Preclinical Safety Testing Of Enhanced-Affinity TCRs · Preclinical Safety Testing Of...

CONFIDENTIAL

Preclinical Safety Testing Of Enhanced-Affinity TCRs

Andrew ‘Jez’ Gerry

Director of Preclinical Research

EMA, 15-16 Nov 2016

This presentation contains “forward-looking statements,” as that term is defined under the Private Securities Litigation

Reform Act of 1995 (PSLRA), which statements may be identified by words such as “believe,” “may”, “will,” “estimate,”

“continue,” “anticipate,” “intend,” “expect” and other words of similar meaning. These forward-looking statements involve

certain risks and uncertainties. Such risks and uncertainties could cause our actual results to differ materially from those

indicated by such forward-looking statements, and include, without limitation: the success, cost and timing of our

product development activities and clinical trials; our ability to submit an IND and successfully advance our technology

platform to improve the safety and effectiveness of our existing TCR therapeutic candidates; the rate and degree of

market acceptance of T-cell therapy generally and of our TCR therapeutic candidates; government regulation and

approval, including, but not limited to, the expected regulatory approval timelines for TCR therapeutic candidates; and

our ability to protect our proprietary technology and enforce our intellectual property rights; amongst others. For a further

description of the risks and uncertainties that could cause our actual results to differ materially from those expressed in

these forward-looking statements, as well as risks relating to our business in general, we refer you to our Quarterly

Report on Form 10Q filed with the Securities and Exchange Commission (SEC) on August 8, 2016 and our other SEC

filings.

We urge you to consider these factors carefully in evaluating the forward-looking statements herein and are cautioned

not to place undue reliance on such forward-looking statements, which are qualified in their entirety by this cautionary

statement. The forward-looking statements contained in this presentation speak only as of the date the statements were

made and we do not undertake any obligation to update such forward-looking statements to reflect subsequent events

or circumstances. We intend that all forward-looking statements be subject to the safe-harbor provisions of the PSLRA.

DISCLAIMER

Workshop on Scientific and Regulatory Challenges of Genetically

Modified Cell-based Cancer Immunotherapy Products European Medicines Agency, London, Nov 2016

2

• The TCR is the natural mechanism for T-cells to distinguish a diseased cell

from a healthy cell

• All proteins, including intracellular ones, are processed and presented as HLA-

peptide complexes which are recognized by TCRs

• Many cancer targets are intracellular – TCR therapeutics can access these

targets

TCRs recognize intracellular cancer antigens

Adaptimmune focuses on developing the best affinity enhanced T cell

therapies for autologous T-cell therapeutics

3



CONFIDENTIAL

Engineering Better T-Cells

Challenges With TCR Therapy

4

Four components to an effective

adoptive therapy:

1. T cell must recognize a cancer

cell via a guiding receptor

2. The guiding receptor must have

two important aspects

Affinity

Specificity

ADOPTIVE T CELL - Most powerful unit in

Immunotherapy

Challenges with TCR Therapy

5

Cancer cell

Apoptosis

T cell Armory Perforin Granzyme

T cell

Cancer cell

Affinity

Specificity

T cell

1. 2.




adoptive therapy:





Affinity

Specificity

3. The T cell needs to be resistant

to suppression


Immunotherapy


6

T cell

Cancer cell

Inhibitory

mechanisms

of cancer cells

make T cells

insensitive

Make T cells

resistant to

suppression




adoptive therapy:





Affinity

Specificity


to suppression

4. The T cell (either alone or via

other mechanisms) needs to

‘break cancer immune

tolerance’


Immunotherapy


7

T cell

Cancer cell

Make T cells

resistant to

suppression

Epitope spreading

Epitope spreading

1

2

34




adoptive therapy:





Affinity

Specificity


to suppression

4. The T cell (either alone or via

other mechanisms) needs to

‘break cancer immune

tolerance’

