From eligibility to CDx: developing and implementing ... · Profile Multiple Technologies and...

Copyright ©2016 Q2 Solutions. All rights reserved.

From eligibility to CDx: developing and implementing

effective biomarker strategies for Immuno-oncology trials

Patrice Hugo, Ph.D., Chief Scientific Officer

Patrick Hurban, Ph.D., Senior Director and Global Head, Genomic Development/Esoteric Assays

Biomarker and Diagnostics World Congress May 18, 2016

2 COMPANY CONFIDENTIAL

• Over 45 immuno-oncology drugs approved (US)*

• 57 immuno-oncology drugs in development*

• Over 250 studies registered/ongoing*

• Increasing number of relevant publications annually**

The Opportunity for Immuno-Oncology (IO): The Future of Cancer Treatment

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**PubMed; keywords ‘cancer immunotherapy’

*UBS Immuno-oncology Monthly Handbook (Jan 2015)


Examples of Immuno-oncology therapies

• Immunomodulatory cytokines/receptors (ex: OX40,

CSF-1R)

• Bi-specific T cell engagers –BiTEs-

• Chimeric antigen receptors (CARs)

• Checkpoint inhibitors (ex: CTLA4, PD-1/PD-L1)

• Anti-cancer vaccines

• Adoptive cell transfer

• Immunosuppressive metabolism inhibitors (ex: IDO)

Novel Immunotherapies: Oncology’s “Breakthrough” Drugs From hypothesis to realization and refinement

www.researchcancerimmunotherapy.com

http://www.researchcancerimmunotherapy.com/overview/targeted-cancer-research

https://www.google.com/search?q=cancer+immunotherapy+timeline+pd-l1&biw=1384&bih=617&tbm=isch&tbs=simg:CAQSEglE18J7x_1PsFyELhFs8h6EC-A


Classification of Immuno-Oncology Therapies Immunomodulatory mAbs as Checkpoint Inhibitors: A Revolution

Source: Galluzi et al., Oncotarget, 5: www.impactjournals.com/oncotarget/

Checkpoint inhibitor posterchild:

Anti-PD-1/PD-L1 antibodies

Brahmer et al, N Engl J Med 2015; 373:123-135


Expansion of PD-1/PL-L1 drugs into multiple indications and combinations adds complexity and opportunity

Mono therapy Combination

Phase I

Phase II

Phase III

BMS-936559

MEDI4736 (I/II)

Nivolumab + iliolumbar

Advanced Solid Tumors

MPDL3280A + vemurafenib (Phase Ib)

MEDI4736 + dabrafenib + trametinib or trametinib alone (I/II)

Nivolumab ± ipilimumab

Nivolumab + ipilimumab

Nivolumab + ipilimumab

Nivolumab sequentially with ipilimumab Nivolumab

Nivolumab + multiple class 1 peptides & montanide ISA 51 VG

Nivolumab

Pembrolizumab

Pembrolizumab

Melanoma

MPDL3280A + erlotinib (Phase Ib) MPDL3280A

MPDL3280A

MEDI4736 + tremelimumab (I/II)

Nivolumab ± gemcitabine/cisplatin, pemetrexed/cisplatin, carboplatin/paclitaxel, bevacizumab, erlotinib, ipilimumab Nivolumab

Pembrolizumab

Pembrolizumab (II/III) NSCLC

MPDL3280A ± bevacizumab vs sunitinib

Nivolumab + sunitinib, pazopanib, or ipilimumab

Nivolumab

Nivolumab

Pembrolizumab + pazopanib

Pidilizumab ± dendritic cell/RCC fusion cell vaccine

Renal Cell Carcinoma MPDL3280A

Solid or Hematological Malignancies

Pembrolizumab

Colon Cancer

Pembrolizumab

Nivolumab ± ipilimumab (I/II)

Gastric, SCLC, TNBC, HNC, Urothelial

Nivolumab ± ipilimumab

Glioblastoma

Nivolumab

Hepatocellular

Pembrolizumab Hodgkin Lymphoma,

Myeloma, MDS, NHL

Pidilizumab (I/II) Malignant Gliomas

Pembrolizumab Melanoma, NSCLC

Pidilizumab + gemcitabine

Pancreatic

Pidilizumab + sipuleucel-T + cyclophosphamide

Prostate Cancer

MPDL3280A + bevacizumab and/or chemotherapy

MPDL3280A + cobimetinib

MEDI4736 + tremelimumab MEDI4736

MSB0010718C

Anti-LAG3 (BMS-986016) ± nivolumab

Nivolumab

Nivolumab + interleukin-21

AMP-554

Solid Tumors

Pembrolizumab (NSCLC)

