A Platform for Designing Genome-Based Personalized Immunotherapy or Vaccine against Cancer

PLoS One. 2016 Nov 10;11(11):e0166372. doi: 10.1371/journal.pone.0166372. eCollection 2016.

Abstract

Due to advancement in sequencing technology, genomes of thousands of cancer tissues or cell-lines have been sequenced. Identification of cancer-specific epitopes or neoepitopes from cancer genomes is one of the major challenges in the field of immunotherapy or vaccine development. This paper describes a platform Cancertope, developed for designing genome-based immunotherapy or vaccine against a cancer cell. Broadly, the integrated resources on this platform are apportioned into three precise sections. First section explains a cancer-specific database of neoepitopes generated from genome of 905 cancer cell lines. This database harbors wide range of epitopes (e.g., B-cell, CD8+ T-cell, HLA class I, HLA class II) against 60 cancer-specific vaccine antigens. Second section describes a partially personalized module developed for predicting potential neoepitopes against a user-specific cancer genome. Finally, we describe a fully personalized module developed for identification of neoepitopes from genomes of cancerous and healthy cells of a cancer-patient. In order to assist the scientific community, wide range of tools are incorporated in this platform that includes screening of epitopes against human reference proteome (http://www.imtech.res.in/raghava/cancertope/).

MeSH terms

  • Cancer Vaccines / genetics*
  • Cancer Vaccines / therapeutic use
  • Computer Simulation
  • Epitopes / genetics
  • Gene Expression Regulation, Neoplastic
  • Genome, Human
  • Genomics / methods*
  • Humans
  • Immunotherapy / methods*
  • Internet
  • Mutation
  • Neoplasms / genetics*
  • Neoplasms / prevention & control
  • Peptides / genetics
  • Peptides / therapeutic use
  • Precision Medicine

Substances

  • Cancer Vaccines
  • Epitopes
  • Peptides

Grants and funding

Authors are thankful to project Open Source Drug Discovery (OSDD) and GENESIS BSC0121.