Innovative Cancer Vaccine · 2020-07-08 · IFN-γ, IL-12, etc. IL-12 etc. Proliferation, Maturation, Migration to Tumor site Th0 IL: Interleukin IFN: Interferon Th0: Naïve T Helper

Shun Doi, PhD, President and CEOCYTLIMIC Inc.

https://www.cytlimic.com/

Innovative Cancer Vaccine:

Fruit of Integration of

AI and Immunology

BIO Asia – TaiwanSession 2 “AI for Biotech & Healthcare”July 24, 2019

➢ CTL is main player in Cancer Immunotherapy

➢ Why and How AI in Cancer Vaccine?

➢ Cancer Vaccine: History of Failure, Challenges

➢ Cytlimic approaches to overcome Challenges

✓ Optimized Shared-antigen Peptides – advent of AI

✓ Optimized Combination Adjuvants – to boost CIC

➢ CYT001: Cytlimic’s Lead vaccine for HCC

➢ Future of AI in cancer vaccine

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Table of Contents

Development of Innovative Cancer Vaccine

CTL: Cytotoxic T Lymphocyte, CIC: Cancer-Immunity Cycle, HCC: Hepatocellular Carcinoma

© CYTLIMIC Inc. 2019 Proprietary

The Novel Prize in Physiology or Medicine 2018

Discovery of ICI (Immune-Checkpoint Inhibitors) to Release Negative Regulations to CTLs (Cytotoxic T Lymphocytes),

to let those CTLs kill cancer cells

CTLA-4 PD-1

3


BUT …

CTLA-4 PD-1

The improvements in clinical responses and overall survivals by ICI alone are still limited e.g., ORR are in 20% level, except for a certain lymphoma

Combination drugs/therapies for further improvements are highly desired

Drugs/therapies that tern “Cold Tumor* to Hot” are promising as such combination

* Tumor where CTLs are not or rarely infiltrated

4


Antigenpresentation

Injection of antigen peptides

Tumor cells

Killing by CTLs

CTL

CTL

Th1

CTL

IFN-γ, IL-12, etc.

IL-12etc.

Proliferation, Maturation,Migration to Tumor site

Th0IL: InterleukinIFN: InterferonTh0: Naïve T Helper CellTh1: T Helper 1 CellCTL: Cytotoxic T LymphocyteHLA: Human Leukocyte Antigen

Lymph nodes

9mer amino acids

HLA-Class Imolecule

Cancer Vaccine

Injection of antigen peptides induces Proliferation, Maturation, Migration to tumor sites of CTLs through activation via DCs,

to kill cancer cells

CTLCytotoxic T

Lymphocytes

DCDendritic Cell

Helper T cell

5


Launched : anti-CTLA-4 (Ipilimumab) 2011, anti-PD-1 (Nivolumab) 2014, …

Two approaches: Accelerator and/or Releasing Brake

The initial success of ICIs makes experts recognizethe importance and power of T cells (CTLs),

in cancer therapy.

Tumor cells

SurgeryChemotherapy

Radiotherapy

CancerImmunotherapy Accelerator

ReleasingBrake

Immune-CheckpointInhibitor

Peptidevaccine

ICIpeptide

１２

6

© CYTLIMIC Inc. 2019 Proprietary 7

NEC Headquarter Building(Tokyo)

Year Events

1990 Fundamental research in AI(Central Research Laboratories, NEC)

1998～ MHC-binding peptide prediction with AICollaboration with Prof. Keiko Udaka,Kochi University

2001～ Development of WT1 peptide vaccine

2008～ First-in-Human study of WT1 vaccine, atKochi University

2012～ Development of CYT001 vaccineCollaboration with Yamaguchi Universityand Kochi University

2016/12 Establishment of CYTLIMIC Inc.

AI approach – History in NEC


CancerCell

Tumorcell

Antigenpeptides

How to find peptides, binding to HLA molecule, and induce anti-tumor immunity

How to find HLA binding peptides ?

HypothesisThere must be a “rule” between the binding affinity

and binding-peptide sequence.

9mer amino acids

HLA-Class Imolecule

QuestionHow to find the rule, within minimum experiments?