Nivolumab ± ipilimumab (I/II)

AMP-514 + MEDI4736

MPDL3280A + radiation therapy MPDL3280A + carboplatin + paclitaxel / nab-paclitaxel

Pembrolizumab

Pembrolizumab

MPDL3280A

Pembrolizumab (I/II)

Pembrolizumab (I/II)

Pembrolizumab (I/II)2

Pembrolizumab + dabrafenib (I/II) + trametinib

Pembrolizumab + cisplatin + 5-FU3

Tremelimumab and / or MEDI4736 + radiation

MPDL3280A ± lenalidomide

MPDL3280A ± bevacizumab vs sunitinib

MPDL3280A + bevacizumab

MPDL3280A + RO6895882

MPDL3280A + carboplatin + nab-paclitaxel

MPDL3280A + RO5509554

MPDL3280A + RO7009789

MPDL3280A + obinutuzumab4

MPDL3280A + Interferon alfa-2b / ipilimumab

MPDL3280A

Avelumab

Skin Cancer

Avelumab

MPDL3280A + INCB024360

MPDL3280A + carboplatin + paclitaxel ± bevacizumab

Biomarker driven therapy

May 2015

Source: Quintiles Internal Analysis, Clinicaltrials.gov, BioPharm Clinical & ADIS Database,

Dolan, 2014, Cancer Control. 2014:231-237


Novel Immuno-Oncology Drugs in the Pipeline

Source: Nature Biotech. 33:7 73-67, 52015


Current Challenges Turning a fatal disease into a chronic treatable disorder

Over 800 cancer drugs in clinical trials -

almost all are targeted at particular gene

products

Some Fundamental Problems in Cancer

Treatment

• Cancer is rarely detected early

• Cancer develops resistance rapidly to

targeted therapies and chemotherapies

due to the development/expansion of

resistance mutations

• Many patients do not respond to

immunotherapies. Immunotherapies are

changing the approach to treating cancer

by treating the immune system rather than

the cancer but not all patients respond

Source: Sharma, Allison: Cell, April 2015


Immuno-oncology: A Comprehensive Biomarker Approach is Needed

Tumor – Immune Biology

• Target protein expression

• Serum soluble proteins

• Circulating tumor cells

• Circulating free DNA

• Tumor gene expression


Immuno-oncology Research Requires Diverse Resources An integrated scientific approach can help drive a successful I-O clinical study

Flow Cytometry

Immunoassay

IHC

Genomics

Anatomic

Pathology

Target

Occupancy

Cytokine

Panels

ISH

Immune

Repertoire

Tumor

Antigens

Effector

Function

Immuno-

phenotyping

Immuno-

monitoring

Tumor

Lysates,

Cell Sorting

Digital

Pathology

Gene

Expression

Profile

Multiple Technologies and Methods Integrated Scientific Teams

Immunologists

Geneticists

Technical Experts

Pathologists

Clinical Scientists

Bioinformaticists


The Overlooked Fundamentals: Sample Quality Methods and best practices to maximize integrity of clinical specimens

Pre-Analytics

Standardized collection

methods

Established guidelines (fixatives, fixation time,

etc.), collection device, biopsies versus blood,

etc.

Proper shipping/handling Logistics infrastructure, insulated shippers

Stabilization/Preservation PAXgene tubes, cfDNA tubes, ethanol fixation

Sample Processing

Cell Enrichment Cell purification, PBMC isolation, CTC isolation,

FFPET macrodissection

Ex vivo assays Cell stimulation, drug treatment, co-culture

Sample QC Pathology review (% tumor), tissue quantity,

viability assessment

Nucleic Acid Preparation

FFPET-specific protocols (e.g.

degraded material)

FFPET extraction and purification methods,

optimized target capture protocols, increased

depth of coverage, specialized bioinformatics


Routinely collected clinical samples

Data can be mined for immune-oncology characterization

Anatomic Pathology and Immuno-Oncology Predicting and assessing a patient’s response to checkpoint inhibitors

