An Open-label, Phase IB Study of NEO-PV-01 + Adjuvant with Nivolumab in Patients with Melanoma, Non-Small Cell Lung Carcinoma, or Transitional Cell Carcinoma of the Bladder

Patrick A. Ott,1 Aung Naing,2 Ramaswamy Govindan,3 Kim Margolin,4 Melissa A. Moles,5 Richard B. Gaynor,5 Matthew J. Goldstein,5 Siwen Hu-Lieskovan6

1Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA; 2Department of Investigational Cancer Therapeutics, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX; 3Division of Medical Oncology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO; 4Department of Medical Oncology & Therapeutics Research, City of Hope, Los Angeles, CA; 5Neon Therapeutics, Inc., Cambridge, MA; 6Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles (UCLA), Los Angeles, CA

Presented at the Annual Congress of the European Society for Medical Oncology (ESMO): September 8–12, 2017; Madrid, Spain.

Background• Cancer cells contain unique, somatic DNA mutations that result in altered amino

acid sequences known as neoantigens1,2

• Tumor neoantigens are not subject to the immune dampening effects of central tolerance and are expressed only in tumors, rendering them exquisitely tumor specific1,2

• Growing evidence supports a central role for neoantigens as targets for tumor-directed immune responses.1,2 Tumor mutational burden, as well as neoantigen load, have been associated with antitumor activity of checkpoint inhibitors1,3,4

• Immune responses to neoantigens depend on the ability of major histocompatibility complex molecules to effectively bind a small peptide (epitope) containing the altered amino acid sequence and present it to a T cell. Such an epitope can be generated synthetically and used in a vaccine2,5

• Vaccines targeting neoantigens offer a highly specific way of inducing de novo, and expanding existing, tumor-specific T-cell responses1,2,5–7 (Figure 1)

Figure 1. NEO-PV-01 Personalized Neoantigen Vaccine Mechanism of Action

Poly-ICLC, polyinosinic-polycytidylic acid-polylysine carboxymethylcellulose; TLR3, Toll-like receptor 3.

Objectives

Primary• To evaluate the safety of NEO-PV-01 + adjuvant (a personalized neoantigen vaccine) with

nivolumab in patients with unresectable or metastatic melanoma, smoking-associated non-small cell lung cancer (NSCLC), or transitional cell carcinoma (TCC) of the bladder who have received no more than one prior systemic treatment

Secondary• To determine antitumor activity at Week 24, assessed by overall response rate and

clinical benefit rate

• To determine the response conversion rate, defined as improvement in response category at Week 24 vs Week 12

• To evaluate progression-free survival, overall survival, and duration of response

Exploratory• To characterize immune responses including evaluation of antigen-specific CD4+ and

CD8+ T-cell responses in the peripheral blood and tumor

• To correlate patient responses with exploratory biomarkers, such as programmed death-ligand 1 (PD-L1) expression and somatic mutations

Study Design• NEO-PV-01 + adjuvant is a personalized neoantigen vaccine custom designed

specifically for the molecular profile of each individual’s tumor (Figure 2)

> The vaccine is composed of a set of up to 20 neoantigen peptides of 14–35 amino acids in length, designed based on DNA mutations present in each patient’s tumor

> Peptides are pooled together in four groups of up to five peptides each, and mixed with the adjuvant polyinosinic-polycytidylic acid-polylysine carboxymethylcellulose (poly-ICLC) at the time of administration

• NT-001 is a single-arm, phase IB trial of NEO-PV-01 + adjuvant (poly-ICLC) in combination with the programmed death 1 (PD-1)-directed antibody nivolumab in patients with advanced melanoma, smoking-associated NSCLC, or TCC of the bladder (Figure 3) (NCT02897765)

• Key patient eligibility criteria are described in Table 1

• Approximately 30 patients will be enrolled in each disease group for a total of approximately 90 patients

> If ≥ 15 patients in each disease group do not have ≥ 1% PD-L1 expression as characterized in their pre-treatment tumor biopsy, additional patients may be enrolled

• The study opened in November 2016 and will be conducted at approximately 10 sites in the US; six sites are currently open. Approximately 25 patients have been enrolled to date

Figure 2. NEO-PV-01 Product Process

DNA, deoxyribonucleic acid; RNA, ribonucleic acid.

Figure 3. NT-001 Study Schema

NSCLC, non-small cell lung cancer; PD, progressive disease; RECIST, Response Evaluation Criteria in Solid Tumors; TCC, transitional cell carcinoma.

