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En masse discovery of anti-cancer human monoclonal antibodies by de novo assembly of immunoglobulin sequences from transcriptomes and genome sequences of cancer tissues

Cellular & Molecular Immunology volume 16, pages 943–945 (2019)Cite this article

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Characterization of the tumor-infiltrating B cell immunoglobulin (Ig) repertoire is critical to understanding B cell immunity in tumors and developing monoclonal antibody therapy. However, the generation of specific antibodies for cancer therapy1,2 is a major endeavor, involving a lengthy process of antigen identification, immunization, hybridoma production and, in most cases, antibody humanization. As a radical departure from the conventional approach, we hereby describe a rapid and potentially en masse identification of cancer-specific antibodies directly from human cancer tissues by de novo assembly from transcriptome and genome sequences. Our integrated computational framework was developed and successfully tested for antibody discovery by mining 1945 solid tumor RNA-sequencing-based samples for abundant Ig CDR3 sequences among the TCGA database of glioblastoma multiforme (GBM), lower grade glioma (LGG), lung adenocarcinoma (LUAD), lung squamous carcinoma (LUSC), pancreatic adenocarcinoma (PAAD), and skin cutaneous melanoma (SKCM).

Considering the predominate abundance observed in BCR density and clonality of LUAD cohorts, the sample that ranked first in abundance of Ig transcripts to total RNAseq reads was selected for experimental validation (Fig. 1c). We were able to assemble 1675 IgH, 2999 IgK, and 1959 IgL CDR3 sequences from this sample, which provided massive amounts of antibodies for further characterization. Based on the abundance, alignment score and BCR gene usage of assembled CDR3 sequences, the three IgH and six IgL sequences of this sample were selected (Fig. 1c) for manual curation. Sequence information and gene usage of CDR3 sequences are presented in Fig. 1d. Co-enrichment of CDR3 of the H and L chains suggests that they are likely paired, as suggested by parallel studies in T cells.4 However, it is not possible to determine to pair by frequency alone. Nevertheless, since our goal is to identify cancer-reactive antibodies rather than describing endogenous antibody responses, we combined the 3H chains and 6L chains at random in a pairwise fashion and tested whether Igs were produced. These antibodies were linked to mouse IgG2a heavy chain and k light chain to facilitate future studies of human tissues that may have endogenous human IgG. As shown in Fig. 1e, out of 18 combinations, 13 combinations resulted in significant levels of antibodies in transient transfection and thus gave us valuable tools to evaluate antibody specificity.

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Acknowledgements

Part of the study was performed when the authors were at the Children’s National Medical Center.

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  1. These authors contributed equally: Peng Zhang, Hung-Yen Chou

Authors and Affiliations

  1. Division of Immunotherapy, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA

    Peng Zhang, Hung-Yen Chou, Pan Zheng & Yang Liu

  2. The Institute for Biomedical Sciences, The George Washington University, Washington, DC, 20037, USA

    Hung-Yen Chou

  3. Center for Cancer and Immunology Research, Children’s Research Institute, Children’s National Health System, Washington, DC, 20010, USA

    Lei Young

  4. OncoImmune, Inc, Rockville, MD, 20852, USA

    Pan Zheng & Yang Liu

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  1. Peng Zhang
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Contributions

Pe.Z. and H.-Y.C. performed the experiments and analyzed the data. L.Y. helped with the experiments. Y.L. and Pa.Z. supervised the studies, designed the experiments and wrote the manuscript along with Pe.Z. and H.-Y.C.

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Correspondence to Pan Zheng or Yang Liu.

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Competing interests

Y.L. and Pa.Z. are co-founders of and have equity interests in OncoImmune, Inc. The remaining authors declare no competing interests.

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Zhang, P., Chou, HY., Young, L. et al. En masse discovery of anti-cancer human monoclonal antibodies by de novo assembly of immunoglobulin sequences from transcriptomes and genome sequences of cancer tissues. Cell Mol Immunol 16, 943–945 (2019). https://doi.org/10.1038/s41423-019-0299-9

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