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Dissecting therapy-induced T-cell responsesin melanoma
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Tumor-infiltrating lymphocyte (TIL) therapy of melanoma
Patient pretreated withlymphodepletingchemotherapy
TIL are grown from melanoma
tumors
Infusion of TIL + IL-2
Rapid Expansion
- 50% response rate in trials in multiple centers (US, Israel)- Clinical effect at least partially mediated by cytotoxic T cells
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Dudley et al. Curr. Opin. Immunol. 2009
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- Which cytotoxic T cells mediate cancer regression?- Could we specifically boost their numbers?
Tumor-infiltrating lymphocyte (TIL) therapy of melanoma
?
Patient pretreated withlymphodepletingchemotherapy
TIL are grown from melanoma
tumors
Infusion of TIL + IL-2
Rapid Expansion
![Page 5: Dissecting therapy-induced T-cell responses in melanoma · Tumor-infiltrating lymphocyte (TIL) therapy of melanoma Patient pretreated with lymphodepleting chemotherapy TIL are grown](https://reader031.vdocuments.us/reader031/viewer/2022011914/5fbd8f60b794822b78252cbc/html5/thumbnails/5.jpg)
- Survival benefit in metastatic disease- Data from murine models suggest a role for cytotoxic T cells
Anti-CTLA4 therapy of melanoma
Hodi et al. NEJM 2010
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- Which cytotoxic T cells mediate cancer regression?- Could we specifically boost their numbers?
- Could we distinguish responders and non-responders?
Anti-CTLA4 therapy of melanoma
Hodi et al. NEJM 2010
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How a T cell sees a target cell How an MHC tetramer sees a T cell
Detecting tumor-specific cytotoxic T cells
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How an MHC tetramer sees a T cell
Anti-CD8
MA
RT-
1 M
HC
tetra
mer
Detecting tumor-specific cytotoxic T cells
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How an MHC tetramer sees a T cell
Detecting tumor-specific cytotoxic T cells
Hundreds of different melanoma-associated T cell antigens have been described
Two problems:1. Generation of very large collections of MHC tetramer reagents is not possible with
standard technology
2. Even if you would have such a collection, the amount of biological material is limiting
Anti-CD8
MA
RT-
1 M
HC
tetra
mer
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Generation of pMHC multimers by UV-induced peptide exchange
Toebes et al. Nat. Med. 2006Bakker et al. PNAS 2008
H2NNH
HN
NH
HN
NH
HN
NH
O
O
O
O
O
O
O O
NH O
OH
O2N
GILGFVF(o-NO2)L
UV-light 365 nm
O
ON O
NH O
OH+H2NNH
HN
NH
HN
NH
HN
NH2
O
O
O
O
O
O
O
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Generation of pMHC multimers by UV-induced peptide exchange
Toebes et al. Nat. Med. 2006Bakker et al. PNAS 2008
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Generation of pMHC multimers by UV-induced peptide exchange
Toebes et al. Nat. Med. 2006Bakker et al. PNAS 2008
Disintegration
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Generation of pMHC multimers by UV-induced peptide exchange
Peptide 1 Peptide 2 Peptide 3
Disintegration
Rescue Peptides
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UV-sensitive ligand pre-cleavage(KILGJ*VFJV)
UV-sensitive ligand post-cleavage(visualization of the reaction intermediate)
In crystallo exchange with HIV RT468-476(ILKEPVHGV)
In crystallo exchange with HIV Env120-128(KLTPLCVTL)
In crystallo MHC ligand exchange
Celie et al. JACS 2009
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Generation of pMHC multimers by UV-induced peptide exchange
Peptide 1 Peptide 2 Peptide 3
Disintegration
Rescue Peptides
Allows the creation of very large MHC multimer collections for all prevalent HLA class I alleles
- HLA-A1, -A2, -A3, -A11, -B7, -B57 (Toebes et al. Nat. Med. 2006, Bakker et al. PNAS 2008)- HLA-A24, -B40, -B58 (G. Grotenbreg, NUS, Singapore)
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How to monitor hundreds of T cell populations per patient?
Aim: Detection of low frequency T cell populations
~ 0.02% of CD8 T cells
Required: record >50,000 CD8 T cells ~ 2 ml fresh blood
For 100 potential antigens: ~ 200 ml blood
25 parallel measurements per sample: ~ 8 ml blood
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What if you couple the same pMHC to multiple fluorophores & start combining?