STEP1: Finding the rule

Binding Tests(at Kochi Univ.)

Next test candidates

Results of the tests

Update ofRules

Sequence Affinity

ABCDEFGHI 4.5

BCDEFGHIJ 6.2

CDEFGHIJK 3.5

・・

・・

・・

PQRSTUVWX 8.2

QRSTUVWXY 3.3

RSTUVWXYZ 6.4

Our answer: Active Learning, an AI algorithm

MPRAPRCRAVRSLLRSHYREVLPLATFVRRLGPQGWRLVQK

GDPAAJFRALVAQCLVCVPWDARPPPAAPSFRQVSCLKELV

ARVLQRLCERGAKNVLAFGFALLDGARGGPPEAFTTSVRSYJ

LPNTVTDALRGSGAWGLLLLRRVGDDVLVHLLARCALFVLVI

APSCAYQVCGPPLYQLGAATQARPPPHASGPRRRLGCERW

NHSVREAGVPLGLPAPGARRRGGSASRSLPLPKRPRRGAAPJ

EPERTPVGQGSWAHPGRTRGPSDRGFCVVSPARPAEJEATN

LEGALSGTRHSHPSVGRQHHAGPPSTSRPPRPWDTPCPPVY

AMTKHFLYSSGDKEQLRPSFLLSSLRPSLTGARRLVETIFLGSW

MPGTPNRRLPRLPQRYWQMRPLFLELLGNHAQCPYGVLLKI・

Candidates peptides

(9 amino acids)

STEP2: Finding peptides

Antigen proteinamino acids sequence

9mer amino acids

HLA-Class ImoleculeAI

algorithm


P RQ S T UVWX

Peptide A Peptide B Peptide C

P RQ S T UVWX

Peptide XJapanese: 85%

Caucasian: 60%

Challenges・Costs・Personalization

A single peptide can induce anti-tumorresponse in patients having different HLA types.

HLA type

Multi-HLA peptide, another advantage of AI algorithm

ConventionalVaccine

CYTLIMICVaccine

Binding peptide sequence depends on HLA type

HLA A*24:02 HLA A*02:01 HLA A*02:06

P RQ S T UVWX

P RQ S T UVWX

Human LeukocyteAntigen


Year/month

Name Company Indication

2012/2 OTS102 Oncotherapy (J) PDAC

2012/12Tecemotide(Stimuvax)

Merck KGaA (G)(Oncothyroen)

NSCLC

2013/9 MEGE-A3 GSK (UK)MelanomaNSCLC

2016/3Rindopepimut(Rintega)

Celldex (USA) Glioblastoma

2016/11 IMA901 IMMATICS (G)Renal CellCarcinoma

2018/5 ITK-1 BrightPath (J)Prostate Cancer

Cancer Vaccine, History of failure …

No one succeeded yet in Phase III. What was wrong?


Chen DS, et al. Immunity. 2013;39(1):1-10.

12

Optimized Combination Adjuvants, best boosting the

Cancer-Immunity Cycle

CYTLIMIC Bets-In-Class Vaccine Design Concept

Optimized Shared-antigen Peptides, escaping self-tolerance,

and immunogenic


Challenges

CYTLIMIC Development Approaches

What combinationmost effectively boosts

Cancer-Immunity Cycle?

Combination of clinical-stage adjuvant

materials; Poly ICLC and LAG-3Ig

Challenge #2

How can we findOptimized Shared-antigen peptides?

(neoantigen-like*)

AI-based prediction & screening by patient‘s

samples to find cryptic* Multi-HLA peptides

Challenge #1

CYTLIMIC Development Approaches


HCC Patients s

(Yamaguchi Univ. Medical School)

