Transcript Biopsies of recurrent ovarian cancers for molecular profiling, can we

Biopsies
of recurrent epithelial ovarian cancers
for molecular profiling
Can we do without them?
Clare Scott MBBS PhD FRACP
Medical Oncologist RMH, RWH
Laboratory head, WEHI
Royal Melbourne Hospital
WHY BIOPSY?
Most women with
high-grade epithelial ovarian cancer OC
are treated with platinum/taxane chemotherapy
Therapies targeting defined molecular defects
are not yet approved
Chemotherapy success is limited and
it is imperative that we continue to drive
recent molecular advances
Would you want
Last Century’s medicine: surgery, carboplatin, taxol…..?
Last Century’s medicine: carboplatin, taxol…..
and BTW more chemo doesn’t work (paraphrased by IMcN)
….two large randomised trials, one conducted by the
Gynecologic Oncology Group (GOG) and the other by the
European Organisation for Research and Treatment of Cancer
(EORTC),
have shown that administration of the taxane paclitaxel in
combination with cisplatin significantly improves the
duration of progression-free survival and overall survival in
women with advanced epithelial ovarian cancer compared
with cisplatin–cyclophosphamide therapy
(McGuire et al, 1996; Piccart et al, 2000).
The “One size fits all approach” has failed
The promise of personalized cancer care
rests on our ability to truly
understand and respond effectively to the
biologic differences between patients
Peppercorn et al J Clin Oncol 2010
How do we define these differences?
Don’t treat very different subsets of
epithelial ovarian cancer as if they are one disease
Crum et al Curr
Op Obst
Gynaecol 2007
Vaughan et al, Nat Rev Ca, Oct 2011
Don’t treat one sub-type as if it is one disease
C1
C2
C3
C4
C5 C6
MYCN
MYCN inhibitors (Norris / Haber
/ Chesler)
? Impact on mortality of this
lethal subset of 15-20%
of HG serous OC
Tothill et al Clinc Canc Res 2008
Helland et al PLoS One 2011
Serous OC
Trastuzumab and Lapatinib:
>50% reduction in the
mortality of this lethal
subset of 15-20% of Breast
Cancer
Perou et al Nature 2000
Breast Cancer
Design clinical trials to match treatment
to molecular patterns
Which means we need to design smaller trials
that are tissue-driven
to match a woman’s ovarian cancer to the
treatment most likely to address
the drivers and susceptibilities of her cancer
What are the issues here?
What is Molecular Profiling?
The study of specific patterns (“signature”) of:
Protein
mRNA
Proteomics, IHC
gene expression profiling, RNASeq,
OncotypeDX, ISH for RNA
DNA
Sequencing, ISH for DNA amplific,
WGS/NGS, incl CNV
(Copy number variation) and SNPs
Epigenome DNA Methylation, histone marks,
ChIP-seq
Molecular Profiling
The study of specific patterns, or signature
of DNA, RNA and protein:
….and how this signature correlates molecular patterns with a
phenotype of interest.
Diverse molecular profiling platforms and strategies can be
implemented during drug development to identify biomarkers
useful for patient stratification.
“Detecting Gene Alterations in Cancers”
Diverse molecular profiling platforms and strategies
can be implemented during drug development to identify
biomarkers useful for patient stratification.
Frequency of Somatic Gene Mutations in
Epithelial Ovarian Cancer
Approximately 10–20% of high grade ovarian cancers are associated with germline
mutations in BRCA1/2 (Pal et al. 2005). Somatic alterations in BRCA1/2 and
other genes associated with DNA repair are seen in approximately 50% of
high grade ovarian cancers (TCGA 2011).
Type I tumors have low grade serous, clear cell, endometrioid, and mucinous
histological features: BRAF and KRAS somatic mutations are relatively
common in these tumors, which may have important therapeutic implications.
Type II tumors are high grade serous cancers of the ovary, peritoneum, and
fallopian tube, high grade endometrioid and poorly differentiated ovarian cancers as
well as carcinosarcomas: high levels
of genomic instability with few
common mutations, other than TP53, which is altered in over 90% of the
cases (Kurman and Shih 2011; Landen, Birrer, and Sood 2008; TCGA 2011). PIK3CA
and RAS signaling pathways are altered in 45% of the cases, but somatic mutations
are rare and gene amplifications are far more common (TCGA 2011).
