Advanced prostate cancer is highly heterogeneous but this inter-patient heterogeneity has until recently not been understood. We have through an international research effort dissected the molecular landscape of advanced castration resistant prostate, elucidating key molecular targets in this group of diseases. We have also shown that PARP inhibitors have antitumor activity against a significant proportion of these cancers, mainly in men whose cancers harbor DNA repair defects.

1. Prostate Cancer:
From Genomics To Therapy
Johann Sebastian de Bono
Director, Drug Development Unit
Professor of Experimental Cancer Medicine
The Institute of Cancer Research and Royal Marsden
London, United Kingdom
Qiagen Meeting January 2016

4. Prostate Cancer
• Most common cancer in men and second most common
lethal cancer in men; metastatic disease invariably lethal
• Many new treatments
– Abiraterone, enzalutamide, cabazitaxel, radium 223
• Molecularly highly heterogeneous
– No stratified treatment to date
de Bono et al, NEJM 2011; de Bono et al, The Lancet 2010; Scher et al, NEJM 2012;
Parker et al, NEJM 2014; Robinson et al, Cell 2015.

5. Seminar on prostate cancer published in The Lancet, 11th June 2015

6. Therapy: PARP Inhibitors in Advanced Prostate Cancer

7. Hypothesis
A molecular subclass of prostate cancers have DNA
repair defects that render them vulnerable to synthetic
lethal therapeutic strategies utilizing PARP inhibition.

8. Synthetic Lethality: Targeting the Achilles’ heel
• Synthetic lethal strategies pursue this Holy Grail: Killing tumor
cells but sparing normal cells.
• “Synthetic lethality” occurs when there a potent and lethal
synergy between two otherwise non-lethal events: in this
case a highly specific PARP inhibitor induces a DNA lesion and
a tumor-restricted genetic loss of function for the DNA repair
pathways required to repair it.”
Farmer et al, Nature 2005; Bryant et al, Nature 2005; Fong et al, NEJM 2009

10. • Investigator-initiated multi-stage Phase II trial
– NCT-01682772; CR-UK/11/029
• Adaptive design focused on predictive biomarker identification
– Test set (all comers; Part A) and validation set (patient selection; Part B)
– Possibility to proceed to a randomized Phase II of PARPi vs placebo
• Open label, Olaparib (tabs) 400mg BID
Study Objectives
• To evaluate the antitumour activity of olaparib in mCRPC
• To identify and clinically qualify a predictive biomarker suite
for PARP inhibitor antitumour activity in CRPC
Trial design
Like the first abiraterone Phase I/II trial and the olaparib
first in man Phase I trial, this trial was written at Flims.

11. • Primary endpoint: Response Rate
– Response as per RECIST 1.1
– PSA decline >50% (PCWG-2)
– CTC conversion (>5 to <5/7.5ml)
Confirmed by a second assessment >4 weeks later
• Secondary endpoints included:
– rPFS, OS, duration of responses, safety-tolerability.
• Exploratory endpoints:
– Study of diffusion-weighted MRI as response biomarker
Trial design
No. HR (95% CI) p-value No. HR (95% CI) p-value
rPFS CTC conversion 46 0.48 (0.23, 0.996) 0.049 40 0.37 (0.18, 0.77) 0.007
OS CTC conversion 49 0.32 (0.13, 0.77) 0.011 47 0.31 (0.14, 0.68) 0.004
4 weeks 8 weeks
CTC Conversion for these 49 patients: Association with rPFS, OS

12. • po= RR 5%; p1= RR 20%
• α=0.02; β=0.10
Trial Design: Elucidating the Predictive Biomarker Suite
Investigator Initiated Trial Written at AACR/ESMO/ECCO Flims Workshop
TO-PARP-A; What I am presenting today.
Written with Shahneen Sandhu, now at Peter Mac, Melbourne

13. • po= RR 5%; p1= RR 20%
• α=0.02; β=0.10
Trial Design: Elucidating the Predictive Biomarker Suite
TOPARP-Part C

