The adaptive immune system defends the human body from pathogens through the recognition ability of antigen receptors from B and T cells. Different organs play various immune function roles, and therefore present varied B and T cell gene expression and immune repertoire profiles. Abnormality of these profiles may reflect immunological disorder, presence of neoplastic tissue, or response to infectious agent. High-throughput sequencing technology has facilitated the understanding of gene expression and related cell functions, but in-depth understanding of B and T cell phenotype and clonotype profiling is an emerging application that has yet to take full advantage of sequencing technology for diagnosis and prognosis of disease.

Here, we share results of RNA sequencing of immune system tissues; including B cell and T cell specific gene expression and full-length immune repertoire profiling. Total RNA was extracted from various tissue samples including healthy donor peripheral blood mononuclear cells (PBMC), lymph nodes, bone marrow, spleen, thyroid, thymus and colon, as well as diseased PBMC and colon samples. RNA-seq and Immune-seq libraries were made from these samples and sequenced on Illumina NextSeq2000. Gene expression analysis and immune repertoire profiling from RNA-seq data were performed using edgeR and TRUST4. Immune repertoire sequencing data was processed using pRESTO and IgBlast. We correlated RNA-seq with Immune-seq results for B-cell receptor and T-cell receptor clonotypes. Differential expression and clonotype profiling comparisons were also performed between normal and diseased RNA samples. The effect of reference on immune repertoire detection sensitivity and accuracy was further investigated by comparing IMGT reference and AIRR-C Human IG Reference Sets.

This study has identified tissue specific B/T cell phenotype and clonality patterns that relate to tissue functions and disease progression. RNA-seq enables highly multiplex immunophenotyping which is traditionally performed by flow cytometry. RNA-seq can detect high-abundant clones that correlate with Immune-seq, with the latter targeted approach providing more in depth clonality signatures. References comparison results show the importance of continued community effort to develop more representative and accurate immunorepertoire germ line references for clonotype annotation in diverse populations. Integrating both RNA sequencing and immune repertoire sequencing approaches allows accurate phenotype and clonotype determination for immune landscape in various tissues.

Citation Format: Chen Song, Evan Janzen, Tessa Devoe, Ariel Erijman, Gautam Naishadham, Li Song, Bradley W. Langhorst. RNA sequencing approaches enable tissue specific B and T cell gene expression and immune repertoire profiling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7045.