Phase I study:HSP70 mRNA transfected DCTherapy for unresectable or

recurrent HCC patients

Selection ofTarget Antigens- Proteome- mRNA- Histopathology

MPRAPRCRAVRSLLRSHYREVLPLATFVRRLGPQGWRLVQKGDP

AAJFRALVAQCLVCVPWDARPPPAAPSFRQVSCLKELVARVLQR

LCERGAKNVLAFGFALLDGARGGPPEAFTTSVRSYJLPNTVTDAL

RGSGAWGLLLLRRVGDDVLVHLLARCALFVLVIAPSCAYQVCGP

PLYQLGAATQARPPPHASGPRRRLGCERWNHSVREAGVPLGLP

APGARRRGGSASRSLPLPKRPRRGAAPJEPERTPVGQGSWAHPG

RTRGPSDRGFCVVSPARPAEJEATNLEGALSGTRHSHPSVGRQH

HAGPPSTSRPPRPWDTPCPPVYAMTKHFLYSSGDKEQLRPSFLLS

SLRPSLTGARRLVETIFLGSWMPGTPNRRLPRLPQRYWQMRPLFL

ELLGNHAQCPYGVLLKIMPRAPRCRAVRSLLRSHYREVLPLATFVR

RLGPQGWRLVQKGDPAAJFRALVAQCLVCVPWDARPPPAAPSF

RQVSCLKELVARVLQRLCERGAKNVLAFGFALLDGARGGPPEAFT

TSVRSYJLPNTVTDALRGSGAWGLLLLRRVGDDVLVHLLARCALF

VLVIAPS

AI-basePredictionsystem

･･･

Patients

Target HLAHLA A*24:02, 02:01, 02:06

･･･

ELISPOT assay(patients samples)

Identification ofImmunogenic

Peptide Cocktail

Screening

Use of AI-based discovery tool and Dendritic Cell therapy patient samples enables the discovery of rarely existing cryptic multi-HLA peptides

NEC

Binding assay

TargetAntigens

HLA A*24:02, 02:01, 02:06

Kochi Univ.

HSP70 Multi-HLA Class I peptideGPC3 Multi-HLA Class I peptide

Discovery of optimized shared-antigen peptides

14


Peptides HLA allele

HSP70 GPC3

122 138 297 335 371 448 166 170 222

BindingAssay

24:02-5.82 -4.37 -5.21 -6.17 -5.50 -5.49 -4.70 -7.43 -5.34

02:01-4.59 -4.76 -4.33 -4.86 -4.90 -5.56 -5.31 -5.07 -6.21

02:06-5.53 -5.59 -5.58 -5.07 -5.37 -4.28 -6.14 > -3 -5.21

ELISPOTAssay

2402/(except 0201,0206)

4/5 3/6 1/2 2/2 6/7 6/7 3/5 2/2 3/5

0201/(except 2402,0206)

0/1 0/2 0/1 0/1 2/3 1/3 1/2 0/2 2/2

Other combination

1/1 0/2 0/1 0/1 1/3 0/3 0/2 1/2 1/2

Total5/7 3/10 1/4 2/4 9/13 7/13 4/9 3/6 6/9

Note:✓ PBMC of Yamaguchi HSP70 DC therapy patients (total 13 samples, Slide

14) were used to conduct ELISPOT and ELISA assays✓ Positivity criteria: Significantly higher in either ELISPOT or ELISA (ELISPOT

p<0.05, ELISA p<0.015)

Selection of optimized shared-antigen peptides

Reference: Menez-Jamet J. et al, Optimized tumor cryptic peptides: the basis for universal neo-antigen-like tumor vaccine, Ann. Transl. Med., 2016, 4(14), 266.

15


Challenge #2 Novel combination adjuvant

Reference: Kano Y., Tamada K., Doi S. et al, Cancer Science, 2016, 107: 398-406

Peptide + IFA

Peptide + Poly IC Peptide + LAG-3Ig

Peptide + Poly IC + LAG-3Ig

* registered in Japan

DiscoveredPoly IC (TLR3, MDA5 agonist) + LAG-3Ig (MHC Class II agonist)

Tumor growth (P815 mastocytoma tumor)

Possible combinations of clinical-stage adjuvant materials (～10) weretested using tumor-bearing mouse model, to find novel synergistic pair

CYT001 – CYTLIMIC Lead Vaccine


CYT001 - CYTLIMIC Peptide Vaccine

Optimized Shared-antigenMulti-HLA-reactive peptides

Optimized combination ofadjuvants in clinical-stage

Shared antigens highly expressed in various tumors

including HCC, EsC, GaC, etc.(2 patents filed)