14. Biomarker studies
• Mandated pre-and post-PARPi fresh tumour biopsies.
• Planned studies to analyse predictive biomarker suite:
– Whole exome and transcriptome analyses (HiSeq)
– Targeted NGS for validation (MiSeq; Qiagen M&Mv2)
– ctDNA: serial plasma samples (MiSeq; Qiagen M&Mv2)
• PD studies in tumour tissues
– Gamma H2AX foci, RAD51 foci, 53BP1 foci

15. 15
Statistical Analysis Plan
Predictive Biomarker Definition
Definition of Biomarker positive (B+) patient
Presence of a homozygous deletion AND/OR a putative deleterious
mutation in a gene reported to be involved in DNA repair and/or
sensitivity to PARP inhibition

16. Trial population
• Metastatic CRPC after 1-2 lines of taxane chemotherapy.
• Documented progressive disease by RECIST or PSA (PCWG2).
• ECOG Performance Status 0-2.
• Appropriate organ-function: Hb >10g/l, Neut>1.5x109/l,
Plt>100x109/l, Bilir<1.5x ULN, AST/ALT<2.5x uLN (x5 liver mets),
Creatinine<1.5x ULN.
• No prior PARPi, platinum, cyclophosphamide or mitoxantrone.
• CTC count of ≥5 cells/7.5mls blood at screening.

17. Clinical trial results
Patients characteristics
Median age (range) 67.5 y (40-79)
ECOG-PS 0-1 44 (80%)
ECOG-PS 2 6 (20%)
Time from CRPC:
median (IQR)
2.2 y (1.7-3.9)
Baseline PSA:
median (IQR)
349.5 ug/l
(153-806)
Baseline ALP:
median (IQR)
169 IU/l (97-
407)
Baseline Hb:
median (IQR)
11.2 g/l (9.1-
15.3)
Baseline LDH:
median (IQR)
260.5 IU/l
(196-525)
Baseline CTC counts:
median (IQR)
37 CTC/7.5ml
blood (14-110)
Prior lines of treatment n (%)
Docetaxel 50(100%)
Cabazitaxel 29 (58%)
Abiraterone* 48 (96%)
Enzalutamide* 14 (28%)
Palliative radiotherapy 18 (26%)
Patients dosed 50
Evaluable for response 49
* CYP-17 inhibitor and/or enzalutamide 50/50 (100%)

18. Biomarker studies
Paired CRPC biopsies for NGS
• 43/49 biopsies positive and
suitable for NGS (87%)
• 35/43 had sufficient tumor for WES
• 37 archival, castration-sensitive,
matched samples were also
retrieved (including all 6 patients
with negative fresh biopsy*).
Liver: 6 (12%)
Nodes: 16 (32%)
Bone marrow: 28 (56%)
The 6 pts with negative fresh biopsies were not responders but had exome NGS from FFPE.
All CRPC samples sequenced by targeted NGS (MiSeq). All BRCA/ATM copy number data
validated by digital droplet PCR (BioRad).

19. Primary endpoint analysis
Response to olaparib in sporadic mCRPC
Response rate: 32.7%
(16/49 evaluable patients)
95% C.I.: 20.0-47.5%

20. Our First Responder
• 70 years old patient with no family history
– Acute urinary retention in Dec 2011
• Staging: T4 tumour with extension into bladder base, pelvic
nodes and metastatic bone disease
• Biopsy confirmed adenocarcinoma of prostate with Gleason
score of 4 + 5 (9) in 10/10 cores, up to 80% core involvement

21. 0
10
20
30
40
50
60
70
De
c-
11
Ja
n-
12
Fe
b-
12
M
ar-
12
Ap
r-
12
M
ay-
12
Ju
n-
12
J
ul-
12
Au
g-
12
Se
p-
12
Oc
t-
12
No
v-
12
De
c-
12
Ja
n-
13
Fe
b-
13
M
ar-
13
Ap
r-
13
M
ay-
13
Ju
n-
13
J
ul-
13
Au
g-
13
Se
p-
13
Oc
t-
13
LHRH analogue +
Bicalutamide
LHRH analogue
Then XRT to
Prostate
Docetaxel
CYP17
inhibitor
Time
PSA
Detailed Case Study: TO-PARP Responder
PARPi
6m TTP
CYP17i refractory
4m PFS on D