Integrating TCR research and development

Alignment of Multiple disciplines

8

Treating

PatientsMaking

TCRs

Engineering

T cells

Target

identification

and

validation

Clinical and

Regulatory

CMC

Safety

Testing

(Preclinical)

Translational

Sciences

Engineering

TCRs



9

ADAPTIMMUNE SPEARTM T-cell PLATFORM

uniquely overcomes these hurdles

Target Identification

TCR Identification

TCR Engineering – Optimized Affinity

TCR Safety Testing

Generation 2 T cells

Specific

Peptide

Enhanced

Affinity

Receptor



CONFIDENTIAL

Engineering Better T-Cells

Platform Technology

10

Research Pipeline

Research Pipeline

11



Engineering Better T cells

T Cell Receptor (TCR) Engineering

12

MHC

Peptide antigen

TCR

Workshop on Scientific and Regulatory Challenges of Genetically Modified Cell-based

Cancer Immunotherapy Products European Medicines Agency, London, Nov 2016

13

Specificity and non-specificity

Types of safety signal



e.g. another family

member, or Titin

• Preclinical package covers in vitro potency, safety and specificity

• In vivo animal models are not informative for assessing TCR specificity

and safety for a number of reasons

– Mainly due to MHC and proteome mis-matches

• Following 2 SAEs on MAGE-A3a3a protocol, we developed a battery of

tests that cover parallel approaches to identifying alternate reactivities

– Molecular characterisation of TCR:peptide binding preferences to

generate a motif for searching against the proteome for potential

cross-reactive peptides

– Screening cells, tissues and cellular models for actual cross-

reactivities

Adaptimmune’s preclinical safety package

Primary aim to identify potential on- and off-target reactivities

14



[Cameron, Gerry et al, Sci Trans Med, 2013,

Linette et al, Blood, 2013]

Molecular Analysis

Human Cell Testing

Potency/efficacy

Adaptimmune’s preclinical safety package

Primary aim to identify potential on- and off-target reactivities

X- ScanMotif

BLAST

Fresh tissue, organotypic and iPS models (Key tissues)

Standard Cell Screen (>100 cell types)

Peptide family

members

2D cell line cytokine

response and cytotoxicity

3D cell-lines

Motif Peptide

Screen

Motif Mass Spec

Search

Whole

Blood

Assay

Allo-reactivity

assay

Primary tumours (if available)

Antigen-driven proliferation

Overexpression

studies

Clin

ica

l Can

did

ate

TC

R



1. T cell must recognize a

cancer cell via a guiding

receptor

Engineering better T cells

Platform technology

16

Cancer cell

Apoptosis

T cell Armory Perforin Granzyme

T cell

Cancer cell

Affinity

Specificity

T cell

1. 2.



1ST select the right TARGETS ….

Engineering Better T Cells

The spectrum of potential cancer targets for immunotherapy

see http://cancerimmunity.org/peptide/ for a list of tumour antigens reported in the literature