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Generate fluorochrome conjugated MHC multimers
Mix to create a collectionof differentially encoded MHC multimers
Assembly of combinatorial codes on T cell surfaces
Analysis by flow cytometry
T cell T cell T cell
Self-assembling molecular codes
Hadrup et al. Nat. Methods 2009
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Example of a combinatorial coding read-out
8 colors 28 T cell reactivities
APC QD 605 QD 625 QD 655 QD 705 QD 800 PE-Cy7
APC
QD 605
QD 625
QD 655
QD 705
QD 800
PE
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Selection of melanoma-associated epitope panel
Cancer-testis antigen
31%
Overexpressed44%
Differentiation18%
Mutation5%
Not fully characterised
2%
Antigen class distribution
Cancer-Germline
31%
Panel of 216 melanoma-associated peptides• public databases
• literature analysis
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Panel of 216 melanoma-associated peptides• public databases
• literature analysis
Cancer-testis antigen
31%
Overexpressed44%
Differentiation18%
Mutation5%
Not fully characterised
2%
Antigen class distribution
Cancer-Germline
31%
e.g. MAGE family
e.g. MART-I
e.g. Meloe-I
e.g. CDK4R24C
Selection of melanoma-associated epitope panel
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Dissecting therapy-induced T cell responses in melanoma: POC
Patient pretreated withlymphodepletingchemotherapy
TIL are grown from melanoma
tumors
Infusion of TIL + IL-2
Rapid Expansion
- Do we detect tumor-specific T cell responses in the cell product?- If so, what do these T cells recognize?
- Does composition of the cell product predict post-treatment immune reactivity?
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MART‐1 (#78)(0.087%)
ELAGIGILTV
pt.LN
MART‐I (#78)(0.113%)
ELAGIGILTV
MART‐I (#78)(0.074%)ELAGIGILTV
pt.CR pt.ER
Numbers represent the % MHC tetramer+ T cells out of total CD8+ cells
Identification of diverse T cell populations in HLA-A2+ TIL products
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pt.MA
MART‐1 (#78)(4.581%)
ELAGIGILTV
gp100 (#56)(0.071%)
IMDQVPFSV
pt.MV
MAGE‐A10 (#59)(0.137%)
GLYDGMEHL
MART‐1 (#78)(0.150%)
ELAGIGILTV
Meloe‐1 (#80)(0.344%)
TLNDECWPA
Numbers represent the % MHC tetramer+ T cells out of total CD8+ cells
gp100 (#56)(0.045%)
IMDQVPFSV
MART‐1 (#78)(0.018%)
ELAGIGILTV
pt.LR
SSX‐2 (#114)(0.628%)KASEKIFYV
MAGE‐A10 (#59)(0.015%)
GLYDGMEHL
pt.HE
Identification of diverse T cell populations in HLA-A2+ TIL products
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Gp100 (#36)1.897%
YLEPGPVTA
Gp100 (#56)0.083%
IMDQVPFSV
Gp100 (#39)0.131%
VLYRYGSFSV
MART‐1 (#78)1.210%
ELAGIGILTV
pt.LD
gp100 (#36)0.453%
YLEPGPVTA
gp100 (#38)0.376%
ITDQVPFSV
gp100 (#39)0.010%
VLYRYGSFSV
gp100 (#42)0.016%
AMLGTHTMEV
gp100 (#44)0.028%
KTWGQYWQV
gp100 (#56)(0.42%)
IMDQVPFSV
Meloe‐1 (#80)(1.45%)
TLNDECWPA
MART‐1 (#78)0.633%
ELAGIGILTV
pt.KS
Identification of diverse T cell populations in HLA-A2+ TIL products
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Summary of identified T cell responses in 15 T cell products
Epitope
PSC
CZE
RA
V
RTE
MZU LR LN KS
MV
CR
ER MA
LD SW HE
Mart-1ELA
gp100IMA
gp100YLE
gp100VLY
gp100ITD
gp100AML
gp100KTW
TRP2VYD
TRP2SVY
MAGE A10GLY
MAGE C2LLF
MAGE C2ALK
MAGE C2VIW
SSX-2KAS
Meloe-1TLN FrequencyTelomeraseRLF 0.01 - 0.99 %
M CDK4ACD 1.00 - 4.99 %
U MG50RLG > 4.99 %
Patient
Diff
eren
tiatio
nC
ance
r / T
estis
OE
0gp100IMD
U
M
OE
Can
cer/
Ger
mlin
e
D
iffer
entia
tion
Frequency0.01 - 0.99 %1.00 - 4.99 %> 4.99 %
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Summary of identified T cell responses in 15 T cell products
Epitope
PSC
CZE
RA
V
RTE
MZU LR LN KS
MV
CR
ER MA
LD SW HE
Mart-1ELA
gp100IMA
gp100YLE
gp100VLY
gp100ITD
gp100AML
gp100KTW
TRP2VYD
TRP2SVY
MAGE A10GLY
MAGE C2LLF
MAGE C2ALK
MAGE C2VIW
SSX-2KAS
Meloe-1TLN FrequencyTelomeraseRLF 0.01 - 0.99 %
M CDK4ACD 1.00 - 4.99 %
U MG50RLG > 4.99 %
Patient
Diff
eren
tiatio
nC
ance
r / T
estis
OE
0gp100IMD
U
M
OE
Can
cer/
Ger
mlin
e
D
iffer
entia
tion
• Total of 39 melanoma-reactive T cell responses in 15 T cell products
• Number of responses ranges from 0 to 8
• Predominant recognition of MDA and C/G antigens
• T cell reactivity is highly patient-specific
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Summary of identified T cell responses in 15 T cell products
Epitope
PSC
CZE
RA
V
RTE
MZU LR LN KS
MV
CR
ER MA
LD SW HE
Mart-1ELA
gp100IMA
gp100YLE
gp100VLY
gp100ITD
gp100AML
gp100KTW
TRP2VYD
TRP2SVY
MAGE A10GLY
MAGE C2LLF
MAGE C2ALK
MAGE C2VIW
SSX-2KAS
Meloe-1TLN FrequencyTelomeraseRLF 0.01 - 0.99 %
M CDK4ACD 1.00 - 4.99 %
U MG50RLG > 4.99 %
Patient
Diff
eren
tiatio
nC
ance
r / T
estis
OE
0gp100IMD
U
M
OE
Can
cer/
Ger
mlin
e
D
iffer
entia
tion
- Are these T cell populations relevant for melanoma recognition?- Does this analysis predict post-treatment immune reactivity?