22. 14.10.201318.07.2013

23. 14.10.201318.07.2013
Response in porto-caval (top row) and right external iliac nodes (bottom row)
A similar trend was see at all nodal disease sites(supraclavicular, retroperitoneal, pelvic, sigmoid mesentery)

24. Fused MRI DWI - Anatomical Whole Body MRI DWI – b 900
Baseline Post Tx Post Tx
Whole Body MRI showing almost complete resolution of the liver metastases (red
arrow), retroperitoneal and pelvic lymph nodes (yellow arrows) after 12 weeks.
(The signal in the clavicles is artefactual; signal in the spleen is normal.)
Baseline
Pre-Treatment Post-Treatment Pre-Treatment Post-Treatment

25. chr9: One copy loss of
CDKN2A and CDKN2B
chr5: One copy
loss of APC
chrX: Amplification
of AR and AMER1
chr13: One copy loss of
RB1 and BRCA2
chr2: One copy
loss of ERCC3
Gene ExonicFunc Chr Start End Ref Obs
Var reads/
Total reads
Normal
BRCA2
frameshift
substitution
13 32954225 32954252
CCATCTTGTTCTGAG
GTGGACCTAATAG
CA 8/16 0/57
SU2C TO-PARP First Responder Analyses
Somatic Cell Biallelic BRCA2 loss

26. 26
ID
Maximum %
PSA decline
Measurable
disease
Best
RECIST
response
Confirmed
CTC
conversion
Baseline CTC
count (/7.5ml
blood)
Maximum %
CTC decline
Time on
treatment
(weeks)
DNA repair
genes defect
#1 84.7 % No No 87 100 % 73.1 Positive
#5 51.2 % No Yes 24 100 % 58 Positive
#6 29.3 % Yes SD Yes 105 97.1 % 15.9# Positive
#8 47.3 % No Yes 38 94.7 % 60 Positive
#11 No decline Yes PD Yes 6 83.3 % 9.7 Negative
#14 82.6 % No Yes 102 100 % 36.3 Positive
#15 79.9 % Yes PR Yes 18 100 % 35.9 Positive
#16 86 % Yes PR Yes 5 100 % 40+ Negative
#17 94.6 % Yes PR Yes 8 100 % 24 Positive
#20 87.9 % Yes PR N/E <5 100 % 47.9 Positive
#26 No decline No Yes 12 100 % 17* Positive
#30 69.9 % No Yes 100 100 % 44+ Positive
#35 94.7 % Yes PR Yes 513 100 % 40+ Positive
#36 58.7 % No Yes 22 100 % 56.7 Positive
#39 68.2 % Yes PR Yes 24 100 % 44+ Positive
#48 No decline Yes SD Yes 9 100 % 38.7 Positive
*Patient discontinued due to AE; #Patient had serial dose reductions for anemia

28. 28

29. PALB2: Partner and localizer of BRCA2. Pt 60: Biallelic HDAC2 loss and low HDAC1/2

30. Biomarker studies
DNA repair defects associate with response
DNA repair defects
Responder
Total
(N=49)No
(N=33)
Yes
(N=16)
Biomarker Negative 31 2 33 (67.3%)
Biomarker Positive 2 14 16 (32.7%)
Fishers’ exact p-value p<0.001
Sensitivity 87.5%
Specificity 93.9%
OR (95% CI), p value
*
108.5 (13.84, 850.5), p<0.001
* Estimated from a logistic regression model

31. Patients with and without DNA Repair Defects
Time to progression and Overall Survival

32. Changes in PSA and CTC Counts
Mean counts during treatment by biomarker

33. Individual CTC Counts for TOPARP-A Patients
Molecular Characterization was prospectively planned
but only available retrospectively-100
0
100200300
0 4 8 12 16 20 24 28 32 36 40 44 48 52 56 60 64
Weeks from C1D1
Biomarker negative Biomarker positive