17

Cancer testis antigens

expression restricted to immune-

privileged tissuee.g. MAGE family / NY-ESO

Differentiation antigens

tissue restricted expressione.g. Tyrosinase / gp100

Overexpressed antigens

overexpressed in tumour cellse.g. WT1 / telomerase

Tumour specific antigens

not expressed in normal tissuesViral antigens e.g. EBV/HPV

Mutated antigens e.g p53

Neo-antigens

Ideal

Good

Depends on tissue

Depends on extent of

normal tissue

expression

Ubiquitous antigens

expressed in all cellse.g. Her2/neu

Unlikely to be suitable

tumour

selectivity

Prevalence




Finding the Right Targets

19

Tumour

cell

Mass

spectrometry

Confirms surface expression and

expression on tumour cells (i.e. not

normal tissue) Only low risk targets selected for TCR

programs




Finding the Right Targets

19

Tumour

cell

Mass

spectrometry

Confirms surface expression and

expression on tumour cells (i.e. not

normal tissue) Only low risk targets selected for TCR

programs



Molecular Analysis

Human Cell Testing

Potency/efficacy

Adaptimmune’s standard preclinical package

Assessing safety

X- ScanMotif

BLAST



Peptide family

members



3D cell-lines

Motif Peptide

Screen

Motif Mass Spec

Search

Whole

Blood

Assay

Allo-reactivity

assay



Overexpression

studies

Clin

ica

l Can

did

ate

TC

R





• Exchange of each aa for all other possibilities to generate a binding

motif

• Searching with the motif against the human genome

– [ACFGIKLMNQRSTVWY]-[ACGILMQSTVY]-[DNT]-[KR]-[FW]-[CEGHILMNQTVW]-[FHNQSTVWY]-[CDEGMNQS]-[AFILMTV]

Peptide screening ‘X-scan’ (AFP SPEAR T-cells)

TCR peptide recognition mapping using combinatorial amino acid substitutions

p1 p2 p3 p4 p5 p6 p7 p8 p9

XMNKFIYEI

FXNKFIYEI

FMXKFIYEI

FMNXFIYEI

FMNKXIYEI

FMNKFXYEI

FMNKFIXEI

FMNKFIYXI

FMNKFIYEX

21

• Requires assessment of

tissue distribution of other

‘targets’

Analysis of peptide recognition – Family members

How well are peptides recognised?

22



• Non-related proteins derived from X-scan motif proteome search

• Over-express and screen for T cell reactivity

• If other peptides are recognised, a risk assessment is required on

those proteins

Analysis of peptide recognition – Mimotypes

How well are peptides recognised?

23



Molecular Analysis

Human Cell Testing

Potency/efficacy


Assessing safety

X- ScanMotif

BLAST



Peptide family

members



3D cell-lines

Motif Peptide

Screen

Motif Mass Spec

Search

Whole

Blood

Assay

Allo-reactivity

assay



Overexpression

studies

Clin

ica

l Can

did

ate

TC

R



Alloreactivity screen (AFP SPEAR T-cells)