APC activation and control of immunosuppressive mechanism

(2 patents filed)

+Poly-ICLC(Hiltonol®)

Oncovir

LAG-3Ig(IMP321)Immutep

Vial A Vial B Vial C

GPC3Class Ipeptide

HSP70Class Ipeptide

Cross-reactivity to HLA*A- 24:02, 02:01,02:06, covers 85% of Japanese andabout 60% of Caucasian*

* German: 58%, etc.Caucasian

SC injections simultaneously at both underarms and both groins

peptide Hiltonol IMP321

18


Poly ICLC binds to TLR3 (Toll-Like Receptor 3)and MDA5 (Melanoma Differentiation Antigen 5)of Antigen Presenting Cells (APCs), andactivates APCs through this “danger signal”mimicking viral infection.

LAG-3Ig binds to MHC (Major HistocompatibilityComplex) Class II molecules of APCs, andactivates APCs through MHC Class II signaling.

Poly ICLC

LAG-3Ig

TLR3/MDA5 agonist

MHC Class II agonist

CancercellAdjuvants, synergistically

activates DCs

PeptidesAntigen presentation

PeptidesAntigen presentation

CTL

CTL

CD4 + T cellhelp

Proliferation, Maturation,Migration to Tumor site

HelperT cell

Pre-existingpeptide

The combination of Poly ICLC (Hiltonol, Oncovir) and LAG-3Ig (IMP321, Immutep) synergistically activates antigen-specific CTL reactions as effective combination adjuvants.

Reference: Kano Y. et al., Cancer Science, 2016, 107: 398-406

HSP70peptide

GPC3peptide

Mechanism of Action

GPC3reactive

CTL

HSP70reactive

CTL

HSP70reactive

CTL

HSP70reactive

CTL

GPC3reactive

CTL

GPC3reactive

CTLMHC Class II

receptor

MHC Class Ireceptor

DC

TLR3 MDA5

Combination adjuvants boost peptide-specific CTL reactions

Hiltonol

IP321

19


Partnering for adjuvant supply

20

A pharmaceutical corporation dedicated to the development of nucleic-acid-based clinical immunotherapies for cancer and other diseases.Oncovir Hiltonol (Poly ICLC) is supplied to Cytlimic and used in Cytlimic CYT001 cancer vaccine under collaboration agreement between Oncovir and Cytlimic, to synergistically boost patient immune responses to vaccine antigens together with Immutep Efitilagimod Alpha.

https://www.oncovir.com/

A globally active biotechnology company developing LAG-3 related immunotherapeutic product. Immutep Eftilagimod Alpha (LAG-3Ig, IMP321) is supplied to Cytlimic and used in Cytlimic CYT001 cancer vaccine under collaboration agreement between Immutep and Cytlimic, to synergistically boost patient immune responses to vaccine antigens together with OncovirHiltonol.

https://www.immutep.com/

https://www.immutep.com/


Name PhaseTarget disease, patients

Study Period(Status)

Study Site(PI)

YNP01

1IIT (Specified Clinical Trial)*

jRCTs061180058

Advanced solid tumor (HCC, GI), n=17

2016/1~2019/3

(completed)

Yamaguchi Univ.(Prof. Hiroaki Nagano)

YCP02

1IIT (Specified Clinical Trial)*

jRCTs061180033

Resectable HCC(Neoadjuvant, adjuvant vaccine)n=20 (planed)

2018/1~(active,

recruiting)

Yamaguchi Univ.(Prof. Hiroaki Nagano)

CRESCENT1

1b Investigator-Initiated Clinical Trial

jRCT2031190072

Unresectable HCCn=6

2019/8~(not yet

recruiting)

Chiba Univ.(Prof. NaoyaKato)

CYT001 - Clinical Trials

* Specified Clinical Trial: Clinical trial conducted under Clinical Trial Act (Act No.16 of April 17, 2017)

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▌Study name⚫A phase I study of combination immunotherapy with HSP70 derived peptide, GPC3

derived peptide, Poly ICLC and Soluble LAG-3 for patients with advanced or metastatic solid cancer (jRCTs061180058)

