Download The integration of personalized treatment with

The integration of
personalized treatment
with clinical research:
CoPPO
Copenhagen Prospective
Personalized Oncology
Ulrik Lassen, Professor, MD, PH.D.
Phase 1 Unit, www.rigshospitalet.dk/phase1
Department of Oncology, Rigshospitalet
Phase 1 Unit 2005 • In recent years, the technical demands of early clinical trials have
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increased.
As a consequence, the department has opened a dedicated unit for
experimental cancer therapy and phase 1 trials in 2005 with new
facilities
Only one dedicated Phase 1 Unit in Denmark assures sufficient
volume and track record
This ensures that patients from all over the country can be referred
to clinical trials, including phase 1 trials with no costs incurred on the
referring hospital.
Recruitment of patients from all Denmark (5.6 million) in phase 1
studies in Copenhagen (plus Nordic patients)
But how to become competitive?
Governmental initiatives and goals 2014-17
• A further increase of 10% in the number of clinical trials
with public-private partnership (both pharma - and
academic trials).
• Attraction of more than 20-30 new trials by the enterprise
(medical devices and pharmaceuticals).
• Increase of 5% in the number of clinical trials with medical
devices with public-private cooperation.
• Increase of 5 per cent in the number of subjects
participating in clinical trials with public-private cooperation
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• Continued engagement for the high quality of clinical
research with public-private cooperation.
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NATIONAL EXPERIMENTAL
THERAPY PARTNERSHIP
Research
• The NEXT partnership brings Denmark together as
a unified investigational site with national
recruitment and patient database.
• NEXT offers the pharmaceutical industry and
hospital researchers a one-stop shop: easy access
to Denmark’s strongest clinical research
environments within the early phases of clinical
research, national recruitment of patients and
optimised administrative and regulatory processes.
INNO+
NEXT partnership envisions Denmark as a world-class country of choice for early clinical
testing of new drugs in patients which will strengthen early clinical research in Denmark
and provide Danish patients early access to novel medical therapy.
• The Phase 1 Unit at Rigshospitalet has been appointed as a
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national pilot center for early phase oncology/hematology studies.
The pilot center will chair a national steering group to coordinate
the associated network (Herlev, Odense, Århus and Aalborg)
The network will generate innovative initiatives making Denmark
a preferred partner for early drug development and increase the
number of clinical trials
The network will also act as a platform for coordinating
investigator-initiated trials, including translational research.
A transnational analytical unit will collect data, including
molecular biomarkers for correlation with clinical data from the
national clinical databases and registries
Novartis, MSD and Roche are part of the INNO+ NEXT Oncology
program – more companies have applied
Perspectives of INNO+
• INNO+ is establishing a structural mutual binding collaboration
for early phase oncologic and hematologic trials
• The pilot center will have patients referred from the whole
country (central referral) and act as the only Danish dedicated
Phase 1 unit
• When applicable, all partners will enrol patients: - Phase 1a
(first in humans) primarily at the pilot center - Other Phase 1
trials at more sites when needed - Phase 2 trials at all sites
• More Phase 1 trials will continue into Phase 2 to be performed
at all sites, thereby increasing the number of trials offered to all
patients and partners of INNO+
Studies performed in the Phase 1 Unit
• First-in-humans, phase 1a
• Dose-finding (including add-on)
• PK/PD interaction studies (DDI)
• Standardized diets
• Phase 1b
• Early phase 2
• Randomized phase 2 with PK/PD
• Tumor basket and umbrella studies
Innovation
Tumor regression was seen in 30% of patients
with mutations, compared to 10% of patients
without mutations.
There may be an advantage by selecting patients
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Yap T et al. 2010
New track for early clinical trials
Yap T et al. 2010
The academic medical center precision medicine tumor board model.
