to CRPC-AR SU2C patients.

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