Frequency of Somatic Gene Mutations in Epithelial
Ovarian Cancer
The most common ‘actionable’ alterations with potential for small molecule targeted
therapy in EOC tumors are in the PIK3CA/PTEN and KRAS/BRAF signaling pathways
Integrated genomic analyses of ovarian carcinoma
The Cancer Genome Atlas Research Network
high-grade serous ovarian cancer: TP53 mutations in almost all (96%);
low prevalence but statistically recurrent somatic mutations in
NF1, BRCA1, BRCA2, RB1, TP53, CSMD3, FAT3, GABRA6 and CDK12;
113 significant focal DNA copy number aberrations
Promoter methylation events involving 168 genes
4 ovarian cancer transcriptional subtypes,
3 microRNA subtypes,
4 promoter methylation subtypes and
1 transcriptional signature associated with survival duration,
BRCA1, BRCA2 and CCNE1 aberrations impact on survival
Homologous recombination is defective in about half of HG-SOC
NOTCH and FOXM1 signalling are involved
Design clinical trials to match treatment
to molecular patterns
What are the ethics to be considered by clinical
resaerchers, clinicians (standard of care),
patients and their supporters?
Ethics of Mandatory Research Biopsy for Correlative End
Points Within Clinical Trials in Oncology
What is a biopsy? (What about ascites?)
Peppercorn et al J Clin Oncol 2010
Ethics of Mandatory Research Biopsy for Correlative End
Points Within Clinical Trials in Oncology
In the era of molecularly targeted therapies and
continued poor outcomes, there is a pressing need
to improve our understanding of the biology of cancer
and to improve outcomes for future patients
The promise of personalized cancer care rests on our
ability to truly understand and respond effectively to the
biologic differences between patients
Peppercorn et al J Clin Oncol 2010
Ethics of Mandatory Research Biopsy for Correlative End
Points Within Clinical Trials in Oncology
Given the reality of constrained health care resources,
there is a need to determine
which patients may benefit from an intervention and
which should be treated with an alternative strategy.
There are moral dimensions to both our need for better
treatments and better use of health care resources.
Peppercorn et al
Ethics of Mandatory Research Biopsy for Correlative End
Points Within Clinical Trials in Oncology
There is a need to acknowledge that patients with cancer
seeking access to investigational therapy are
frequently under duress from their illness and
may be interested in trial participation primarily due to
expectation of direct personal benefit.
Peppercorn et al
Ethics of Mandatory Research Biopsy for Correlative End
Points Within Clinical Trials in Oncology
Any study using research biopsies in this population must be:
well designed to address the scientific question,
obtain the biopsy with minimal possible risk and
ensure that research participants are fully informed of the
risks, rationale, and requirements of the study,
as well as of treatment alternatives.
Peppercorn et al
Ethics of Mandatory Research Biopsy for Correlative End
Points Within Clinical Trials in Oncology
In addition, the scientific justification for
a mandatory biopsy design
as opposed to optional biopsy
or use of clinical specimens for correlative end points
must be carefully considered in trial design and review.
Peppercorn et al
Ethics of Mandatory Research Biopsy for Correlative End
Points Within Clinical Trials in Oncology
We feel that if these guidelines are respected, an informed
adult with cancer can both understand and voluntarily
consent to participation in a clinical trial involving
mandatory research biopsy for scientific end points.
Such trials may be necessary to ultimately defeat
cancer, and our patients can be valued and
respected partners in this effort.
Peppercorn et al
A major impediment to
successful targeting of therapy in OC is
poor availability to OC tissue,
particularly upon OC recurrence.
Biopsy of recurrent OC would massively improve our
ability to attack the
genetic drivers and susceptibilities of a woman’s OC and
improve the possibility of “allocating” each patient to
the most appropriate treatment available.
Without biopsying individual OC,
improved survival may remain elusive.
in vivo platinum
DNA repair gene mutation