• Total of 39 melanoma-reactive T cell responses in 15 T cell products
• Number of responses ranges from 0 to 8
• Predominant recognition of MDA and C/G antigens
• T cell reactivity is highly patient-specific
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Isolation of a melanoma-reactive T cell populations for functional validation
Numbers represent the % MHC tetramer+ T cells out of total CD8+ cells
MAGE-A105.3%
GLYDGMEHL
MAGE-C2 0.2%
ALKDVEERV
MAGE-C20.9%
LLFGLALIEV
CDK4 R24C2.3%
ACDPHSGHFV
MAGE-C21.5%
VIWEVLNAV
MG-500.8%
RLGPTLMCL
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Recognition of autologous melanoma by identified T cell populations
MAGE-A10
ALK
MAGE-C2 LLF
MAGE-C2 VIW
MAGE-C2
MG50
CDK4R24
C
0
20
40
60
80
100T2 no pep T2 pulsed w pep Autologous tumor
%C
D8+
IFN
g+
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• Total of 19 post-infusion responses in 10 HLA-A2+ TIL-treated patients
• 79% of pre-infusion responses is seen back in post-infusion PBMNC
• 95% of T cell responses in PBMNC post-therapy is predicted by in vitro reactivity
Detecting post-therapy T cell reactivity in patients treated with TIL
gp100 (#36)0.148%
YLEPGPVTA
gp100 (#38)0.106%
ITDQVPFSV
gp100 (#39)0.222%
VLYRYGSFSV
Meloe-1 (#80)(0.366%)
TLNDECWPA
MART-1 (#78)0.302%
ELAGIGILTV
pt.KSPost-Infusion PBMNC
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Conclusions
We have developed and validated technology for the high-throughout
detection of therapy-induced melanoma-specific T cell reactivity
T cell responses in TIL cell products are diverse, biased towards MDA and
C/G antigens, and highly variable between patients
In ‘young TIL’, individual T cell responses are generally of a (surprisingly)
low magnitude
T cell responses in TIL cell products predict immune reactivity post-therapy
- No epitope spreading -
Is it possible to influence TIL cell product composition?
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F20.433 0.044 0.033
F40.0070.005
F70.212 0.022 0.006
CDK4R24C Mage A10 Mage C2 72 Mage C2 73 Cyclophilin B
F12
F1
F9
0.016
0.160
F5
Individual tumor fragments yield distinct TIL products
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Dissecting melanoma-specific T cell responses upon other immunotherapeutic treatments?
Immune reactivity induced by anti-CTLA4 or anti-PD1 treatment?
Immunological consequences of combination therapy?
(e.g. BRAF inhibition plus anti-CTLA4)
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MHC-based monitoringJenny Shu
Manuel FankhauserPia Kvistborg
Mireille ToebesArne Bakker
Carsten Linnemann
Chemical BiologyBoris Rodenko
Huib Ovaa
CCIT, CopenhagenSine Hadrup
Charlotte Albæk Thrue
Surgery Branch, NIH Steven Rosenberg
Mark Dudley
Clinical translationBianca HeemskerkAnnelies Jorritsma
Raquel GomezNienke van RooijBastiaan NuijenChristian BlankJohn Haanen
Self-destructive MHC ligands & combinatorial coding
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F20.433
F40.005
F70.212
F12
F1
F9
0.016
0.160
F5
Individual tumor fragments yield distinct TIL products
CDK4R24C
0
0.1
0.2
0.3
0.4
0.5
F1 F2 F4 F5 F7 F9 F12
% C
DK
4 te
tram
er p
ositi
ve c
ells
% C
DK
4R24
C-s
peci
fic C
D8+
T ce
lls
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T cell T cell T cell
Self-assembling molecular codes
Hadrup et al. Nat. Methods 2009