Bioinformatics of T-cell and Primary Tumor Cells- Fundamental of Adoptive T-cell Immunotherapy

Epitope discovery of tumor antigen and mutant proteins has enabled a better application of T-cell immunotherapy. Genomic profiles analyzed by genomic expression and single nucleotide polymorphisms (SNP) by genome-wide association studies (GWAS) are an essential fundamental to screen and define T-cell therapeutic targets. To determine tumor antigens or mutant proteins related to T-cell targets with their TCR or CAR reconstruction, we will introduce the SNP technique related to primary tumor cells for personalized T-cell immunotherapy, including global and local SNP detection of the therapeutic targets. Moreover, the use of mRNA genomic expression can discover gene expression signature and further uncover tumorassociated antigen (TAA) or tumor-specific antigen (TSA) for T-cell immunotherapy. Accompany with the ongoing development of next-generation sequencing, epitope discovery of tumor neoantigen and mutant proteins will be irreplaceable for a novel generation of T-cell adoptive immunotherapy. System biology, which is a mathematical modeling of complex biological systems,can integrate data of SNP signature and genomic expression signature. Thus, a new bioinformatics platform with the analysis of GWAS and genomic expression profile along with system modeling is an essential fundamental for T-cell adoptive immunotherapy.

Keywords: And system modeling, Genome-wide association studies (GWAS), gene expression signature (GES), Networks, Proteomics, Single nucleotide polymorphisms (SNP), System biology, T-cell adoptive immunotherapy, Therapeutic targeting, Transcriptome.