34. Biomarker studies
BRCA2 loss sensitizes to olaparib
ID Germline hit?
Response
Y/N
RECIST
response
PSA fall
>50%
CTC
conversion
Time on
trial
(weeks)
14 YES YES N/A YES YES 36
15 YES YES PR YES YES 36
17 NO, SOMATIC fs + het-del YES PR YES YES 24
20 NO, SOMATIC fs + het-del YES PR YES N/E 40+
30 YES YES N/A YES YES 40+
35 NO, SOMATIC hom-del YES PR YES YES 24+
39 NO, SOMATIC hom-del YES PR YES YES 40+

35. Somatic homozygous deletion of BRCA2

36. Another BRCA2 Responder
BASELINE
WEEK 12
• Radiological PR lasting 9 months.
• Previously unknown germline BRCA2
mutation + loss of 2nd copy in tumor
(no family history of cancer)
0
20406080
100
CTCcount
0 10 20 30 40
Weeks of treatment
0
250500750
10001250
PSA(ng/ml)
0 10 20 30 40
Weeks of treatment
CTC COUNT PSA
Is BRCA carrier CRPC underdiagnosed? Probably.

37. Biomarker studies
ATM defects and response to olaparib
ID alteration detected
Response
Y/N
RECIST
response
PSA fall
>50%
CTC
conversion
Time on
trial
(weeks)
1
SOMATIC p.N2875S
(kinase domain)
YES N/E YES YES 73
5
GERMLINE stop gain p.W2638*
(kinase domain)
YES N/E YES YES 56+
6
SOMATIC fs deletion p.-2288fs
(kinase domain)
YES SD
NO
(30%)
YES 17*
12
GERMLINE fs del p.-1970 +
SOMATIC p.I2752F
(kinase domain)
NO PD NO NO 11
36
GERMLINE fs del p.-1267fs +
SOMATIC LOH
YES SD YES YES 57
*Patient 6 came off study after repeated dose reductions for anemia

38. • Prolonged response in a patient post
docetaxel, cabazitaxel, abiraterone and
enzalutamide.
• The patient is still responding after 10+
months. Has stopped opioids and his
mobility has improved.
• Germline FS del ATM + LOH in tumor.
• Transcriptome analysis: very low ATM
expression in tumor. 05
10152025
CTCcount
0 10 20 30 40
Weeks of treatment
0
250500750
100012501500
PSA(ng/ml)
0 10 20 30 40
Weeks of treatment
CTC COUNT
PSA
TO-PARP Responder: Biallelic ATM Loss
Patient on trial > 1 year

39. TO-PARP Responder:
ATM Genomic characterization by LOH analysis.
Chromoso
me Start End
Mean
Zygosity
Deviation
Log2
Coverage
Ratio
Copy
Number
Ratio Probability Classification
Heterozygous
SNPs
Targeted
Exons
11 106647135 108723102 0.414 -0.607 0.656561 1 1 Copy 41 208 ATM, GUCY1A2
ATM
ATM is on a region of one copy loss in the tumor.
The reference allele is lost in the tumor and the frameshifted variant allele is retained.

40. ATM expression across a cancer compendium
Red arrow is this patient’s ATM expression
TO-PARP Responder Case 3:
Low ATM mRNA Expression

41. 41
T001014 Pre – Castration Resistant Prostate Cancer (Poorly diff adenocarcinoma)
IHC: Nuclear H score: 0 Cytoplasm H score: 0
IHC: Nuclear H score: 0 Cytoplasm H score: 0 Responding patient

42. Biomarker studies
ATM Truncating Mutation and response to olaparib
Baseline +3 months
PSA
CTC count
NGS of the baseline bone marrow biopsy revealed a somatic missense mutation
within the ATM PI3K catalytic-domain (p.N2875S) without evidence of genomic
loss of the second allele and maintained ATM expression by IHC.
? Dominant negative (Bakkenist & Kastan, Nature 2003); Haploinsufficiency?