No

targ

et

230 6

99

BPO

T

1331-8

234

BR

IP

1333-8

276

CG

P04

1349-8

396

CV

I6184

1416-1

191

DU

G150

AA

S125

AH

T192

FB466 L

CL

F B469 L

CL

FH24

FB572 L

CL

FH25

FB578

FH28

FH10

FH36

FH18

FH21

FH39

FH23

FH41

FH42

FH75

FH43

FH77

FH8

FH46

FH53

ISH

3

FH58

ISH

4FH

6

ISH

5

FH67

J0528239

KT14

OLG

A

LSR

5702

RM

L

MW

X3891

MYE2001

SC

L -116A

MYE2002

T7527

MYE2004

TIS

I

Hep

G2

0

1 0 0 0

2 0 0 0

3 0 0 0

4 0 0 0W 84

IFN

y p

g/m

l

W 8 4 / n td

W 8 4 / td

No

targ

et

230 6

99

BPO

T

1331-8

234

BR

IP

1333-8

276

CG

P04

1349-8

396

CV

I6184

1416-1

191

DU

G150

AA

S125

AH

T192

FB466 L

CL

F B469 L

CL

FH24

FB572 L

CL

FH25

FB578

FH28

FH10

FH36

FH18

FH21

FH39

FH23

FH41

FH42

FH75

FH43

FH77

FH8

FH46

FH53

ISH

3

FH58

ISH

4FH

6

ISH

5

FH67

J0528239

KT14

OLG

A

LSR

5702

RM

L

MW

X3891

MYE2001

SC

L -116A

MYE2002

T7527

MYE2004

TIS

I

Hep

G2

0

2 0 0 0

4 0 0 0

6 0 0 0

8 0 0 0W 85

IFN

y p

g/m

l

W 8 5 / n td

W 8 5 / td

No

targ

et

230 6

99

BPO

T

1331-8

234

BR

IP

1333-8

276

CG

P04

1349-8

396

CV

I6184

1416-1

191

DU

G150

AA

S125

AH

T192

FB466 L

CL

F B469 L

CL

FH24

FB572 L

CL

FH25

FB578

FH28

FH10

FH36

FH18

FH21

FH39

FH23

FH41

FH42

FH75

FH43

FH77

FH8

FH46

FH53

ISH

3

FH58

ISH

4FH

6

ISH

5

FH67

J0528239

KT14

OLG

A

LSR

5702

RM

L

MW

X3891

MYE2001

SC

L -116A

MYE2002

T7527

MYE2004

TIS

I

Hep

G2

0

2 0 0 0

4 0 0 0

6 0 0 0

8 0 0 0W 86

IFN

y p

g/m

l

W 8 6 / n td

W 8 6 / td

ntd

AFP TCR

Alloreactivity assay

Positive

control

25

• Looking for response against another unidentified peptide on a

different HLA

Screen T cells against panel of 55 EBV-transformed B cells expressing

a wide range of different HLAs

38 HLA-A, 63 HLA-B and 28 HLA-C

• AFP SPEAR T-cells showed response to 2 cell lines

Express unique alleles HLA-B*1501 and C*0404 – clinical exclusions



• HLA-A*0202 alloreactivity in pericytes

Alloreactivity screen (AFP SPEAR T-cells)

There may be lineage-specific alloreactivities

26

Molecular Analysis

Human Cell Testing

Potency/efficacy


Assessing safety

X- ScanMotif

BLAST



Peptide family

members



3D cell-lines

Motif Peptide

Screen

Motif Mass Spec

Search

Whole

Blood

Assay

Allo-reactivity

assay



Overexpression

studies

Clin

ica

l Can

did

ate

TC

R



• Bank of primary cells, covering multiple organ systems and cell types

– Over 100 non-fetal cell types (multiple donors sources of each if possible)

Primary normal cells, low passage (2 to ~10)

Tumour lines, generally high passage

– Coverage is boosted by tumour cell lines, but

Majority are epithelial.

Risk of genetic instability.

Safety assessment – Cell and tissue screen

28



Safety assessment – Cell and tissue screen

Over 100 cells covering multiple key lineages and tissues (selected examples)

29

• Respiratory

• Digestive

• Genito-urinary

• Musculoskeletal

• Endocrine

• Lymphatic

• Cardiovascular

• Nervous (CNS and PNS)

Endothelium

Astrocytes

Neurons

Pericytes

Epithelium,

Schwann cells

iPS neurons

Epithelium

Pneumocytes

Fibroblasts

Endothelium

Smotth muscle

Fibroblasts

Myocytes

Arterial and venular endothelium

Smooth muscle

Whole blood and cell subsets

Thyroid fibroblasts

Adrenal cortical cells

Preadipocytes

Pancreatic Islets

Renal proximal and distal epi

Glomerular epi

MesangialMelanocytes

Keratinocytes

Skeletal muscle cells and myoblasts

Chondrocytes

Osteocytes

Follicular papillary cells

Hepatocytes

Kuppfer cells

Biliary epithelium

Stellate cells

Tonsil epi

Splenocytes

Lymphocytes

30

Cellular Dynamics Inc. iCell Cardiomyocytes

Cells, tissues and models - Cardiovascular

iPS CM - Spontaneously electrically active and contractile (beating) myocytes



• Improved assay formats and HCS equipment

available

• Assess safety and potency of TCRs in the same well

– co-culture and multicolour fluorescently labelled

Ag+ cell lines or primary tumour material and Ag-

primary cells from the same tissue with T cells in

the same well eg Melanoma cultured with

Melanocytes and Keratinocytes

• Other techs – lots becoming available

– Air-liquid interface

– Primary tissues

– Fluid based systems

– Organs on chips

Design the models based upon the science and relevance….

