Mini-reviewHigh-throughput sequencing of the immune repertoire in oncology: Applications for clinical diagnosis, monitoring, and immunotherapies
Introduction
Diagnostic, monitoring and therapeutic options for cancers are currently still limited. These limitations create immense threats to human health, and thus there is an urgent need for more effective diagnostics and treatments [[1], [2], [3], [4]]. In recent years, immunotherapy has become a promising and powerful tool for combating cancers [[5], [6], [7], [8]]. The great successes of immune checkpoint blockade inhibitors (e.g., PD-1/PD-L1 antibody or CTLA-4 antibody) and engineered immune cells (e.g., chimeric antigen receptor (CAR)-T cells or neoantigen-specific T cell receptor (TCR)-T cells) in the application of cancer therapy mark the beginning of a new era in medicine [[9], [10], [11], [12], [13]]. However, given that multifaceted factors that define immune profiles combine to represent the varying “cancer-immune set points” in individual cancer patients with the treatment of immunotherapeutics, such as PD-1/PD-L1 and CTLA-4 antibodies, only a subset of people exhibit efficient immune responses to immunotherapy, suggesting that the identification of elements of cancer immunity and immune profiles merits the prediction and optimization of the therapeutic response for tumor eradication [14]. Thus, a profound understanding of the mechanisms of cancer immunology is necessary. Adaptive immunity, which plays a critical role in an effective anti-tumor immune response [15], requires functional B cells bearing a diverse repertoire of B-lymphocyte antigen receptors (BCRs, Fig. 1A) and functional T cells bearing a diverse repertoire of T-lymphocyte antigen receptors (TCRs, Fig. 1B). In general, the repertoire of BCRs or TCRs is extremely large and can be shaped by age [16], exogenous antigens, and endogenous factors [[17], [18], [19]]. Changes in these repertoires occur during the pathogenesis of oncological diseases. The development of novel methods for analyzing or evaluating the repertoires of BCRs or TCRs will therefore facilitate the development of diagnostic and monitoring tools, as well as effective immunotherapies.
In the 1990s, Sanger sequencing technology provided a platform for the low-throughput analysis of the repertoire of BCRs or TCRs in typically up to a few hundred B or T cells. This analysis promoted an understanding of adaptive immunity in some diseases and allowed the design of more effective vaccines against some pathogens [[20], [21], [22]]. Nonetheless, low-throughput analysis of BCRs or TCRs has limited our broader understanding of the immune repertoire. The advancement of next-generation sequencing technology has led to the development of high-throughput sequencing of immune repertoire (HTS-IR) technology for the deep sequencing of BCR or TCR gene sequences, allowing large-scale and quantitative analyses of the astronomically large BCR or TCR repertoires [23,24]. The HTS-IR method has made it possible to delineate a much broader picture of BCR or TCR repertoires, track the dynamic evolution of B or T cell clones [25], and elucidate the structural composition and diversity of BCR or TCR repertoires at the single-cell level [17,[26], [27], [28]]. Clinically, the HTS-IR method has recently been employed for the diagnosis and monitoring of minimal residue disease (MRD), oncological recurrence [29] and immune reconstitution after allogeneic hematopoietic stem cell transplantation (HSCT) in B cell or T cell malignancies. Additionally, the HTS-IR assay has also been utilized in quantitative analyses of tumor-infiltrating lymphocytes (TILs) in non-B/T cell malignancies, and the development of prognostic biomarkers [[30], [31], [32]]. Recently, HTS-IR technology has also shown great potential in cancer immunotherapeutics [7,33]. This review will elucidate the generation of BCR and TCR repertoires and the advancement of HTS-IR technology for analyses of the diversity, dynamics, and clonality of B/T cells at the population-cell and single-cell levels. Moreover, this review will generalize the applications of HTS-IR technology in the diagnosis and monitoring of malignant diseases, as well as in immunotherapeutics, such as therapeutic antibodies, CAR-T cell-based adoptive immunotherapies, and neoantigen-specific TCR-T cell-based adoptive immunotherapies.
Section snippets
Advances in HTS-IR at the population-cell and single-cell levels
BCR, which is a membrane-bound form of immunoglobulin (Ig) expressed on the B cell membrane, is composed of two identical heavy (IgH: μ, α, γ, δ, ε) and two identical light (IgL: κ, λ) chains linked by disulfide bonds [23]. TCR is a heterodimer composed of two disulfide bond-linked transmembrane proteins on the T cell membrane surface: one α and one β chain, or one γ and one δ chain [34,35] (Fig. 1A,B). Both intact BCRs and TCRs contain variable (V) and constant (C) domains. The diversity and
Applications of HTS-IR technology in clinical diagnosis and monitoring of cancers
Theoretically, HTS-IR technology for deep sequencing of CDR3 or the variable domains can track B or T cell clones that are involved in B- or T-cell malignancies and non-B or T cell malignancies, highlighting its importance in cancer research and treatment applications (Table 1). On the one hand, given that CDR3 sequences with distinct V(D)J rearrangements constitute desirable biomarkers for tracking malignant B or T cell clones bearing distinct BCRs or TCRs (Fig. 3A) [23], the HTS-IR technology
Applications of HTS-IR in cancer immunotherapy
Recently, cancer immunotherapies, such as therapeutic antibodies and genetically modified T cell adoptive transfer, have exhibited great potential in the treatment of malignant diseases and are becoming hot topics in the area of cancer therapy [5,88]. Monoclonal antibodies that can target or kill tumor cells directly or indirectly have been successfully applied for the treatment of cancer [88]. Genetically modified T cell-based adoptive immunotherapeutics, such as CAR-T cell-based and
Conclusion
HTS-IR technology has been applied in the identification of valuable prognostic biomarkers for tumor surveillance and in the development of cancer immunotherapeutics, such as therapeutic antibodies, CAR-T cell-based adoptive immunotherapy and neoantigen-specific TCR-T cell-based adoptive immunotherapy. In the future, three points should be carefully considered. First, the increasingly large-scale sequencing data provided by developing HTS-IR technologies should be standardized and
Conflicts of interest
The authors have no conflicts of interest.
Acknowledgements
This work was supported by the National Natural Science Foundation of China (No. 81600101 to BX Ye and No.81571147 to XX Xiong) and the Fundamental Research Funds for the Central Universities (No. 2042016kf0078 to BX Ye).
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