A different ontogenesis for chronic lymphocytic leukemia cases carrying stereotyped antigen receptors: molecular and computational evidence

Abstract

Chronic lymphocytic leukemia (CLL) is uniquely characterized by the existence of subsets of cases with quasi-identical, 'stereotyped' B-cell receptors (BCRs). Herein we investigate this stereotypy in 2662 patients with CLL, the largest series yet, using purpose-built bioinformatics methods based on sequence pattern discovery. Besides improving the identification of 'stereotyped' cases, we demonstrate that CLL actually consists of two different categories, based on the BCR repertoire, with important biological and ontogenetic differences. The first ( approximately 30% of cases) shows a very restricted repertoire and is characterized by BCR stereotypy (clustered cases), whereas the second includes cases with heterogeneous BCRs (nonclustered cases). Eleven major CLL clusters were identified with antigen-binding sites defined by just a few critically positioned residues, regardless of the actual immunoglobulin (IG) variable gene used. This situation is closely reminiscent of the receptors expressed by cells participating in innate immune responses. On these grounds, we argue that whereas CLL cases with heterogeneous BCRs likely derive from the conventional B-cell pool, cases with stereotyped BCRs could derive from progenitor cells evolutionarily adapted to particular antigenic challenges, perhaps intermediate between a true innate immune system and the conventional adaptive B-cell immune system, functionally similar to what has been suggested previously for mouse B1 cells.

Over 30% of patients with splenic marginal zone lymphoma express the same immunoglobulin heavy variable gene: ontogenetic implications

“…Despite these shared features, the vast majority of IGHV1-2*04 rearrangements did not fulfill the established criteria for VH CDR3 stereotypy, as defined previously in other lymphoid malignancies, namely CLL, 8,28 mainly because of variable IGHJ gene usage and heterogeneous junctional residues.…”

“…Furthermore, interpretation of results for all cases was performed de novo in the context of this study, following the approaches reported in our recent publications. 8,24,28 Molecular modeling In order to explore the possible modifications in the antibody structure caused by a single amino-acid replacement---namely, the arginine (R)-totryptophan (W) substitution at position VH FR3-75 to obtain an IGHV1-2*04-rearranging antibody---we performed a molecular dynamics study of the human anti-polyhydroxybutyrate antibody F v : IGHV1-2*02 IGKV1-39*01/1D-39*01 (Protein Data Bank code 2D7T). Replacement of the VH FR3-75 R (germline for IGHV1-2*02) by the W residue (germline for IGHV1-2*04) was executed by the COOT algorithm.…”

“…Clustering of VH CDR3 sequences Using the sequence pattern-based methodology described previously by our group, 28 25/345 sequences (7.2%). were assigned to 13 different level zero clusters with restricted (stereotyped) VH CDR3 sequences (Supplementary Table 14).…”

“…The remaining, despite the ubiquitous presence of short shared 'IGHD-derived' motifs within the antigen-binding sites, failed to show significant overall VH CDR3 amino-acid likeness, that is, they did not fulfill the established criteria for VH CDR3 'stereotypy'. 28 …”

Antigens in CLL: themes and variations

“…2 However, the most compelling immunogenetic piece of evidence is the fact that almost 30% of CLL patients share BcRs with restricted, quasi-identical IG sequences. 3 This might justifiably be taken as a convincing hint of restriction also in terms of the antigens selecting CLL progenitors. Elucidation of the identity of the respective antigens combined with knowledge about the actual structure of CLL BcRs should aid in understanding the functional interplay between CLL cells and the (micro)environment, eventually paving the way to the design of rational, individualized treatment.…”