A new two-dimensional analytical method called the pGen-SHM plot can visualize patterns of B-cell receptor repertoire maturation after allogeneic hematopoietic stem cell transplantation that were not apparent from conventional diversity indices. In a small longitudinal study of 12 patients, the method showed a gradual shift toward a pattern resembling that of healthy adults over approximately two years after cord blood transplantation. Early samples after bone marrow transplantation contained two distinct sequence populations, which the researchers interpreted as consistent with mature B cells transferred in the graft and B cells newly generated from hematopoietic stem cells.
The findings support further evaluation of the plot as a potential way to assess humoral immune reconstitution, but the cohort was too small to establish clinical utility. The work, published online in Blood Immunology & Cellular Therapy on August 3, 2026, was led by Yohei Funakoshi, Kimikazu Yakushijin and Hironobu Minami of the Division of Medical Oncology and Hematology at Kobe University Hospital, with Goh Ohji of the Division of Infectious Disease Therapeutics and Takaji Matsutani of Anymics Inc. The investigators examined peripheral-blood B-cell receptor repertoires from six patients who received cord blood transplantation and six who underwent bone marrow transplantation at Kobe University Hospital.
The cord blood group provided 21 samples collected 67 to 662 days after transplantation, while the bone marrow group provided 14 samples collected 67 to 628 days after transplantation. This observational design characterized repertoire distributions over time; it did not test whether the method could predict infection, vaccine responses, survival or other clinical outcomes. Conventional assessments of immune recovery after transplantation often rely on immune-cell counts or IgG levels, but the source release notes that these measures cannot fully show whether a broad population of B cells capable of responding to pathogens has developed and matured.
The B-cell receptor repertoire is the complete collection of diverse receptor sequences in an individual and reflects aspects of B-cell generation, antigen encounter, selection and maturation. Earlier repertoire studies have examined diversity indices, clone-size distributions and CDR3 length, while the optimal computational approach for evaluating immune status from these large datasets has remained unclear. The pGen-SHM plot was designed to retain information about individual sequences by placing two sequence-level features on the same graph: an estimated probability of generation and the degree of somatic hypermutation associated with antigen-driven maturation.
B-cell receptor diversity arises mainly through V(D)J recombination, which generates many possible receptor sequences. For each CDR3 amino-acid sequence, the team calculated pGen, an estimate of the probability that the sequence would arise through this recombination process. The estimate was obtained with a generative V(D)J recombination model using OLGA.
After antigen stimulation, high-frequency mutations can accumulate in the variable regions of immunoglobulin genes, and B cells with improved antigen binding may be selected. The study used the somatic hypermutation rate as an indicator of this affinity-maturation process and calculated it as 100 minus the percentage nucleotide identity of the V region to the IMGT germline reference sequence. Each receptor sequence was then positioned according to its pGen and SHM values, and kernel density estimation represented the repertoire’s distribution through color intensity.
The researchers reasoned that a relatively immature repertoire should contain more readily generated sequences with little somatic hypermutation, producing a concentration in the high-pGen, low-SHM region. Maturation would be represented by movement toward lower pGen and higher SHM. This predicted pattern appeared in the cord blood transplantation group.
Early after transplantation, the sequence distribution was concentrated in the high-pGen, low-SHM region. Over approximately two years, it shifted continuously toward lower pGen and higher SHM and approached the range observed in healthy adults. The proportions of high-pGen sequences and low-SHM sequences were strongly inversely correlated with time after transplantation, providing a quantitative feature associated with the longitudinal change in the plotted distribution.
Publicly available B-cell receptor data from healthy individuals aged zero to 15 years also shifted in the same direction with age, from relatively high-pGen, low-SHM patterns toward lower-pGen, higher-SHM patterns. The similarity between this age-associated distribution and the observed post-transplant change supports the pGen-SHM plot as a candidate measure of repertoire maturation. It does not establish that the post-transplant process is biologically identical to normal development or that cord blood recipients fully replicate healthy maturation.
In addition, conventional diversity indices did not show a clear relationship with time after transplantation in either transplant group. The new visualization exposed the joint distribution of sequence-generation probability and mutation rather than summarizing the repertoire through a single measure of overall diversity. Bone marrow transplantation showed a different early pattern.
Within the first 180 days after transplantation, three samples collected on days 67, 130 and 149 contained clear low-pGen, high-SHM and high-pGen, low-SHM populations. By approximately six months, the low-pGen, high-SHM population was no longer apparent, while the high-pGen, low-SHM population tended to shift toward the maturation pattern seen after cord blood transplantation. Bone marrow grafts contain more mature immune cells than cord blood.
On that basis, the investigators considered the low-pGen, high-SHM population consistent with mature B cells transferred with the bone marrow graft and the high-pGen, low-SHM population consistent with B cells newly generated from hematopoietic stem cells. These are possible cellular interpretations of the measured sequence distributions: the study did not directly trace the origins of the cells in either population. Detailed analysis of the three early bone marrow samples provided an additional association with the observed division.
These samples contained relatively more IgG1 in the high-pGen, low-SHM region and relatively more IgG2 in the low-pGen, high-SHM region. The differing isotype distributions were consistent with the two regions representing biologically distinct groups rather than arbitrary portions of one distribution, but they did not independently establish cellular identity or function. The researchers proposed future work combining flow cytometry, cell sorting and single-cell analysis to determine the origins and functions of the populations displayed on the plot.
Such studies would be needed to test the proposed connection between sequence-level patterns and mature graft-derived cells versus cells arising from hematopoietic stem cells. The pGen-SHM plot is therefore a candidate analytical biomarker rather than a validated clinical test. The team plans prospective studies involving larger numbers of patients and intends to examine the effects of conditioning regimens, immunosuppressive therapy, graft-versus-host disease, corticosteroids, B-cell-depleting therapy and other clinical factors.
It also aims to combine repertoire analysis with cellular methods to characterize the observed populations more directly. Those planned investigations are needed to establish whether the plotted distributions are reproducible, how they relate to immune function and whether the method can support standardized assessment of humoral immune reconstitution. The current study does not show that changes in the plot predict infection, vaccine response or survival, and it does not establish grounds for altering infection-prevention or revaccination practices.
The method’s principal demonstrated capability is to display both continuous repertoire maturation and coexisting sequence populations within a sample. It showed a gradual two-year shift after cord blood transplantation and transiently distinct distributions after bone marrow transplantation, neither of which was clear from conventional diversity indices alone. The plot also offers a way to examine B-cell receptor data in vaccination, infectious disease, cancer immunity and autoimmune disease, but those potential applications remain proposals for future study.
For now, the evidence is limited to longitudinal repertoires from 12 transplant recipients and supports pGen-SHM as a promising method requiring larger prospective cohorts, direct cellular characterization and clinical validation before use in patient management.
Subject of Research: Visualization of B-cell receptor repertoire maturation after allogeneic stem cell transplantation
Article Title: B-cell repertoire analysis visualizes humoral immune maturation after hematopoietic stem cell transplantation
Article References: B-cell repertoire analysis visualizes humoral immune maturation after hematopoietic stem cell transplantation. Original publication (Bibliographic details unavailable.)
Image Credits: AI Generated
DOI: Not provided
Keywords: B-cell receptor repertoire, hematopoietic stem cell transplantation, cord blood transplantation, bone marrow transplantation, humoral immunity, somatic hypermutation, immune reconstitution, repertoire analysis, B-cell, repertoire, analysis, visualizes
News Source: Drew Townsend. (October 26, 2026). Small study maps B-cell maturation after stem cell transplantation. Scienmag.
