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

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/).

MMiRNA-Viewer2, a bioinformatics tool for visualizing functional annotation for MiRNA and MRNA pairs in a network

“…For miRNA (i) The Human Micro-RNA Disease Database (HMDD) [35] (ii) Somatic mutations altering microRNA-ceRNA interactions (SomamiR) Fig. 1 The visualization screenshot of MMiRNA-Viewer 2 [36] (iii) miRbase Database of published miRNA sequences and annotation (miRbase) [37] (iv) Kyoto Encyclopedia of Genes and Genomes (KEGG) [38] whereas for mRNA, (i) Database for Annotation, Visualization and Integrated Discovery (DAVID) [8] (ii) Kyoto Encyclopedia of Genes and Genomes (KEGG) [38] (iii) Catalogue of Somatic Mutations in Cancer (COSMIC) [39] (iiii) Cancertope [40] . The selection criteria were based on the (i) useful information required for microRNA and mRNA (ii) the availability of the database for academic research and (iii) diseases association for both miRNA and mRNA.…”

“…Each gene is linked to HMDD [35], SomamiR [35,36], miRbase [37], KEGG [38]. Each miRNA is linked to DAVID [15], KEGG [38] COS-MIC [39] and Cancertope [40]. Furthermore, to allow efficient and systematic retrieval of statements from pathway databases, directly links results to KEGG.…”

“…Cancertope [40] is a Platform for Designing Genome-Based Personalized Immunotherapy or Vaccine against Cancer. The integrated modules from Cancertope are (i) Epitope Search, (ii) Data Retrieval, and (iii) Browse Gene.…”

Skull base invasive low-grade meningiomas, a distinct genetic subgroup: A microarray gene expression profile analysis

“…Identification of tumors specific gene sequence might allow for the development of cancer-specific immune therapy or vaccine [16]. Vasudevan et al did identify Forkhead Box M1 (FOXM1) as a master transcription factor for meningioma proliferation.…”

“…It is the most common tumor of the central nervous system (CNS), which account for approximately 36.4 % of all primary intracranial tumors and 53.4% of all non-malignant primary brain tumors in the USA [26]. Of meningioma with documented WHO grade, 81.3% of meningioma were WHO grade-I, 16.9%…”