Jürgensmeier J M et al. Clin Cancer Res 2014;20:4425-4435
©2014 by American Association for Cancer Research
Basket trial – 1 specific target
Umbrella trial
25 ongoing Phase 1 trials (11 FIH)
(16 solid tumors, 2 heme malignancies)
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Roche: 7 (4 FIH)
Sanofi: 1 (FIH)
Novartis: 4 (1 includes also heme)
BMS: 1
Genentech 2
MSD: 1
Eli Lilly: 1 (includes also heme)
Genmab: 3 (2 FIH, 1 MM)
Karyopharm: 1 (FIH + 2 Phase 2)
Merck Serono: 2 (includes also heme)
Liplasome: 1, plus other small biotechs
Pending: BMS, Roche, Puma, Celgene, Bayer, AstraZeneca,
Loxo (to start Q2 2016)
Copenhagen Prospective Personalized Oncology (CoPPO):
Sequencing and array-based pipeline for selection of patients to
Phase 1 studies
• Patients with good performance status and tumor
lesions assessable for biopsy are included in a
study of genomic characterization
• A collaboration between the Phase 1 Unit,
Pathology, Genomic Medicine, Clinical Genetics,
Diagnostic Radiology and Bioinformatics at BRIC
• Important for drug development, attracting new
studies and allocating patients for studies
• We are part of an European network and hope to be
able to distribute patients for enrichment of studies
in the future
Complete genomic profile of phase 1 population
• > 300 patients are referred to the Phase 1 Unit every year.
• Every patient will be asked for a signed informed
• Eligible patients are required to fulfill normal criteria for
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entering early phase studies, including normal organ function
and adequate performance status, as well as measurable
disease.
Most patient fulfill these criteria, and it is anticipated that 500
patients will be eligible during the project period (5 years).
Patients will be referred for ultrasound-guided tumor biopsies
with 18 Gauge needle.
Biopsies snap-frozen/RNA-later and paraffin-embedded as
well as verified for their representativeness, tumor cell content,
and suitability for molecular analysis at the Department of
Pathology
A blood sample (7ml) is taken, from which germline mutations
can be subtracted in the tumor/normal analysis
Genome-wide technologies and identification of
tumor specific genetic changes
• The Center for Genomic Medicine functions as core facility for
array and NGS technologies and covers all necessary highthroughput analyses from microarray-based transcriptome
profiling to analysis of SNP arrays (Affymetrix) as well as NGS
(Illumina and Roche platforms).
• The pipeline from biopsy to isolation of DNA and RNA is firmly
established as part of our front-line work-up of carcinoma of
unknown origin and childhood solid tumours, which are subject
to array analysis and exome sequencing, respectively.
• All samples are handled according to standard operation
procedures and quality control parameters according to
MIAME and Tumor Analysis Best Practices Working Group
www.rhmicroarray.com
Tumor and normal DNA is examined by exome
sequencing and tumor mutations are organized
according to the cellular function of the affected
genes
• DNA and RNA are purified from the biopsies stored in
RNAlater® and DNA is isolated from the blood sample.
• Tumor and germline DNA are subjected to whole exome
sequencing (WES) using SureSelect v5 sequence capture
(Agilent) and Illumina HiSeq2500.
• In addition to WES of the DNA isolated from the tumor
containing biopsy, targeted sequencing of 48 important
cancer-related genes is performed with The TruSeq Amplicon
– Cancer Panel (Illumina).
• Sequence information from this panel is obtained by
sequencing on the Illumina MySeq platform.
RNA-sequencing
• From the isolated tumor RNA, an expression array is performed
to molecularly classify the origin of the primary tumor, as well as
to look at the expression level of therapeutic targets.
• In addition to the expression array, RNA-sequencing (Nugens
Ovation RNA-seq system v2) is performed to verify the data
from the expression array, verify the expression of a transcript
harboring an activating mutation, and to investigate whether
chromosomal translocations are the reason for tumor specific
expression of an oncogene.
• These data will be paired with clinical and gene expression
profile to identify potential causative association between
mutations and clinical factors as well as gene expression, gene
activation, and prognosis.
Workflow
• Data are analyzed using CLC Genomics Workbench (Qiagen),
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where data from WES are mapped against hg19, aiming at an
average coverage between 80-100x.