43. Serial Plasma DNA NGS: TOPARP

44. 0
10
20
30
40
50
60
70
80
0 1 2 3 4 5
cfDNA(ng)/mlplasma
Plasma samples
Patient T001-15-V4081-DB
0%
1%
2%
3%
4%
5%
6%
GERM ARCH FRESH
AlleleFrequency(%)
Tissue Samples
ATM N2875S
FGFR2
0%
5%
10%
15%
20%
25%
30%
13-1175-B 13-1288-B 13-1340-B 13-1514-B 13-2026-B 14-196-B
AlleleFrequency(%)
Plasma Samples

45. 0
10
20
30
40
50
60
0 1 2 3 4 5
cfDNA(ng)/mlplasmaPatient T001-14-V4038-TS
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
GERM ARCH FRESH
AlleleFrequency(%)
Tissue Samples
ATM p-1267fs+LOH
RAD51LOH
HNF1A p.A161T
FGFR2 p.S534
0%
10%
20%
30%
40%
50%
60%
70%
80%
13-1186-B 13-1255-B 13-1307-B 13-1471-B 14-163-B
AlleleFrequency(%)
Plasma samples
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
GERM ARCH FRESH
AlleleFrequency
Tissue samples
ATM
RAD51
FANCD2-1
FANCD2-2
FANCD2-3
0%
10%
20%
30%
40%
50%
60%
70%
80%
13-1186-B13-1255-B13-1307-B13-1471-B 14-163-B
AlleleFrequency
Plasma samples

46. 0
5
10
15
20
25
30
35
40
45
50
0 1 2 3 4 5
cfDNA(ng)/mlplasma
Plasma samples
Patient T001-09-V5116-BC
0%
5%
10%
15%
20%
25%
GERM ARCH* FRESH*
AlleleFrequency(%)
Tissue samples
TP53 E286K
NF1 I634T
CTNNB1 T41A
PRDCK S867T
0%
2%
4%
6%
8%
10%
12%
14%
16%
13-507-B 13-538-B 13-559-B 13-761-B 13-1087-B
AlleleFrequency(%)
Plasma samples
0%
10%
20%
30%
40%
50%
60%
70%
AlleleFrequency
Plasma samples
0%
10%
20%
30%
40%
50%
60%
70%
80%
GERM FRESH ARCH
AlleleFrequency
Tissue samples
CDH1
MSH3
ERCC4
ALK-1
ALK-2

47. TO-PARP Trial Conclusions
• Therapeutic trials in CRPC mandating fresh biopsies feasible
and can inform on disease biology
• A proportion of mCRPC have DNA repair defects that can be
targeted through a synthetic lethal strategy by PARPi.
• Approximately 20-30% of mCRPC patients warrant molecular
stratification by analyses of DNA repair gene defects
• It is envisioned that targeted NGS will impact the treatment of
CRPC patients not only in the metastatic setting but also
earlier in the management

48. in partnership with
Acknowledgements
Experimental Cancer
Medicine Centre
• To all patients and their families for their participation and support.
• To the AACR-ESMO-ECCO Flims workshop, where this protocol was developed.
• Supported by Cancer Research UK (CRUK/11/029; C12540/A12829; C1491/A15955;
C12540/A13230) through Collaboration between AstraZeneca and National Cancer Research
Network.
• SU2C-PCF Prostate Cancer Dream Team
• PCF Challenge Award (Knudsen, Feng, Rubin & de Bono).
• All the Cancer Biomarkers group at the ICR
• TOPARP investigators and all the staff at the participating sites, Trial Management Group, Trial
Steering Committee and IDMC. Staff at Clinical Trials and Statistics Units at the ICR.
Prostate Cancer UK is a registered charity in
England and Wales (1005541) and in
Scotland (SC039332). Registered company
2653887

51. Title, Location, Date 51