Analysis Of Tumor TCR Repertoire Characteristics And Establishment Of Bioinformatics Workflow

The immune repertoire(IR)is the entire collection of sequences of antibodies produced by the immune system in an organism.This collection of sequences includes all the antibodies in the immune system that can be directed against various pathogens,cells and molecules.Immunome libraries can be obtained by sequencing DNA or RNA from B cells,antibodies or immunoglobulins in an organism.The study of immunome libraries can provide much valuable information to the fields of immunology,biology,medicine and drug development.The analysis of immunome libraries can reveal the diversity and characteristics of antibodies in organisms in different immune states,including the structure,affinity,specificity,and function of antibodies.This information can help us better understand how the immune system works and its applications in disease and immunotherapy.Currently,with the development of high-throughput sequencing technology,immunome library analysis is gradually coming to attention in the field of immunology research.In order to build an efficient and accurate process for immunome library analysis,we have established a systematic analysis process by combining existing gene assignment and sequence correction tools.The flow covers the upstream analysis process from raw data to quality control,filtering,TCR and BCR sequence identification and extraction,as well as the downstream analysis of immunome library diversity,gene amplification preference,V-J gene sharing and CDR3 length distribution characteristics,and also provides data visualization tools for users to better understand and interpret the results.Based on this,we built a web tool for immunome library analysis process,IRAI(Immune Repertoire Alternative Image),which enables one-stop immunome library analysis.This tool provides researchers with a fast,reliable,and efficient way to analyze immunome libraries,which helps to better understand changes in the immune system under various physiological and pathological states.In this study,a NSCLC(Non-Small Cell Lung Cancer,NSCLC)dataset containing 220 tumor regions,64 non-tumor lung tissue samples and 56 peripheral blood mononuclear cell(PBMC)samples was analyzed using an immunomic library analysis process.It was found that TCR group library diversity and abundance decreased and clonality increased in tumor and paraneoplastic tissues of NSCLC.Peripheral blood hyperclonality typing was significantly higher than in tumor and paraneoplastic tissues,suggesting that NSCLC may cause hyperclonality of peripheral blood cells in patients,activating the biological functions of relevant molecules in the blood,resulting in a global immune response.In addition,it was found that TRAV21 and TRAJ53 genes,TRAJ42 and TRAV38-2DV8 genes are highly shared in TCRαand β in NSCLC,and these highly shared VJ genes may have a synergistic regulatory effect on NSCLC.non-normal hyperclonal amplification of TRAV21 and TRBV6.5may be due to NSCLC,i.e.,these genes could serve as potential tumor markers for NSCLC.In addition,we identified potential NSCLC tumor-associated antigens and neoantigen recognition epitopes in our clone-tracking analysis.Finally,we example analyzed tumor tissues,peripheral blood mononuclear cells and regional lymph node TCR repertoire from six patients with PTC(Papillary Thyroid Cancer,PTC)to explore the commonalities and differences in immunomic libraries among different tumors.We identified a potential upstream regulatory role of the TRBV2 gene on the facilitative TRBJ2-5 gene and an immune response-related binding reference epitope CASSEGTGGGETQYF in papillary thyroid carcinoma.in addition,the TRBV2-1 gene showed a similar high expression in papillary thyroid carcinoma as in NSCLC,suggesting that it could be used as a high-frequency reference gene for immunity in multiple tumor types.