Samples Central AP testing Potential Application How these characterizations can be used in drug studies

Tissue

PD-L1 or related immuno-

modulatory proteins

Tumor-infiltrating

lymphocytes (TILs)

Image Analysis for

multiplex IHC assays

CDx Registrational trial

Predictive Biomarkers for

Optimized Patient Selection



CDx Registrational Trial


• PD-1/PD-L1 expression by

Immunohistochemistry (IHC) in multiple

indications

• Numerous assays and scoring methodologies

• Expression on tumor cells vs. non-malignant cells

• Cutoffs

• Standardization of assay and scoring will be key

• Companion diagnostic (CDx) assay for PD-1

/PD-L1 inhibitors

• Central lab acts as investigative sites (PI and

regulatory support)

• Tumor-infiltrating lymphocytes: Assay

development for CD8, FoxP3 IHC

Anatomic Pathology and Immuno-Oncology Clinical Trials Ongoing biomarker assessments across all phases of development


Situation: Pharma requires pathologist expertise and central testing for

large CDx program

Solution:

– Pathologist familiar with drug MOA engaged to score and refine protocols for multiple

indications in collaboration with Rx pathologist and support from Dx

– Global laboratories trained with expanded pathologist team led by lead pathologist

Result: Global assay deployment, cost and time-savings for pharma, central lab

pathologist support for regulatory discussions

Case Study: Pathologist Expertise for IHC CDx Development of scoring methodology for Rx-sponsored study using Dx-provided assay

Protein

Biomarker

Scoring

Development

Lab

Pharma

Global

Deployment

Dx

Pharma

Dx

Ongoing CDx

Support

Lab

Pharma

Dx



Data can be mined for immune-oncology characterization

Flow Cytometry in Immuno-Oncology New opportunities for immune characterization

Samples Central Flow Analysis Potential Application How these characterizations can be used in drug studies

Blood

Immune Status

• T, B, NK, Monocyte, DC

Cell Subset Activation

Profile

Receptor Occupancy

ExVivo Predictive Assay

Retrospective Data Analysis

Correlation of Activation Profile

to Response




Cancer Immunotherapy Monitoring Flow Cytometry Assays

• Antigen Specific T Cells (Dimers,

Tetramers, Pentamers)

• B Cell Bcl-2 Family Assay

• Bispecific Antibody Assays

• CAR T Cell Assays

• Cell Culture/Predictive Bioassays

• Cytotoxic T Cells (Functional Assays)

• Dendritic Cell Assays (pDC, m1DC, m2DC)

• Leukemia/Lymphoma Assays (EuroFlow)

• Magnetic Bead Separation (RNA, DNA)

• Minimal Residual Disease Assay (CLL, ML,

MM, AML, ALL, NHL)

•

• Myeloid/Fibrocyte Derived Suppressor

Cell Assays

• Phosphorylated Protein Assays (pSMAD,

pCCR5, Whole Blood & PBMC)

• Receptor Occupancy Assays

• T Cell Homing/Activation (ICOS, CD38,

HLA-DR, CD28, CD25, CD69, CD71, CD134)

• T Cell Checkpoint/Exhaustion Assays

(CTLA-4, PD-1, PD-L1, TIM3)

• TIL Assays(Tumor Infiltrating T Cells)

• T Regulatory Cell Assays (surface, FoxP3,

activated)

•


Q2 Solutions Flow Panels Identify Dose Dependent PD Effect of Checkpoint Inhibitor Combination Therapy MEDI4736 (anti-PD-L1) & Tremelimumab (anti-CTLA-4)

Activation & Memory T Cell Panel

Combined data from flow panels running in US, Europe and Asia

Proliferating T Cell Panel

Source: Safety and antitumour activity of durvalumab plus Tremelimumab in non-small cell lung cancer: a multicentre, phase 1b study

Scott Antonia, Sarah B Goldberg, Ani Balmanoukian, Jamie E Chaft, Rachel E Sanborn, Ashok Gupta, Rajesh Narwal, Keith Steele, Yu Gu,

Joyson J Karakunnel, Naiyer A Rizvi

Lancet Oncology 2016. Published February 5, 2016


Beyond IHC and flow cytometry:

Incorporation of genomics due to limitations of other methodologies

(e.g. subjectivity, quantitative ability, low capacity for multiplex, sensitivity, etc.)

