Longitudinal analysis of drift in the circulating human antibody repertoire over four years

  1. Collin Joyce
  2. Benjamin Nemoz
  3. Raiza Bastidas
  4. Bryan Briney
  5. Dennis R. Burton

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Abstract

The human immune system is a sophisticated network of cells and molecules that plays a vital role in safeguarding the body against a broad range of foreign agents. One of the key components of the immune system is the circulating antibody repertoire, a vast collection of different antibodies that recognize and eliminate foreign agents specifically. The diversity and specificity of the circulating antibody repertoire are essential for effective immunity. In a study of ten healthy donors, we previously demonstrated the accessible human antibody repertoire to be on the order of 10 15 -10 18 distinct members, although an individual will only sample a fraction of that repertoire at a given time point. The mode of generation of the naïve antibody repertoire through random recombination before antigen contact suggests that the composition of the circulating antibody repertoire may drift over time, but the magnitude of this drift is poorly understood. Here, we used high-throughput sequencing to analyze two donors from our original study, approximately four years later. Our results reveal conservation of the size, overall diversity, and gross features of the circulating antibody repertoire, such as V- and J-gene usage and CDRH3 length distribution, over time but suggest substantial changes to fine features of the repertoire, such as combinations of V, J, D gene segments and P and N sequences, which may influence primary responses to newly encountered pathogens as well as to immunization procedures.

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  1. PREreview

    This Zenodo record is a permanently preserved version of a PREreview. You can view the complete PREreview at https://prereview.org/reviews/15297872.

    Brief summary of the study - a sentence summarizing the study and general comments that apply across the full paper

    • Joyce, Nemoz et al. investigate the changes of the human antibody repertoire over time by applying high-throughput sequencing on blood samples of two individuals, with two sampling times, 4 years apart. They show that characteristics of the antibody repertoire are conserved over time, but the content differs as much at different time points as between different individuals, revealing high drift. This is an in-depth study with detailed analyses and some caveats (sampling size & depth), which are transparently discussed.

    Major comments  - Comments on the validity or strength of the methodology, experiments and analyses, strength of the conclusions

    • Defining the different features of human antibody repertoires is a challenging task. In this study, the authors used a set of granular features — including the frequencies of V-genes, J-genes, and CDRH3 lengths — to distinguish similarity indexes between time points and individuals. This approach enables differences to be detected with as few as 10⁴ sequences and can serve as a reference method for distinguishing antibody repertoires in future studies.

    • The results of this study identified common clonotypes that are persistent across time points and individuals, which are associated with shorter CDRH3s. While the authors provided hypotheses regarding the presence of these antibodies with shorter CDRH3s, it would be interesting to propose experimental plans, such as studies in animal models or future sampling in geographical areas with known infectious disease outbreaks, to identify the exact origins of these CDRH3-short antibodies.

    Minor comments - Clarifications to statements in the text, interpretation of the results, presentation of the data/figures

    • The authors rightfully point out that antibody studies in humans face many challenges, but a great deal has been investigated in the murine setting. The introduction and discussion would benefit from mentioning and cross-referencing these.

    • Code is well-annotated!

    Conflicts of interest of reviewers

    • No

    Inline commenting section

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    1. Abstract section

      • Comments: 

      • A conclusion section that shows the impact of the results is helpful if added to the abstract section

    2. Introduction section: "The heavy chain variable domain is assembled from three gene segments VH, DH, and JH, that are randomly joined. "

      • Comments: 

      • Please identify the abbreviation as variable (VH), diversity (DH), and joining (JH).

    3. Introduction section: "Recombination requires V(D)J recombinase, a protein complex that includes RAG1, RAG2 and Artemis. Artemis and TdT are responsible for the random (non-templated) addition of P and N nucleotides at VH-DH and DH-JH junctions, "

      • Comments: 

      • Please identify the abbreviations as Recombination Activating Genes 1 and 2 (RAG1 and RAG2)

      • Please identify "Artemis" as DNA CROSS-LINK REPAIR PROTEIN 1C; DCLRE1C (also known as Artemis)

      • Please identify "TdT" abbreviation as Terminal deoxynucleotidyl transferase, also known as DNA nucleotidylexotransferase (DNTT)

    4. Discussion: "In other words, the sampled naïve repertoire of an individual 4 years later is suggested to be as different from that sampled from the individual's prior self as it is between two different individuals at any given time point. "

      • Comments: 

      • Is it possible that this might not be the case with a larger sample sizte? I.e., that it would be possible to correlate individuals over time within a larger cohort?

    5. Discussion: "The broad result of extensive turnover in the naïve repertoire may have been anticipated given the random nature of recombination to generate the repertoire and the limited half-life of naïve B cells in humans (Macallan et al. 2005). "

      • Comments: 

      • This reference is not present in the references section

    Competing interests

    The authors declare that they have no competing interests.

  2. Version published to 10.1101/2025.03.20.644446 on bioRxiv