Identification of somatic mutations is performed using a tumornormal analysis in which the inherited variants are subtracted
from the tumor variants.
The identified somatic mutations are exported into Ingenuity
Variant Analysis (Qiagen) to identify causal variants.
Data from The TruSeq Amplicon – Cancer Panel is analysed
using the CLC Cancer Research Workbench (Qiagen) to
directly call cancer driver mutations.
Gene expression levels and copy number variants are celled
from the two arrays by using Partek software (Partek
Incorporated).
Practical issues
• Bi-weekly tumor board meetings with oncologist,
molecular biologist, biostatisticians (bio-informatic),
pathologists and clinical geneticist
• Turn-around time 4 weeks (2 weeks for initial DNAseq and 4 weeks for RNA-seq and complete report)
• If biopsy is not possible we consider archieval tissue
or blood sample for WES or targeted sequencing
• In case of supected germ-line mutation patients are
offered genetic counselling
• Prior to treatment start and at fixed time points
during treatment, blood samples are taken to track
selected mutations in cfDNA
Ethical aspects
• Obtaining a wide genomic profile of tumor tissue requires a
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parallel investigation of germline DNA in order to detect tumor
specific mutations.
There exists a minor risk that mutations that is not disease
related could be identified.
Handling of incidental knowledge has to be taken into account
when introducing genomic screening in personalized
medicine.
Participants have to be aware of this possibility and have to be
well informed of consequences.
The implications and procedures involved in the analysis and
handling of patient data are discussed prior to consent.
There are four possible outcomes of exome sequencing
Possible outcomes
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Finding of gene alterations considered being the cause of the
hereditary disease. In this case the patient will be offered genetic
counselling.
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Finding of gene alterations that cannot be determined accurately.
Thus, it is unclear whether these are associated with the disease.
In some cases it may be necessary to examine several members of
the family, the patients can decide the level of information.
3.
No specific gene alterations associated to disease are found.
However, in the future, some of the genes may be associated with
disease. In case, the patient or the family will be informed if
additional information is encountered.
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When studying all genes with exome sequencing, there is a risk
that gene alteration not associated with heritable disease is found,
so called incidental findings. This could be genes associated with
an increased risk of a disease of the nervous system. Such a finding
may have implications for the patient or other family members.
Endpoints
• Results are reviewed by a tumor board that verifies the clinical
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relevance of the findings and defines an “actionable” target.
The treatment suggested by the tumor board can be either a drug
under development or a marketed drug.
If no actionable target can be revealed from the screening, the
patient will be allocated to a non-matched, random available slot in a
phase 1 trial.
Specific targets, for which Phase I trials exist but are based on the
assessment and/or verification of the target as such or of other
members of the target’s pathway at the protein level, can be further,
investigated in the parallel FFPE biopsy by using
immunohistochemical techniques.
To assess the antitumor effects of treatments, tumor response will be
evaluated using RECIST criteria.
Progression free survival (PFS) from the treatment will be compared
to PFS of the most recent standard treatment (PFS ratio).
Expression profiles are refined according to
actionable targets
• FGFR-pathway
• Notch pathway
• RAS-RAF-MEK-ERK pathway
• PTEN/PI3K/AKT/mTOR
• ALK and ROS1
• EGFR, HER2, HER3, HER4 and TRK-fusions
• C-met and IDH1
• Protein and ligand expression
- in relationen to Mab in development:
CEA, TF, mesothelin, EGFR, HER2, FAP, LAMP1
• Immunoscore: MSI, mutational load, PD-L1
ERBB2 c.929C>A p.S310Y
PIK3CA c.3140A>G p.H1047R
APC c.5432C>T p.S1811L
APC c.7498C>G p.Q2500E
ESR1 c.1571A>T pH524L
RAD51C c.61C>G p.P21A
The perspectives of gene profiling
• Enrichment of population for phase 1 studies
• Attracting more studies and offering personalized
therapy for the patients
• Recruiting patients
• Referring patients for appropriate studies locally and
globally
• Offering treatment with selected marketed targeted
agents
Challenges
• Driver versus pasenger mutations
• Finding the right agents
• Tumor heterogeneity
• Identifiyng valid immune profiles
Future directions: liquid biopsies
• We now have facilities for liquid biopsies to study
circulating DNA and have an established
collaboration with Nitzan Rosenfeld in Cambridge
• Patients are having this performed every 4 weeks
during therapy (more frequent at start)
• Patients will be re-biopsied at progression to study
longitudinal changes
• One particular study allows screening for mutations
based on cfDNA in a national screening program
Glioblastoma
• We will perform molecular profiling of newly diagnosed and recurrent GBM
by collecting surgical specimens for DNA sequencing and RNA
expression
• Test individualized therapy for GBM by:
• Including patients with primary GBM and relevant individual
molecular profiles in trials with targeted therapy.
