Immunoglobulin Gene Repertoire Diversification and Selection in the Stomach – From Gastritis to Gastric Lymphomas

Abstract

Chronic gastritis is characterized by gastric mucosal inflammation due to autoimmune responses or infection, frequently with Helicobacter pylori. Gastritis with H. pylori background can cause gastric mucosa-associated lymphoid tissue lymphoma (MALT-L), which sometimes further transforms into diffuse large B-cell lymphoma (DLBCL). However, gastric DLBCL can also be initiated de novo. The mechanisms underlying transformation into DLBCL are not completely understood. We analyzed immunoglobulin repertoires and clonal trees to investigate whether and how immunoglobulin gene repertoires, clonal diversification, and selection in gastritis, gastric MALT-L, and DLBCL differ from each other and from normal responses. The two gastritis types (positive or negative for H. pylori) had similarly diverse repertoires. MALT-L dominant clones (defined as the largest clones in each sample) presented higher diversification and longer mutational histories compared with all other conditions. DLBCL dominant clones displayed lower clonal diversification, suggesting the transforming events are triggered by similar responses in different patients. These results are surprising, as we expected to find similarities between the dominant clones of gastritis and MALT-L and between those of MALT-L and DLBCL.

Aging affects B‐cell antigen receptor repertoire diversity in primary and secondary lymphoid tissues

“…Clonally related sequences (based on VDJ segment identity and CDR3 similarity) were aligned using the well-known sequence alignment tool ClustalW2 [38], in order to confirm that the CDR3 in the clonally related sequences were highly homologous. Further analyses were done using our automated pipeline for analyzing Ig gene sequences [39].Estimates of the full repertoire from which each sample were taken, diversity measures and similarity indices of the estimated repertoires were calculated using SPADE C [40], as described in detail in [41]. Briefly, alpha measured the diversity of an individual sample, gamma diversity represents the "global" repertoire diversity across all samples studied in each group of samples, and beta represents the diversity component resulting from the variability between individual repertoires or samples (beta = gamma/alpha).…”

Old questions, new tools: does next-generation sequencing hold the key to unraveling intestinal B-cell responses?

“…Thus, to evaluate over-or underrepresentation of clonotypes, the frequency of certain segment combinations should be compared with the expected frequency if all gene segments were expressed independently. 47 Under the latter assumption, the expected probability of observing a given combination V x J y , P(V x J y ), is the product of the probabilities of observing each of these segments, i.e., P(V x )*P(J y ); the latter probabilities are the observed frequencies of each segment in the database (see appendix in ref. 48).…”

Lineage tree analysis of high throughput immunoglobulin sequencing clarifies B cell maturation pathways

“…Sequence data were processed as described [41] [44]. Briefly, an in-house program deletes duplicate sequences (which might be a product of PCR amplification), and leaves only the unique sequences for the analysis.…”

“…Previous studies demonstrated the usefulness of this method and resulted in new insights regarding differences in GC dynamics in aging or between different tissues [35]- [37],in autoimmune diseases [38], chronic inflammation [39], lymphomas [40], and chronic gastritis and gastric lymphomas [41]. This method was also used to determine clonal relationships of Ig genes from different tissues [39] [42].…”