▌Dose

▌Vaccination Schedule

▌Patient: 17

Level Peptides Adjuvants

HSP70 GPC3 Hiltonol IMP321

Level 1 1.0 1.0 1.4 0.25

Level 2 2.0 2.0 1.4 0.25

Level 3 2.0 2.0 1.4 1.0

(mg/injection)

Download: https://www.cytlimic.com/download/SITC_2018_poster.pdf

YNP01 trial: Study Design

22


▌Endpoints⚫Primarily endpoint: Safety

⚫Secondary endpoints: Peptide-specific immune responses, biomarker response, clinical response

YNP01: Endpoints and summary of results

23

Summary

Safety All AEs related to CYT001 were Grade 1/2

Vaccine-specific immune response

88% (15/17) responded, Prompt (most responders in 1 mo.) and Strong (IFNɤ ELISPOT≧3+, in grades -/1+/2+/3+/4+/5+)

Anti-tumor response(RECIST v1.1)

DCR: 29% (5/17), SD – 5 pts., PD – 12 pts. (no CR, PR)

Tumor marker decrease: 58% (10/17)Median OS: 10.3 mo. (95% CI 5.52–20.4 mo.)Median PFS: 1.9 mo. (95% CI 1.2–3.0 mo.)Long survivor (≧ 24 mo.): 3 pts. (HCC) (HCC: 75% (3/4))

Biomarker response TIM3+/CD4 decreased in Level 3 after 1 course (p=0.012)

Sub-class analysis Longer survival in pts. with lower PD-1+/CD4, TIM3+/CD4, TIGIT+/CD8 than higher ones, respectively


(1) Safety

Level 1(n=3)

Level 2(n=3)

Level 3(n=11)

irAE(Grade 1/2)

Total 2 1 7

Edema 1 0 1

Fever 0 0 2

Injection site reaction/Skin reaction

1 1 6

note: There is no irAE as Grade 3/4. (ir: immune related)

Other AE

Grade 1+2 3 4 3

Grade 3 8 7 4

note: All of Other AEs are not related to CYT001.There is no AE as Grade 4.

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Level # Patients HSP70 (%) GPC3 (%)

# Pts.

Post CTL grade >

Pre CTL grade

Level 1(Post CTL≧3+)

3 2(0)

2(0)


3 1(0)

2(0)


11 8(6)***

9(5)***

all 17

11 (65%)* 13 (76%)*

15 (88%)**

(2) Antigen-peptide specific immune response

(Notes)✓ CTL grade: -/+/2+/3+/4+/5+✓ Among 10 responses to HSP70, 8 (80%) were observed after 1 course (*)✓ Among 12 responses to GPC3, 9 (75%) were observed after 1 course (*)✓ Response to at least one of antigen-peptides (**)✓ Among responders, strong responses (ELISPOT≧3+, after 1 course) were observed only in

Level 3 (***)

25


Note: Solid brown line– Level 3 pts., Dashed line– Level 1 or 2 pts.

In patients recieving Level 3 dosage, the population of TIM3+ cells in CD4+ T cells was decreased significantly, and MDSC (CD11b+CD33+HLR-DR-/PBMC) showed trend to decrease, after 1 course of treatment.

Biomarkerts tested: Proportion of CD4+T cells/ CD8+T cells/ Monocyte cells/ Tregcells (FrⅠ,Ⅱ, Ⅲ)/ MDSC (CD11b+CD33+HLA-DR-)/ Memory T cells, Exhaustion marker (PD-1, LAG-3, TIM3, TIGIT) on CD4/8+ T cells

(3) Biomarker response in PBMC

26

0

2

4

6

Pre Post

MDSCCD11b+CD33+HLA-DR-/PBMC

P=0. 132 (Level3)

0

3

6

9

12

Pre Post

TIM-3/CD4

P=0.012 (Level3)


(3) Anti-tumor response (Swimmer plot)

✓Best response: SD (long-SD for > 38 months)✓Disease control rate (DCR)：29%

as of 2019/7

27


p=0.0399 p=0.0245 p=0.0578 p=0.2495 p=0.2374

p=0.3327 p=0.2679 p=0.5661 p=0.0317 p=0.4732

Surface marker expression on the PBMC (pre-treatment) and prognosis(Cut-off value = median value, Gehan-Wilcoxon test)

Suggesting that the overall survival of CYT001 treatment could be improved by the combination with ICI treatment.