Table 1. Key Patient Eligibility CriteriaKey Inclusion Criteria

• Histologically-confirmed disease having received ≤ 1 prior systemic therapy:

> Unresectable or metastatic Stage III–IV melanoma

> Unresectable or metastatic Stage IIIB/Stage IV smoking-associated NSCLC

> Unresectable or metastatic TCC of the bladder, urethra, ureter, or renal pelvis

• Measurable disease not treated with local therapy within 6 months of study treatment

• ECOG PS ≤ 1

• ≥ 18 years of age

• Adequate hematologic, hepatic and renal function

Key Exclusion Criteria

• Prior treatment with:

> Immunotherapeutic agents including any anti-PD-1 or anti-PD-L1 antibody therapya

> Systemic anticancer therapy within 28 days of first dose of study therapy

• Treatment with non-oncology vaccine therapy for prevention of infectious diseases:

> During the 4-week period prior to first dose of nivolumab therapy

> During the period of NEO-PV-01 + adjuvant or nivolumab administration and until ≥ 8 weeks after the last dose of the booster vaccine

• Condition requiring systemic treatment with either corticosteroids or other immunosuppressive medications within 14 days prior to the first dose of nivolumabb

• Active or history of autoimmune diseasec

• Mucosal melanoma and uveal melanoma

• Patients with NSCLC and known ALK translocations or EGFR mutations who have not received prior treatment with ALK or EGFR inhibitor

aWith the exception of melanoma patients having received and progressed on anti-cytotoxic T lymphocyte associated protein 4 (CTLA4); bInhaled or topical steroids and adrenal replacement doses (≤ 10 mg daily prednisone equivalents) are permitted in the absence of active autoimmune disease; cExceptions are permitted for vitiligo, type I diabetes mellitus, residual hypothyroidism due to autoimmune condition requiring only hormone replacement, psoriasis not requiring systemic treatment, or conditions not expected to recur in the absence of an external trigger.ALK, anaplastic lymphoma kinase; CTLA4, cytotoxic T lymphocyte associated protein 4; ECOG PS, Eastern Cooperative Oncology Group performance status; EGFR, epidermal growth factor receptor; NSCLC, non-small cell lung cancer; PD-1, programmed death 1; PD-L1, programmed death-ligand 1; TCC, transitional cell carcinoma.

Treatment• The schedule of treatments and assessments is shown in Figure 4

• During pre-treatment, patients undergo a baseline tumor biopsy, and collection of peripheral blood mononucleocytes (PBMCs)

• Human leukocyte antigen typing is performed for each patient

• Whole exome DNA sequencing and RNA sequencing is performed on both the tumor and peripheral blood sample in order to identify the mutations specific to the patient’s tumor

• The NEO-PV-01 vaccine is designed based on computational immunogenicity analysis of the mutations in each patient’s tumor using Neon Therapeutic’s proprietary algorithm, RECON

• Starting on Day 1, all patients will receive nivolumab 240 mg by intravenous infusion over 30 minutes every 2 weeks. Nivolumab will be continued until disease progression

• Serial tumor biopsies will be performed and PBMCs collected

• Patients who have not achieved a confirmed complete response by Week 12 will begin vaccination with NEO-PV-01 + adjuvant (subcutaneous injection) at Week 12

• Each patient scheduled to receive NEO-PV-01 + adjuvant will receive five vaccinations during the priming phase, on Days 1 and 4 of Week 12 and then weekly for 3 weeks (Weeks 13, 14, and 15). Patients will also receive booster vaccinations 4 and 8 weeks following the completion of the priming vaccine Weeks 19 and 23)

Figure 4. Treatment and Assessment Schedule

NSCLC, non-small cell lung cancer; PD, progressive disease; TCC, transitional cell carcinoma; Vax, vaccination.

Study Assessments

Safety • Safety assessments include evaluation of adverse events (AEs), serious AEs, symptom-

directed physical examinations, measurement of vital signs, Eastern Cooperative Group performance status, and safety laboratory assessments

Efficacy • Radiographic assessments to evaluate response to treatment (defined by Response

Evaluation Criteria in Solid Tumors) will be conducted at Weeks 8, 12, and 24

Immune Profiling and Monitoring• Detailed analysis of robust neoantigen peptide T-cell responses detected by ELISPOT

will be performed (Figures 5 and 6), including:

> Determination of the precise epitope specificity of T cells

> Assessment of the phenotype of T-cell subsets (Th1 vs Th2, T effector vs memory cells, cytokines)

> Evaluation of presence and abundance of regulatory cells such as T-regulatory cells or myeloid-derived suppressor cells

• Serial tumor biopsies will be assessed, including whole exome sequencing, RNA sequencing, and immunohistochemistry

Figure 5. Immune Profiling: Informs and Improves

ELISPOT, enzyme-linked immunospot; ICS, intracellular cytokine staining; IHC, immunohistochemistry; TIL, tumor infiltrating lymphocyte.

