Cancer Letters

Cancer Letters

Volume 416, 1 March 2018, Pages 42-56
Cancer Letters

Mini-review
High-throughput sequencing of the immune repertoire in oncology: Applications for clinical diagnosis, monitoring, and immunotherapies

https://doi.org/10.1016/j.canlet.2017.12.017Get rights and content

Highlights

  • Stepwise V(D)J recombination mainly contributes to the repertoires of the B-cell receptor (BCR) or T-cell receptor (TCR).

  • HTS-IR technology allows a high-resolution and panoramic analysis of B- or T-cell repertoires at population- or single-cell level.

  • HTS-IR technology has been applied for the identification and development of prognostic and therapeutic tumor biomarkers.

  • Application of HTS-IR in therapeutic antibodies, CAR-T or neoantigen-specific TCR-T cell-based adoptive immunotherapy.

Abstract

The diagnostic, monitoring and therapeutic options for cancers currently remain limited. These limitations represent a large threat to human health. Adaptive immunity, which is dependent on diverse repertoires of B cell receptors (BCRs) and T cell receptors (TCRs), plays a critical role in the anti-tumor immune response. Modulation and surveillance of adaptive immunity has become a powerful weapon to combat cancers. Recently, the high-throughput sequencing of immune repertoire (HTS-IR) technology, which provides a robust tool for deep sequencing repertoires of BCRs or TCRs, has been applied in the development of tumor biomarkers and immunotherapeutics for cancers. This review will first provide an overview of the advancement of HTS-IR technology at the population-cell and single-cell levels. It will then provide a current summary of the applications of HTS-IR technology in the diagnosis and monitoring of minimal residual disease (MRD), focusing on immune reconstitution after the treatment of allogeneic hematopoietic stem cell transplantation (allo-HSCT) in B/T-cell malignancies, and the precise detection of tumor-infiltrating lymphocytes (TILs) in non-B/T-cell malignancies. Finally, current advances of HTS-IR technology in cancer immunotherapeutic applications, such as therapeutic antibodies, CAR-T cell based-adoptive immunotherapies, and neoantigen-specific TCR-T cell-based adoptive immunotherapies, will be introduced.

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).

References (112)

  • J.J. Calis et al.

    Characterizing immune repertoires by high throughput sequencing: strategies and applications

    Trends Immunol.

    (2014)
  • F.W. Alt et al.

    Mechanisms of programmed DNA lesions and genomic instability in the immune system

    Cell

    (2013)
  • M. Bruggemann et al.

    Has MRD monitoring superseded other prognostic factors in adult ALL?

    Blood

    (2012)
  • J.J. van Dongen et al.

    Minimal residual disease diagnostics in acute lymphoblastic leukemia: need for sensitive, fast, and standardized technologies

    Blood

    (2015)
  • J.W. Sweetenham

    Following aggressive B-cell lymphoma

    Blood

    (2015)
  • D.M. Kurtz et al.

    Noninvasive monitoring of diffuse large B-cell lymphoma by immunoglobulin high-throughput sequencing

    Blood

    (2015)
  • S.J. Dawson et al.

    Large B-cell lymphoma: is the future written in the blood?

    Lancet. Oncology

    (2015)
  • M. Roschewski et al.

    Circulating tumour DNA and CT monitoring in patients with untreated diffuse large B-cell lymphoma: a correlative biomarker study

    Lancet Oncology

    (2015)
  • A.J. Barrett et al.

    The role of stem cell transplantation for chronic myelogenous leukemia in the 21st century

    Blood

    (2015)
  • H.J. Deeg et al.

    Malignancies after hematopoietic stem cell transplantation: many questions, some answers

    Blood

    (1998)
  • A.D. Posey et al.

    Distinguishing truncated and normal MUC1 glycoform targeting from tn-MUC1-specific CAR T cells: specificity is the key to safety

    Immunity

    (2016)
  • N. Leffers et al.

    Prognostic significance of tumor-infiltrating T-lymphocytes in primary and metastatic lesions of advanced stage ovarian cancer

    Cancer Immun. Immunother. CII

    (2009)
  • B. Ye et al.

    Genetically modified t-cell-based adoptive immunotherapy in hematological malignancies

    J. Immune Res.

    (2017)
  • S.L. Topalian et al.

    Immunotherapy: the path to win the war on cancer?

    Cell

    (2015)
  • B. Li et al.

    Landscape of tumor-infiltrating T cell repertoire of human cancers

    Nat. Genet.

    (2016)
  • E. Tran et al.

    T-cell transfer therapy targeting mutant KRAS in cancer

    N. Engl. J. Med.

    (2016)
  • Chimeric antigen receptor-modified T cells in chronic lymphoid leukemia; chimeric antigen receptor-modified T cells for acute lymphoid leukemia; chimeric antigen receptor T cells for sustained remissions in leukemia

    N. Engl. J. Med.

    (2016)
  • S.A. Grupp et al.

    Chimeric antigen receptor-modified T cells for acute lymphoid leukemia

    N. Engl. J. Med.

    (2013)
  • D.L. Porter et al.

    Chimeric antigen receptor-modified T cells in chronic lymphoid leukemia

    N. Engl. J. Med.

    (2011)
  • D.S. Chen et al.

    Elements of cancer immunity and the cancer-immune set point

    Nature

    (2017)
  • Q. Qi et al.

