14-16 November 2018


Day One
Thursday November 15, 2018

Day Two
Friday November 16, 2018

Registration & Morning Refreshments

Chair’s Opening Remarks

Public vs Private Neoantigens – Can Both Be Used Therapeutically?


  • Neoantigens can be shared between patients (public) or unique to an individual patient (private)
  • Therapeutics targeting public neoantigens can be “off-the-shelf” but patient selection is key –
    likely only a subset of solid tumors display these targets
  • Most solid tumor patients could benefit from personalized immunotherapy against private
    neoantigens – neoantigen identification and product manufacturing are critical
  • An ability to elicit profound T cell responses in humans is a likely obligate requirement of both approaches

An Integrated Machine-Learning Approach to Improve the Prediction of Clinically Relevant Neoantigens


  • Current neoantigen discovery algorithms are not optimal to predict presentation to the cell surface
  • Here, we outline a high-performing machine learning approach, trained on massspectrometry
    data, that predicts naturally processed and presented antigens
  • The predictor is integrated with several immune parameters, such as HLA binding, in a deep
    learning layer to predict bone fide neoantigens
  • We illustrate its application to significantly improve the identification of neoantigen targets for personalized cancer immunotherapy

Morning Refreshments & Networking

11.30 TESLA Consortium: Update on Neoantigen Predictions

  • Over two dozen distinct computational pipelines exist for neoantigen prediction
  • These pipelines utilize over a dozen different parameters to select peptides for vaccines
  • The identity of the key factors in the selection of validated peptides are not clear
  • Using 4 different bioassays, including patient-derived cells, the consortium is characterizing the key factors in peptide prediction

Fred Ramsdell, Vice President of Research, Parker Institute for Cancer Immunotherapy

12.00 Neoantigen Prediction: Approach and Validation

  • Neoantigen identification for cancer immunotherapy remains a significant challenge
  • Tumor immunopeptidomics combined with deep learning provides a powerful approach for neoantigen prediction
  • Gritstone’s EDGETM prediction model identifies therapeutically relevant neoantigens

Roman Yelensky, Chief Technology Officer, Gritstone Oncology

12.30 Immunitrack: a unique platform for supporting immuno-oncology projects

  • PrDx: a best-in-class peptide:MHC stability predictor, trained on proprietary peptide:MHC I & II stability assay data. The PrDx software can generate up to 80% less false-positives (compared to netMHC) with the identification of larger subsets of T-cell epitopes
  • Best-in-class peptide/MHC stability and affinity assays (US and European client contracts).
  • Addresses the unmet client production need for customized MHC/epitope complexes and reagents.

Sune Justesen, CSO, Immunitrack

11.30 Neoantigen-targeting T Cell Therapy for Brain Cancer

  • Overview of the neoantigen landscape for malignant gliomas
  • Development of vaccine and T cell therapies targeting the novel H3.3K27M-derived neoantigen
  • Unique challenges related to antigen heterogeneity of malignant gliomas

Hideho Okada, Professor & Director of UCSF Brain

Tumor Immunotherapy Program, University of California, San Francisco

12.00 Neoantigen Targeted CD8 T Cell Responses Via Optimized DNA Immunotherapy

  • Tumor neoantigen targeting has emerged as a viable approach for treating cancer
  • Beyond prediction and selection algorithms, neoantigen delivery platforms and platform potency are important considerations to drive neoantigen targeted immune responses in vivo
  • Plasmid DNA based ASPIRE® platform for development of neoantigen targeted personalized cancer immunotherapy

Niranjan Y. Sardesai, CEO & President, Geneos Therapeutics

12.30 Th1 Epitopes for Versatile Tumor- and Patient-tailored Vaccine Combination Therapies (VCT)

  • EpiThany develops multiantigen cancer vaccines from a neo-repertoire of Th1-selective epitopes arising from overexpressed tumor antigens
  • Multiple Phase 1 patient studies of our vaccines have demonstrated antigen-specific IFNg T cell titers comparable or superior to neo-epitope platforms, epitope spreading, and enhanced survival
  • Retrospective analyses of archived epitopes for immune phenotype (Th1 or Th2) and a spectrum of genomic features suggests sequence homology to bacterial/fungal species may confer immunogenic properties

William Watt, Chief Executive Officer, EpiThany

Lunch & Networking

14.30 High-dimensional Mass Cytometry Epitope Mapping and Profiling of Neoantigen-specific T Cells in non-small Cell Lung Cancer Patients Treated with Atezolizumab.

  • Mass cytometry and highly-multiplexed combinatorial peptide-MHC tetramer staining was used to longitudinally monitor neoantigen-specific CD8+ T cells in PBMC from 14 NSCL cancer patients treated with atezolizumab
  • 782 candidate tumor neoantigens as well as 73 control peptides (mostly virus-derived epitopes) were screened across all patient samples
  • T cell reactive for 13 different neoantigens were identified by unbiased analysis across all patients
  • 9 out of 13 Neoantigen specific T cell responses were detected in patients with objective response (n=8) compared to only 4 hits in patients with progressive disease.

Mahesh Yadav, Research & Early Development Scientist, Genentech

15.00 Beyond Algorithms: the ATLAS Bioassay Method for Neoantigen Identification and Characterization

  • HLA agnostic assay identifies CD4 and CD8 T cell neoantigens
  • Uniquely distinguishes mutations that elicit stimulatory and inhibitory T cell responses
  • Personalized neoantigen vaccine using ATLAS entering clinical development

Jessica Flechtner, Chief Scientific Officer, Genocea Biosciences

14.30 Personalized Adoptive NeoE-specific TCR-T Cell Therapies for Cancer

Validation beyond Predictions: imPACTTM technology for the identification and isolation of neoE-specific T cells that constitute the intrinsic immune response in cancer patients

  • Expanding the neoE specific T cell repertoire beyond HLA-A2
  • Precision genome engineering of primary human T cells –  PACT’s non-viral technology for personalized neoE TCR engineering
  • Functional characterization of personalized adoptive neoE-specific TCR-T cells – the path to clinical development

Alex Franzusoff, Chief Scientific Officer, PACT Pharma

15.00 Personalized Adoptive T Cell Therapy Targeting MDS Stem Cell Neoantigens

  • The need for neoantigen validation
  • Do we know what fraction of potential neoantigens are recognized by T cells?
  • Why adoptive transfer and not vaccination?

Antonella Vitiello, Founder & CEO, PersImmune

Afternoon Refreshments

From Sample to Neoantigens for Vaccines: Key Challenges and Solutions

  • Sean Boyle Director Bioinformatics Applications, Personalis


  • Improving neoantigen identification
  • Elaborating TME, immuno-modulators and vaccine response biomarkers
  • Overcoming poor sample quality and quantity for NGS sequencing
  • Overcoming sequencing gaps that can harbor neoantigens
  • cfDNA neoantigens: dealing with tumor heterogeneity
  • Validation and regulatory issues on the way to commercialization

Clinical Considerations for Neoantigen-based Cancer Therapy – A Regulatory Perspective

  • Laronna Colbert Medical Officer, Office of Tissues & Advanced Therapies, CBER, FDA


  • Current landscape of Neoantigen-based cancer therapies
  • Challenges in clinical trial design
    1. Study population
    2. Target identification and selection
    3. Safety and Efficacy Endpoints
  • Opportunities to further advance the field


Chair’s Closing Remarks