Identification of Immunogenic Neo-epitopes for the Development of Personalised Pancreatic Cancer Vaccines
Condition: The Initial Aim of This Project is to Perform in Vitro Validation of Neoepitope Candidates Selected From Available Mutanome Data
Study type: Observational

Summary: 
      Human pancreatic cancer has a very poor prognosis with an overall survival rate of less than
      5%. Current treatment regimens are ineffective and even if the patient responds to initial
      treatments, relapse is common due to the survival of small populations of resistant cancer
      cells.

      The immune system is capable of recognising and eliminating invading organisms by virtue of
      differences in their appearance when compared to normal components of the body. Cancer cells
      also have a different appearance compared to normal cells. However, these differences are
      often too small and weak to stimulate the immune system sufficiently to respond effectively
      to eliminate the tumour.

      Our aim is to analyse the small differences between healthy and cancer cells in pancreatic
      cancer patients. Analysis of the genetic information from 100 pancreatic cancer patients has
      allowed us to design molecules that display each of these small differences. We now intend to
      analyse each of these, with respect to their ability to stimulate an immune response against
      cancer. We then intend to take all validated molecules and incorporate them into vaccines
      carried by viral vectors. These vaccines can be used to train the patient's immune system to
      respond more effectively when it encounters these particular differences in the patient's
      body and thus mount an efficient attack on the cancer cells specifically.

      Surplus material from blood donations will be used to isolate individual components of the
      immune system, which can be examined for their response to these altered molecules in the
      laboratory. On completion of this project, we will have viral vaccine libraries that can be
      tested in future research projects. Ultimately, we hope to transfer this regime to the clinic
      by selecting an appropriate viral vaccine library to deliver as a personalised therapeutic
      that can eliminate cancer and prevent cancer recurrence within each patient.
    

Detailed description: 
      Background Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive tumour
      types, with an extremely poor prognosis. Without active treatment, patients with metastatic
      PDAC have a mean survival of 3-5 months [1]. Current advances in surgical and adjuvant
      treatments have failed to improve overall survival rates since the 1970s. Thus, new treatment
      strategies, that are not cross resistant with conventional chemotherapy-based regimes are
      imperative. Recently, attention in cancer therapy has focused more heavily on immune-based
      strategies as these therapies act through a mechanism that is distinct from chemotherapy or
      radiation therapy and represent a non-cross-resistant treatment option [2]. Immune based
      therapies aim to stimulate robust T cell responses against tumour antigens. However,
      significant challenges exist in the development of these regimes. These include poor
      immunogenicity of the tumours and the presence of a highly immunosuppressive environment
      within the tumour [3, 4]. The clinical potential of various tumour vaccination strategies has
      been demonstrated in early phase clinical trials, with some promising immunological and
      clinical responses in PDAC patients [5-8]. A number of hurdles still need to be overcome in
      the development of an ideal PDAC vaccine. Crucially, specific tumour antigens must be
      identified that elicit a strong and specific immune response as failure of past cancer
      vaccine trials can be attributed in large part to selection of inappropriate tumour antigens
      that have weak inherent immune potential [9, 10]. Current advances in high throughput
      profiling technologies as enabled rapid determination of the genomic states of cancer cells
      such that comprehensive data regarding individual mutanomes is now available [11, 12]. It is
      also now possible to select missense mutations identified through the exome sequencing on the
      basis of their HLA binding capacity for production of synthetic peptides that can be
      presented by a desired HLA molecule [12, 13]. The development of this platform has allowed us
      to analysed published data from 100 PDAC patients [14] and establish a dataset containing
      high-affinity HLA-A2 and HLA-DP4 (the most abundant HLA class I and II molecules [15, 16])
      and HLA-E*01:01 and HLA-E*01:03-restricted neo-epitopes for analysis as peptide vaccine
      candidates.

      Hypothesis Sequence analysis has allowed us to develop a peptide library of neo-epitopes that
      are expressed at high frequency in patient populations and have high binding affinities
      compared to their wild-type counterpart to HLA-A2, HLA-DP4, HLA-E*01:01 or HLA-*01:03
      molecules. We hypothesise that a number of these will be sufficiently immunogenic to
      stimulate a T cell interferon-γ (IFN-γ) response in vitro, that will translate to an in vivo
      anti-tumour response. Immunogenic neo-epitopes can then be combined in a peptide vaccination
      program using adjuvants such as oncolytic viruses for targeted delivery and expression within
      tumours of PDAC patients to stimulate robust and long-term anti-tumour responses.

      Aim The initial aim of this project is to perform in vitro validation of neo-epitope
      candidates selected from available mutanome data to determine their immunogenicity using
      peripheral blood mononuclear cells (PBMCs) from healthy individuals.

      Research Plan PBMC samples from healthy individuals will be HLA typed using commercially
      available reagents from thermofisher scientific. HLA-A2, HLA-DP4, HLA-E*01:01 and/or
      HLA-E*01:03 positive samples will be pulsed with peptides selected after bioinformatics
      analysis of available sequence data. IFN-γ and interleukin-2 (IL-2) production by the T cells
      in the samples will be evaluated by ELISA after two rounds of stimulation within a two weeks
      time as a measure of peptide immunogenicity. Once immunogenic peptides have been identified,
      their wild-type counterparts will be analysed in parallel to confirm specificity for the
      mutated epitope. Immunogenic peptides whose wild-type counterparts do not elicit immune
      responses will then be selected for inclusion in an oncolytic virus-based vaccine to be
      analysed in vivo using transgenic HLA-A2/HLA-DP4 mice [17].
    

Intervention name(s): Peptides
Intervention type(s): Other
Intervention description(s): Peptides will be added to PBMCs in in vitro cell culture.
Observational model: Other
Time perspective: Prospective
Sampling method: Probability Sample
Study population: 
        Healthy blood donors, who donate their blood at the Blood Donation Centres in London.
      
Biospecimen description: 
      Human blood from healthy donors, who donate blood at the Blood Donation Centres.