No DNA repair gene mutation
PDX Sensitive
>/100d
PARP inhibitors
? Immune therapy
? Model of BRCA1/2 mutation
carriers resistant to PARP inhibitors
?anti-angiogenic therapy
PDX Resistant
<100d
PDX Refractory
PD on Platinum
PARP inhibitor AND
Oncogene inhibitors /
BH3 mimetics
Oncogene inhibitors /
BH3 mimetics
Monique Topp, WEHI
BILL GATES
As we look ahead into the next century
leaders will be those
who empower others
It is up to us to lead
by empowering future researchers and patients
with research repositories and processes
that are relevant for this century
of molecular technological advances
No technology can rescue us from our
cumbersome last century habits
Back to the biopsy:
Alternatives to solid tissue?
Ascites
A Blood test????
Timing?
At relapse?
What about at First Diagnosis?
Back to the biopsy:
Tumor heterogeneity
Does everything end up in the blood?
Just A Blood test????
Breast Cancer
Circulating tumor DNA was successfully detected in 29 of the 30 women
(97%) in whom somatic genomic alterations were identified;
Circulating tumor DNA levels showed a greater dynamic range, and
greater correlation with changes in tumor burden, than did CA 15-3 or
circulating tumor cells.
Breast Cancer
…when mutations could be detected in the primary tumor and
subsequently in the plasma, the variation in the number of copies of
circulating tumor DNA was reasonably correlated with responses to
treatment.
In addition, there was a significant relationship between the number
of copies in blood and the ultimate prognosis of the patient.
Breast Cancer
“…..could more reliably predict patients who might not need further
therapy or identify those with localized breast cancer who would be
adequately treated by lumpectomy alone.”
“…..might be used to screen for recurrences in asymptomatic patients
with previously diagnosed early-stage disease...”
“….identification of new mutations in circulating tumor DNA over
time might inform the clinician about tumor evolution and provide evidence
to support new treatment targets not identifiable in the primary”
Pancreatic Cancer
Ovarian Cancer
Ovarian Cancer
Ovarian Cancer
Plasma of (OC) cancer patients contains cell-free tumor DNA
that carries information on tumor mutations and tumor burden.
Individual mutations have been probed using allele-specific
assays, ….developed a method for
tagged-amplicon deep sequencing (TAm-Seq)
Ovarian Cancer
We identified mutations throughout the tumor suppressor gene TP53
in circulating DNA from 46 plasma samples of advanced OC patients.
We demonstrated use of TAm-Seq to noninvasively identify the origin
of metastatic relapse in a patient with multiple primary tumors.
This low-cost, high-throughput method could facilitate analysis of
circulating DNA as
a noninvasive “liquid biopsy” for personalized cancer genomics.
Ovarian Cancer
Editor’s Summary
Through several experiments, the
authors were able to show that TAmSeq is a viable method for sequencing
decision-making on an individual basis.
….. once optimized, this ''liquid
biopsy'' approach will be amenable to
personalized genomics, where the level
and type of mutations in ctDNA would
inform clinical plasma of patients with
less advanced cancers.
BUT it will take a while…(!!!!)
to be able to glean all we need to know
from the blood (a liquid biopsy)
In the meantime, we need tissue biopsies
to establish actionable molecular
abberations
(if not surgery itself…..)
Collecting tissue,
and analyse it,
to empower clinical researchers
to design appropriate clinical trials
for their patients
to target therapy to drivers/susceptibilities of OC
To move on from last century’s medicine
Patient diagnosed with HG-EOC

Diagnostic sample collected and analysed

Recurrent disease – sample collected and compared

Can additional analysis inform choice of therapy?

Iterative……
Professor Paul Waring (Principal Investigator)
Professor Michael Quinn (Chair, governance committee)
Dr Orla McNally (Surgical Lead)
Professor David Bowtell (Genomics lead)
Assoc. Prof. Linda Mileshkin (Clinical lead)
Assoc. Prof. Clare Scott (Scientific lead)
Professor Graham Taylor (Diagnostics lead)
Dr. Jayesh Desai (CTA lead)
Dr. Ben Tran (Tumour Board lead)
Dr Kathryn Alsop
Olga Kondrashova (PhD student)