Immuno-Oncology is Genomics Solutions Oriented Molecular methods provide an advantage for complex biomarker analysis

Mutational Load

Gene Expression Signature

Immune Repertoire



Data can be mined for molecular immune-oncology characterization

Genomics in Immuno-Oncology Innovation New opportunities for molecular characterization

Samples Analysis Potential Application How these characterizations can be used in drug studies

Saliva

Blood

Biopsy

Slides

Self-recognition HLA and KIR genotyping

Immune activation B and T-cell repertoire,

Immune gene signature

Tumor

characterization DNA and RNA

Cancer Vaccines and Tumor-

Specific Immune Responses


Refinement of Immuno-

modulatory Therapies

Exploitation of Innate and

Adaptive Immune Response to

Tumors


Novel Antigen Determination Can Kick-Start Immunity

Source: Van Allen et. al. (2015) Science 350(6257):207

• In most cases, somatic mutation calling

from Exomes provides early evidence of

malformed antigens

• Coupling with RNA-Seq is essential to

confer expression of that variant allele

• Clinical group groups by mutation burden

within antigens

• Creating custom antibodies to restore

recognition has increased survivability


Immune Repertoire

• TCR (/, /) and BCR

receptor sequencing to

assess clonal diversity*

• IgVH mutation analysis

(RNA-based)

• Whole-exome deep sequencing to quantify mutational burden

• Identification of ‘neo-antigens’

– Coupled with RNAseq to confirm tumor antigen expression

• BFX and predictive algorithms to generate ‘immunogenicity score’

• DNA damage and mismatch repair:

– MSI instability (PCR and IHC)

– BRCA1 mutation analysis

Genomics Capabilities for Immuno-Oncology Analyzing the tumor: immune system interface

*In development; planned for 2016

HLA and KIR Genotyping

• HLA allele calling from:

–Microarray

–RNAseq

–Targeted DNA sequencing

• KIR genotyping and expression (from PAXgene) using commercial kit (Miltenyi)

http://www.innovations-report.com

Source: Draper et al, Clinical Cancer Research.

October 1, 2015

Mutation Analysis HLA and KIR

Genotyping Immune Repertoire


Checkpoint Inhibitor

Expression

Mutational Load

Gene Expression Signature

Immune Repertoire

Immuno-oncology is Genomics Solutions Oriented Molecular methods provide an advantage for complex biomarker analysis

Assessment Genomics Application

Somatic Mutation Analysis Identify Neo-Antigens

Tumor Exome Sequencing, Breakpoint analysis and Fusion Detection

Gene Expression Profiling Confirm Neo-Antigen Expression, Identify Immune Activation

Pan-Cancer Immune Panel, RNA-Seq, Arrays

Germ Line Variant Analysis Confirm Somatic Mutations and Heritable Lesions

CNV, Structural and Small Variant Detection

HLA Characterization Identify Mutations in HLA

HLA Analysis (DNA, RNA, Arrays)

Antigen-Specific Immune Response Characterize Immune Activation

B/T Cell Repertoire (DNA/RNA), VDJ mutation (DNA/RNA)


Potential Roadmap for Immuno-Oncology Biomarker Strategy Multiple parallel and synergistic pathways maximizing immediate lab opportunities

as well as long term clinical differentiation


Reagent kit production capabilities

& GMP consulting

Companion Diagnostic Development Partner of Choice Extensive expertise to accelerate your tandem development pathway

Clinical Development Preclinical FDA Filing Launch Rx

IVD Feasibility Development IVD Registration Commercialization

& Modification Lab Validation

Clinical

Validation

Marker selection & study design

Deep experience in 3-4 way CDx development relationships

Strategic consulting including regulatory & reimbursement

Global clinical trial wraparound services including Central Lab

Commercial, diagnostic &

market analytics capabilities

Assay development, validation &

scale up

Registration & market access

expertise (510(k); PMA; CE Mark)

Pre-launch medical communications & proficiency training

Q2 Solutions helped develop

≈60% of all FDA approved

oncology

pharmacogenomics drugs as of April 2015


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