• Evaluating the effect of an individualized treatment program on
survival
• Correlate genetic alterations in tumors prior and following therapy with
clinical data to search for possible resistance mechanisms to first-line and
second-line GBM therapy which could be targeted by available drugs.
• Evaluate new drug combinations for GBM treatment preclinically by:
• Identifying or possibly establishing relevant cell models from patient
tumors with specific genetic alterations for evaluation of drugs
identified (Organoids and PDX)
• Evaluating the therapeutic effects of the drugs both under in vitro
and in vivo conditions.
Metastatic breast cancer
• Establishment of a drug-screening platform, facilitating
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individualised cancer therapy of patients with metastatic solid
tumours.
These will be newly diagnosed metastatic breast cancer
patients (c100 patients/year) and patients from the Phase I
Unit (c200 patients/year; mostly with colon cancer) who have
no further treatment options.
(1) Perform molecular profiling through sequencing and kinase
profiling
(2) Establish organoid cultures to identify effective drugs to be
used for each patient
(3) Establish PDX models for each patient for further drug
testing and biological studies
Whole-exome Sequencing to estimate tumor mutational
load and identify immune-profiles to predict clinical benefit
of checkpoint blockade therapy
Hypothesis:
•Methods to identify which tumor-specific mutant peptides (neoantigens) can
elicit anti-tumor T cell immunity that are needed to improve predictions of
checkpoint therapy response
•Massively parallel sequencing data including annotated non-synonymous
somatic variants that have been ‘ translated’ into mutant amino acid changes,
as well as patient-specific HLA alleles, can provide a basis for Precision
Medicine within immuno-oncology
The project has three aims:
•Retrospective analyses to correlate the load neoantigens from WES and
activity of checkpoint inhibitors.
•Retrospective analyses to correlate immune-profiles (TILs and other immunerelated features) and the activity of checkpoint inhibitors.
•Prospective clinical trial of checkpoint-inhibition of non-colorectal cancer
patients with high mutational load or micro-satellite instability (MSI).
•Analysis of gut microbiota and germline genomic alterations in patients treated
with checkpoint-inhibition and the effect on adverse events and response to
therapy.
Aknowledments
NATIONAL EXPERIMENTAL
THERAPY PARTNERSHIP
Rigshospitalet:
Dept. of Oncology: Ida Viller Tuxen, Morten Mau-Sørensen, Kristoffer Rohrberg, Martin Hutchings
Dept. of Pathology: Eric Santoni-Rugui and Jane Preuss Hasselby
Dept. of Genomic Medicine: Finn Cilius Nielsen, Lars Jønson, Olga Østrup and Christina Yde
Dept. of Clinical Genetics: Anne-Mette Gerdes and Karin Waadt
Dept. of Radiology: Mikkel Dam, Flemming Jensen, Bo Nyhus and Birthe Henriksen
The Neuro-Oncology Steering Group
The staff at the Phase 1 Unit
BRIC:
Bioinformatics Centre: Anders Krogh and Ole Winther
Paris:
Institute Gustave Roussy: Jean-Charles Soria
Cambridge:
Cancer Research UK Cambridge Institute, University of Cambridge, Nitzan Rosenfeld
And all the patiens
Funding:
Region Hovedstaden, The Danish Cancer Society and Arvid Nilssons Foundation