Optimization of peripheral blood volume for in silico reconstitution of the human B‐cell receptor repertoire

Abstract

B cells recognize antigens via membrane‐expressed B‐cell receptors (BCR) and antibodies. Similar human BCR sequences are frequently found at a significantly higher frequency than that theoretically calculated. Patients infected with SARS‐CoV2 and HIV or with autoimmune diseases share very similar BCRs. Therefore, in silico reconstitution of BCR repertoires and identification of stereotypical BCR sequences related to human pathology have diagnostic potential. Furthermore, monitoring changes of clinically significant BCR sequences and isotype conversion has prognostic potential. For BCR repertoire analysis, peripheral blood (PB) is the most convenient source. However, the optimal human PB volume for in silico reconstitution of the BCR repertoire has not been studied in detail. Here, we sampled 5, 10, and 20 mL PB from the left arm and 40 mL PB from the right arm of two volunteers, reconstituted in silico PB BCR repertoires, and compared their composition. In both volunteers, PB sampling over 20 mL resulted in slight increases in functional unique sequences (FUSs) or almost no increase in repertoire diversity. All FUSs with a frequency above 0.08% or 0.03% in the 40 mL PB BCR repertoire were detected even in the 5 mL PB BCR repertoire from each volunteer. FUSs with a higher frequency were more likely to be found in BCR repertoires from reduced PB volume, and those coexisting in two repertoires showed a statistically significant correlation in frequency irrespective of sampled anatomical site. The correlation was more significant in higher‐frequency FUSs. These observations support the potential of BCR repertoire analysis for diagnosis.

An ancestral SARS-CoV-2 vaccine induces anti-Omicron variants antibodies by hypermutation

“…Five BCR HC clonotypes, including 27–60, were not found in vaccinees in whom the antibody clones were found. This type of discrepancy is expected to inevitably originate from the incomplete in silico reconstitution of the BCR HC repertoire due to the limitation of the throughput of next-generation sequencing 28 . In this regard, the BCR HC clonotypes are expected to be present in a larger population than we observed herein.…”

Stereotypic persistent B cell receptor clonotypes in Alzheimer’s Disease

“…At least 15 ml of peripheral blood was collected per patient in EDTA tubes (BD Vacutainer K2EDTA tubes, 367525) 29 . Peripheral blood mononuclear cells (PBMCs) and plasma were separated by density-gradient centrifugation using Ficoll (Cytiva Ficoll-Paque Plus, 17-1440-02) solution.…”

An ancestral SARS-CoV-2 vaccine induces anti-Omicron variants antibodies by hypermutation

“…Five BCR HC clonotypes, including 27-60, were not found in vaccinees in whom the antibody clones were found. This type of discrepancy is expected to inevitably originate from the incomplete in silico reconstitution of the BCR HC repertoire due to the limitation of the throughput of next-generation sequencing 23 . In this regard, the BCR HC clonotypes are expected to be present in a larger population than we observed herein.…”