Data from: A public database of memory and naive B-cell receptor sequences

The vast diversity of B-cell receptors (BCR) and secreted antibodies enables the recognition of, and response to, a wide range of epitopes, but this diversity has also limited our understanding of humoral immunity. We present a public database of more than 37 million unique BCR sequences from three healthy adult donors that is many fold deeper than any existing resource, together with a set of online tools designed to facilitate the visualization and analysis of the annotated data. We estimate the clonal diversity of the naive and memory B-cell repertoires of healthy individuals, and provide a set of examples that illustrate the utility of the database, including several views of the basic properties of immunoglobulin heavy chain sequences, such as rearrangement length, subunit usage, and somatic hypermutation positions and dynamics

A Public Database of Memory and Naive B-Cell Receptor Sequences

<div><p>The vast diversity of B-cell receptors (BCR) and secreted antibodies enables the recognition of, and response to, a wide range of epitopes, but this diversity has also limited our understanding of humoral immunity. We present a public database of more than 37 million unique BCR sequences from three healthy adult donors that is many fold deeper than any existing resource, together with a set of online tools designed to facilitate the visualization and analysis of the annotated data. We estimate the clonal diversity of the naive and memory B-cell repertoires of healthy individuals, and provide a set of examples that illustrate the utility of the database, including several views of the basic properties of immunoglobulin heavy chain sequences, such as rearrangement length, subunit usage, and somatic hypermutation positions and dynamics.</p></div

Experimental and informatic design.

<p><b>(a)</b> Peripheral blood samples from three healthy donors were sorted using flow cytometry to isolate naive (CD19⁺ CD27^- IgD⁺ IgM⁺) and memory (CD19⁺ CD27⁺) B cells. For each sample, approximately 10⁷ cells were distributed into two 96-well plates (i.e., into 188 wells, resulting in ~50,000 cells per well), and processed by immunosequencing. <b>(b)</b> Schematic of the ‘urn sampling’ quantitation method. Cells are represented by colored balls, with each color indicating a different clone identity. Each ball (cell) is randomly allocated to a sample bin (well). Occupancy is calculated after censoring count information, and thus is expressed as presence or absence. The majority of clones are present in just one out of 188 wells, indicating that they were almost certainly represented by a single cell in the original sample.</p

V family and V gene usage patterns.

<p>The histograms show the relative percent of total sequences (by occupancy) for each of the IGHV families (as shown under the graphs), for the naive (left panel) and memory (right panel) samples, aggregated for the three donors. Within each family, discrete bands represent each of the individual genes. The most abundant genes within each family are indicated (e.g., 69 in IGHV01 refers to the gene IGHV01-69). Overall, memory samples contain fewer IGHV01 and more IGHV03 family sequences than naive samples, with some gene-level differences evident as well.</p

Comparison of CDR3 lengths in naive versus memory B-cell samples.

<p>(<b>a</b>) The graph shows the normalized percentage of total sequences for the naive (orange) and memory B cells (blue) from donor D2. (<b>b</b>) The graph shows the cumulative percentage of total sequences at a given CDR3 length for all naive and memory samples, as indicated in the inset. The technical replicates for donor D1 overlap closely and are not distinguishable in this figure. The memory repertoire is consistently 3 nucleotides (or 1 amino acid) shorter than the naive repertoire at the same cumulative frequency.</p

Comparison of Somatic Hyper Mutation in paired naive and memory B-cell samples from the same donor.

<p>The figure shows data for the naive (<b>a</b>) and memory sample (<b>b</b>) from Donor 1, which is representative of all three donors. The x-axis corresponds to the number of substitutions differing from the germline V gene sequence, and the y-axis indicates the number of unique sequences that display that number of substitutions. The colors indicate different total well occupancies, with blue indicating singletons present in just one well, and the other colors showing progressively higher well occupancy, as indicated in the figure. The majority of the sequences in the naive B-cell sample have 0 substitutions and correspond to low abundance clones observed in a single well (blue). In contrast, the memory B cell sample from the same individual shows a much broader distribution of substitutions, as well as many more sequences with occupancy greater than 1.</p

T cell receptor gene therapy targeting WT1 prevents acute myeloid leukemia relapse post-transplant.

To access publisher's full text version of this article click on the hyperlink belowRelapse after allogeneic hematopoietic cell transplantation (HCT) is the leading cause of death in patients with acute myeloid leukemia (AML) entering HCT with poor-risk features1-3. When HCT does produce prolonged relapse-free survival, it commonly reflects graft-versus-leukemia effects mediated by donor T cells reactive with antigens on leukemic cells4. As graft T cells have not been selected for leukemia specificity and frequently recognize proteins expressed by many normal host tissues, graft-versus-leukemia effects are often accompanied by morbidity and mortality from graft-versus-host disease5. Thus, AML relapse risk might be more effectively reduced with T cells expressing receptors (TCRs) that target selected AML antigens6. We therefore isolated a high-affinity Wilms' Tumor Antigen 1-specific TCR (TCRC4) from HLA-A2+ normal donor repertoires, inserted TCRC4 into Epstein-Bar virus-specific donor CD8+ T cells (TTCR-C4) to minimize graft-versus-host disease risk and enhance transferred T cell survival7,8, and infused these cells prophylactically post-HCT into 12 patients ( NCT01640301 ). Relapse-free survival was 100% at a median of 44 months following infusion, while a concurrent comparative group of 88 patients with similar risk AML had 54% relapse-free survival (P = 0.002). TTCR-C4 maintained TCRC4 expression, persisted long-term and were polyfunctional. This strategy appears promising for preventing AML recurrence in individuals at increased risk of post-HCT relapse.Juno Therapeutics Immunotherapy Integrated Research Center at the Fred Hutchinson Cancer Research Center Damon Runyon Guillot Family ZachAttacksLeukemia Foundatio