    Diversity and clonal selection in the human T-cell repertoire

    Proc. Natl. Acad. Sci. U.S.A.

    (2014)
  • M.J. Stubbington et al.

    T cell fate and clonality inference from single-cell transcriptomes

    Br. J. Pharmacol.

    (2016)
  • G.C. Wu et al.

    Temporal stability and molecular persistence of the bone marrow plasma cell antibody repertoire

    Nat. Commun.

    (2016)
  • B.J. DeKosky et al.

    Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires

    Proc. Natl. Acad. Sci. U.S.A.

    (2016)
  • J. Michalek et al.

    Definitive separation of graft-versus-leukemia- and graft-versus-host-specific CD4+ T cells by virtue of their receptor beta loci sequences

    Proc. Natl. Acad. Sci. U.S.A.

    (2003)
  • G. Georgiou et al.

    The promise and challenge of high-throughput sequencing of the antibody repertoire

    Nat. Biotechnol.

    (2014)
  • P.G. Thomas et al.

    Ecological analysis of antigen-specific CTL repertoires defines the relationship between naive and immune T-cell populations

    Proc. Natl. Acad. Sci. U.S.A.

    (2013)
  • B.J. DeKosky et al.

    In-depth determination and analysis of the human paired heavy- and light-chain antibody repertoire

    Nat. Med.

    (2015)
  • B.J. DeKosky et al.

    High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire

    Nat. Biotechnol.

    (2013)
  • D. Redmond et al.

    Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq

    Genome Med.

    (2016)
  • H.S. Robins et al.

    Digital genomic quantification of tumor-infiltrating lymphocytes

    Sci. Transl. Med.

    (2013)
  • F. Pages

    Tumor-associated immune parameters for personalized patient care

    Sci. Transl. Med.

    (2013)
  • J.S. Sims et al.

    Diversity and divergence of the glioma-infiltrating T-cell receptor repertoire

    Proc. Natl. Acad. Sci. U.S.A.

    (2016)
  • J.J. Lohmueller et al.

    Antibodies elicited by the first non-viral prophylactic cancer vaccine show tumor-specificity and immunotherapeutic potential

    Sci. Rep.

    (2016)
  • M. Attaf et al.

    Alphabeta T cell receptors as predictors of health and disease

    Cell. Mol. Immunol.

    (2015)
  • H. Spits

    Development of alphabeta T cells in the human thymus, Nature reviews

    Immunology

    (2002)
  • B. Howie et al.

    High-throughput pairing of T cell receptor alpha and beta sequences

    Sci. Transl. Med.

    (2015)
  • J.S. Blachly et al.

    Immunoglobulin transcript sequence and somatic hypermutation computation from unselected RNA-seq reads in chronic lymphocytic leukemia

    Proc. Natl. Acad. Sci. U.S.A.

    (2015)
  • S.D. Brown et al.

    Profiling tissue-resident T cell repertoires by RNA sequencing

    Genome Med.

    (2015)
  • L.E. Mose et al.

    Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V'DJer

    Bioinformatics

    (2016)
  • Cited by (30)

    • High-Throughput immunogenetics for precision medicine in cancer

      2022, Seminars in Cancer Biology
      Citation Excerpt :

      However, only a small fraction of cancer patients experience long-term benefits by immunotherapy, while resistance to therapy and low response rate are major setbacks in these approaches [20]. In this frame, monitoring of TR dynamics during immunotherapy by Immune-seq could guide immunomodulatory and T-cell based interventions [95]. Moreover, data from large-scale Immune-seq studies could serve as a valuable input for personalized designs in each individual malignancy [20].

    • Identification of alpha-enolase as a potential immunogenic molecule during allogeneic transplantation of human adipose-derived mesenchymal stromal cells

      2022, Cytotherapy
      Citation Excerpt :

      These results suggested that the immunogenicity of human Ad-MSCs increased when they were exposed to PBMCs. Comprehensive analysis of the TCR or immunoglobulin repertoire by high-throughput sequencing can be used to assess the enrichment of antigen-specific T- or B-cell clones in many diseases as well as the immunogenicity of specific antigens [32,39]. It may also provide clues for elucidating the underlying mechanisms of anti-tumor immunity in specific tumors [40].

    • Molecular subtyping in pancreatic neuroendocrine neoplasms: New insights into clinical, pathological unmet needs and challenges

      2020, Biochimica et Biophysica Acta - Reviews on Cancer
      Citation Excerpt :

      Prior PanNEN molecular pathological approaches have used low throughput methods for investigating the contributions of specific molecules, which may not accurately contextualize these molecules within the landscape of molecular disruptions occurring in tumors. High throughput sequencing and multi-platform technologies [19] have led to new insights into molecular subtyping that are associated with the development of specific PanNENs. These techniques also show the heterogeneity of PanNENs, revealing key molecular events that contribute to PanNEN recurrence.

    • Adaptive immune receptor repertoires, an overview of this exciting field

      2020, Immunology Letters
      Citation Excerpt :

      From both basic research and clinical perspectives AIRRseq has revolutionized the study of the immune repertoire. Clinical applications of AIRR analysis comprise identification of diagnostic biomarkers, design of therapeutic antibodies, and development of new vaccines [72–80]. Lymphoid malignancies are a good example of AIRRseq application to identify potentially lymphocyte clones, and to track them over time in longitudinal data from the same individual, before and following therapeutic treatment.

    View all citing articles on Scopus
    View full text