31

In-vitro 2D Potency and Safety assays are improving

T cells with ADT TCR vs antigen

positive Melanoma

JULI stage

• Rapid destruction of GFP-labelled HepG2 hepatocellular carcinoma

3D microspheres

Rapid Killing of 3D HCC models by AFP SPEAR T-cells

Can perform similar models with normal cells, co-cultures, iPS cells etc

024

48

72

96

120

144

168

192

216

240

264

288

312

336

360

384

0

5 0 ,0 0 0

1 0 0 ,0 0 0

1 5 0 ,0 0 0

2 0 0 ,0 0 0

2 5 0 ,0 0 0

3 0 0 ,0 0 0

3 5 0 ,0 0 0

4 0 0 ,0 0 0

Me

an

Mic

ro

tis

su

e C

ore

Flu

ore

sc

en

ce

Are

a (

m2)

T c e lls a d d e d - 2 1 7 h rs

H e p G 2 -G F P T a rg e ts + A F Pc 3 3 2

C T L

H e p G 2 -G F P T a rg e ts A lo n e

H e p G 2 -G F P T a rg e ts + N T D C T L

T im e (h )

CONFIDENTIAL 32



• Pick the right target

Favourable expression profile for on-target reactivity (normal vs tumour)

• Identify the right parental TCR

Early cross reactivity profile

Start with multiple parents

• Careful engineering

Step-wise affinity changes from multiple parents to find optimal TCR

• Screening for cross-reactivity in right way

Molecular characterisation, peptide screening and other predictive

models

Cell screening

Relevant organotypic models, depends on the target and safety

concerns

Preclinical Safety Testing Of Enhanced TCRs

Summary



CONFIDENTIAL

TCR engineering alone is not enough

- need to enhance T cells themselves

34

35


Tumour Growth in Sarcoma (Pre-treatment)

BEFORETreatment



36


Results observed with the Engineering optimal affinity NYESO SPEAR T-Cell

BEFORETreatment with NY-ESO

SPEAR T-cell

AFTERTreatment with NY-ESO

SPEAR T-cell

Change in Tumour Size

Months Workshop on Scientific and Regulatory Challenges of Genetically


37


Results observed with the Engineering optimal affinity NYESO SPEAR T-Cell

• Have the guiding receptor with optimal affinity and specificity

• Escape mechanisms present which

• Immune suppression

• HLA down regulation

• Antigen escape

• Reduced DurabilityWorkshop on Scientific and Regulatory Challenges of Genetically



Optimal Phenotype of the Cells

38

39


Lessons from Translational Sciences

Long term respondersare mostly groupedaccording to a TCM profilewith a subset expressinghigh levels of IFN-γ andIL-2 from CD8 cells(green boxes) afterpeptide stimulation

Early relapsers arestrongly groupedaccording to TEMRA andTEM dominated product,or TNF-α producing CD8NY-ESO-1c259T cells(purple boxes)



CONFIDENTIAL

40

Engineering Better T CellsMaking T Cells Resistant To Suppression


adoptive therapy:





Affinity

Specificity


to suppression

Engineering better T cells

2nd generation T cells

41

T cell

Cancer cell

Inhibitory

mechanisms

of cancer cells

make T cells

insensitive

Make T cells

resistant to

suppression



Gen 2 T Cells maintain enhanced killing in the presence of inhibitors

42


Overcoming inhibition in the tumour microenvironment



CONFIDENTIAL

43

Engineering Better T CellsSummary

• Target choice is critical for efficacy and safety profile

• TCR affinity optimization crucial for best TCR-targeted T cell response

• Specificity crucial for lowest toxicity

TCR specificity can be assessed systematically in vitro

• Several next generation technologies making T cells resistant to

tumour microenvironment inhibitory factors

• Several next generation technologies enabling T cells to facilitate

breaking immune tolerance to tumour

Next generation approaches need extra consideration, to be driven by

the mode of action and the science, and appropriate models designed


Summary

44



CONFIDENTIAL

Thank you for your attention!

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