Figure 6. Immune Monitoring Questions and Key Assays

ELISPOT, enzyme-linked immunospot; FACS, fluorescence-activated cell sorting; ICS, intracellular cytokine staining; IHC, immunohistochemistry.

Summary• The NT-001 trial is a phase IB trial designed to evaluate the safety of the personalized

neoantigen vaccine, NEO-PV-01 + adjuvant in combination with nivolumab in patients with unresectable or metastatic melanoma, smoking-associated NSCLC, or TCC of the bladder in patients who have received ≤ 1 prior systemic treatment

• Through the characterization of immune responses and correlation with clinical outcomes following treatment with NEO-PV-01 + adjuvant with nivolumab, the trial aims to inform underlying tumor biology and improve future vaccine design and personalized programs

• The trial is currently recruiting patients

Acknowledgments• This study was funded by Neon Therapeutics.

Disclosures• PAO: Received grants and personal fees from Bristol-Myers Squibb, Celldex Therapeutics, CytomX

Therapeutics, Merck; personal fees from Amgen, Neon Therapeutics, Novartis, Pfizer, Roche/Genentech; received grants from AstraZeneca/MedImmune

• RG: Consulting/advisor for ARAID Pharmaceuticals, Astellas. AstraZeneca, Baxalta, Boehringer Ingelheim, Bristol-Myers Squibb, Celgene, Genentech, INC Pharma, Merck, MSK Pharma, Novartis, Pfizer, Roche; consultant/advisor for and received honoraria from Abbvie; start-up meeting for INC Research

• SH-L: Consulting for Amgen, Emergent BioSolutions, Merck, Novartis, Vaccinex; contracted research for Genentech, Neon Therapeutics, Pfizer, Plexxikon; research support from Bristol-Myers Squibb, Merck (pending); travel support from Amgen, Emergent BioSolutions, Merck, Neon Therapeutics Novartis, Vaccinex

• MAM, MJG, RGB: Employees of Neon Therapeutics

• AN, KM: Nothing to disclose

References1. Yarchoan M, et al. Nature Reviews Cancer. 2017;17:209–222.

2. Martin SD, et al. Annals of Oncology. 2015;26:2367–2374.

3. Farkona S, et al. BMC Medicine. 2016;14:73.

4. van Rooij N, et al. Journal of Clinical Oncology. 2013;31:e439–e442.

5. Le DT, et al. The New England Journal of Medicine. 2015;372:2509–2520.

6. Rizvi NA, et al. Science. 2015;348:124–128.

7. Ott PA, et al. Nature. 2017;547:217–221.

Corresponding author: patrick_ott@dfci.harward.edu

Melanoma

RECISTstaging

Week 1n = 30 per cohort Week 12 Week 24

RECISTstaging

RECISTstaging

Until PDNSCLC(smoking associated)

TCC of the bladder

NEO-PV-01

Nivolumab

Serial tumor biopsies andperipheral blood sampling

Clinicaloutcomes

Rapid exchangetetramers

ELISPOTFlow

cytometry

Tumorcell lines

IHC & TILanalyses

Serial deepsequencing

Vaccinedesign

Personalizedprograms

Clinical feedback loopAllows for intimate understanding of

underlying immunology and tumor biology

ICSbead arrays

Priming Vax Booster 1 Booster 2

Nivolumab: 240 mg flat dose until PD

Blood draw BiopsyLeukapheresis

80 mL 80 mL 80 mL 80 mL

Week 0 8 16 2412

1207TiP

Q?

Tissue

Assay

Do neoantigen-specific

T cells expand?

What are the T-cell phenotypes?

Activated vs suppressive?

Are the T cellspresent at

the tumor site?

Do we see epitope

spreading?

What is the immunesignature at thetumor and how

does it change ontreatment?

ELISPOT,ICS

FACS,phenotyping,

tetramer analysis

IHC analysis,tumor cell

killing assay

Targeted geneexpression

analysis, vaccineepitopes

Mutanomeanalysis by

combinatorialcoding

Biopsy BiopsyLeuka-

pheresis/blood

Leuka-pheresis/

blood

Leuka-pheresis/

blood

Cancer patientbiopsy

Multichannel peptide synthesis

DNA & RNA sequencing

Pooling and fill/finish

n = 1 manufacturing Adjuvant

BioinformaticsMutation calling, selection,

epitope design

Vaccineadministration

T Cell

Dendritic Cell

Tumor Cell

Apoptosis

Neoantigen• Highly Immunogenic• Exquisitely Tumor Specific

Dendritic CellAdjuvant

(Poly-ICLC)

NeoantigenPeptides

Activation of Neoantigen-specific T Cells

Neoantigen-specific T Cells Recognize and Attack Tumor

Personalized Neoantigen Vaccine plus Adjuvant 1

3

2

4Neoantigen-specific T Cells Replicate