(5) Subgroup analysis

28

PD-1/CD4 TIM-3/CD4

TIGIT/CD8


▌A phase I study of combination adjuvant immunotherapy with HSP70 derived peptide, GPC3 derived peptide, Poly ICLC and Soluble LAG-3 for patients with resectable hepatocellular carcinoma (jRCTs061180033)

Treatment period (6 months)

Neoadjuvant therapy(6 injections (weekly))

Adjuvant therapy(10 injections: 4 times weekly + 6 times biweekly

-2 -1 0 1 2 3 4 12

Surgicalresection

Surgical specimen

YCP02 Study

Evaluation of recurrence

Phenotypic analysis of TIL (Tumor infiltrated Lymphocytes) using CyTOF

TIL samples

Pathological analysis to assess if the vaccine shifts “Cold tumor to Hot”

Pathological slides

29


Chen DS, et al. Immunity. 2013;39(1):1-10.

30

On Interim results of YCP02 study (neoadjuvant part)

Trigger

By CYT001 neoadjuvant vaccination,✓ CTLs infiltrate into tumor sites (HCC area)✓ These CTLs recognize vaccine-target antigens✓ Infiltrated T cells (including CTLs and Helper T cells)

express PD-1 exhaustion marker(abstract only, no detail data presented yet)


suppre

ssed

not-

suppre

ssed

Toward ICI-Vaccine combination trial

CTL

CTLCTL

CTL

CTL

CTL

Hot, but suppressed Cold and suppressed

Cold, and not-suppressedHot and not-suppressedNo Cancer growth

HOT COLD

Cancercell

Cancercell

Cancercell

Cancercell

Cancercell

Cancercell

Cancercell

Cancercell

Cancercell

The interim analysis results suggest that CYT001 terns “Cold

tumor to Hot”, thus the combination to anti-PD-1 drug

improves the clinical response of anti-PD-1 drug.

CytlimicVaccineVialCVialA VialB

Accelerator

CytlimicVaccineVialCVialA VialB

Accelerator

Cancercell

Cancercell

Cancercell

CancercellCTL

CTLCTL

CTL

ICICI

Brake×

ICI

Brake×

CI

31


IndividualizedNeo-antigen vaccine

(Personalized vaccine)

Optimized Shared-antigenMulti-HLA peptide vaccine

(One-fit-all vaccine)

Advancing AI technologies for Cancer Vaccine

Future of AI in Cancer Vaccine （NEC）

transgene

32


The author gratefully acknowledges the following contributors for their scientific works and supports:

- Dr. Tomoya Miyakawa*, NEC Corporation

- Prof.Dr. Keiko Udaka, Kochi Medical School

- Prof.Drs. Masaaki Oka, Hiroaki Nagano, Shoichi Hazama, and doctors and laboratory members involved in YNP01 and YCP02 studies, Yamaguchi University School of Medicine

- Prof.Dr. Koji Tamada, Dr. Daisuke Umezu, Yamaguchi University School of Medicine

- Prof.Dr. Naoya Kato, Dr. Sadahisa Ogasawara, and doctors and laboratory members involved in CRESCENT1 study, Chiba University School of Medicine

- Prof.Dr. Akira Saito, Tokyo Medical University

- Drs. Frederic Triebel, Claudia Jacoby, Immutep Limited

- Dr. Andres Salazar, Oncovir, Inc.

- Dr. Shiro Akinaga, AccuRna, Inc.

- Dr. Yoshihide Segawa, Mr. Genji Kawano, Mr. Toru Kano, CYTLILMIC Inc.

and patients participating YNP01, YCP02 and CRESCENT1 studies

Acknowledgements

* Passed away from thyroid cancer in May 2018

Documents

Innovative Cancer Vaccine · 2020-07-08 · IFN-γ, IL-12, etc. IL-12 etc. Proliferation, Maturation, Migration to Tumor site Th0 IL: Interleukin IFN: Interferon Th0: Naïve T Helper