Utilization of Ig heavy chain variable, diversity, and joining gene segments in children with B-lineage acute lymphoblastic leukemia: implications for the mechanisms of VDJ recombination and for pathogenesis

Immunoglobulin (Ig) genes are assembled from germ line variable (V), diversity (D), and joining (J) gene segments during early B-cell differentiation by a site-directed DNA rearrangement mechanism known as VDJ recombination.¹  Further recombination at the heavy chain (H) locus is prevented by a productive V_HD_HJ_H rearrangement that also triggers rearrangements at the light chain (L) loci, most often κ followed by λ.^2,3  During these joining steps, antibody diversity is generated by the following mechanisms: (1) somatic recombination of multiple V_H, D_H, and J_H segments; (2) nucleotide deletions of the 3′-end V_H segment; (3) non-germ line-encoded (N) nucleotide insertions by terminal deoxynucleotidyl transferase (TdT); (4) germ line-encoded palindromic (P) nucleotide additions; (5) transcription of D regions in any of 3 potential open reading frames; (6) fusion and inversion of D regions; and (7) somatic mutation.^4-8 

A complete map of the human Ig V_HD_HJ_H loci has now been constructed on chromosome 14q32.2 in a telomeric-to-centromeric direction.^9,10  The V_H region contains 123 V_H segments, of which 79 are pseudogenes and 44 have an open reading frame.¹⁰  The V_H genes are grouped into 7 V_H families based on their high sequence homology and not by their location on chromosome 14q32. V_H3 is the largest family followed by V_H4 and V_H1.^9,10  V_H6-1 is the most proximal to the D_HJ_H loci.^9,10  The D_H region contains 27 D_H segments, of which 25 have been shown to be involved in creation of human antibody.¹¹  Seven D_H families are classified based on sequence homology. D_H7-27 is closest to the J_H locus.¹¹  Six J_H segments are functional.^12,13  The rearranged heavy chain consists of the 3 high variable regions, complementarity determining regions (CDR1, CDR2, and CDR3), flanked by less variable framework regions (FR1, FR2, FR3, and FR4).⁴  The CDRs, especially CDR3, are considered as the core portion responsible for antigen recognition.⁴  The CDR3 sequence is unique to each rearrangement and therefore identifies individual B cells or clonal B-cell expansion.^4,14,15 

The V_HD_HJ_H gene repertoires are restricted and developmentally regulated at early stages of differentiation.^3,16  In the most immature B-cell precursors (pro-B cells), the IgH genes remain germ line or there is only D_HJ_H joining.^2,17  At the next stage, in early pre-B cells, V_H genes join to the joined D_HJ_H to complete the IgH rearrangement.^2,18  Numerous studies in both mice and humans have shown stage-specific trends in usage of V, D, and J genes, the degree of N nucleotide addition, and the rate of somatic mutation.^8,16-20  In the murine system, a biased use of J_H-proximal V_H segments and a high frequency of absence of N sequences at D_HJ_H joining were demonstrated at fetal stages of development.^19-21  In humans, a similar trend was found by a marked overrepresentation of some V_H (V_H3, V_H5, and V_H6), D_H (D_H7-27), and J_H (J_H3 and J_H4) segments and by a short CDR3 length in fetal liver B cells and in immature B cells.^16-18 

Previous studies have demonstrated a preferential usage of specific V_H genes in B-cell malignancies.^15,22,23  In mantle cell lymphoma, V_H3-21, V_H3-23, V_H4-34, V_H4-59, and V_H5-51 segments have shown to be most widely used.^24,25  In B-cell chronic lymphocytic leukemia (CLL), patients with unmutated compared with somatically mutated V_H genes have a worse prognosis.^26,27  A biased utilization of V_H1-69 combined with selected D_H gene segments and J_H6 has been found in unmutated cases,²⁸  and patients with mutated Ig V_H3-21 genes had significantly shorter survival than other mutated patients.²⁹  In B-lineage acute lymphoblastic leukemia (B-ALL), a privileged usage of V_H6 gene has been shown in both adult and childhood patients.^30-32  Sequence analysis of the CDR region demonstrated that D_H6 (DN1), J_H4, and J_H6 appeared to be overrepresented compared with the expected frequency of use according to the size of each D_H or J_H gene family.^14,33  Several studies have suggested that childhood B-ALL is derived from early fetal life or immature B cells.^31-33  In one study, in-frame and out-of-frame CDR3 joinings were observed in one third and two thirds of the rearrangements in pre-B-ALL, similar to the frequency of occurrence in nonmalignant early pre-B cells,³³  whereas another study found that in-frame CDR3 rearrangement occurred in 78% in children and 64% in adults, similar to that observed in healthy B cells (75%).³⁴ 

Most previous studies of V gene usage in B-ALL have been performed using databases with limitations for the newly identified germ line genes and the completed gene map and in particular have focused on gene family usage rather than location on the chromosome. In particular, awareness of connections among the IgH rearrangement patterns and clinical characteristics has been relatively limited in ALL compared with the more recent studies in CLL. To derive clone-specific oligonucleotides from IgH rearrangements for minimal residual disease (MRD) detection, we prospectively sequenced V_HD_HJ_H regions at presentation in 317 children with B-cell lineage ALL treated sequentially in a single protocol. The aims of this study were to describe V_HD_HJ_H rearrangement profiles in children with B-lineage ALL, to evaluate biologic and structural features in clonal expanded B cells by comparison with previous findings of the human Ig VH repertoire,^9,10  and to investigate the association between rearrangement patterns and clinical characteristics.

Bone marrow (BM) and/or peripheral blood (PB) samples were obtained at presentation and IgH rearrangements sequenced in 317 children with B-lineage ALL enrolled consecutively in Dana-Farber Cancer Institute (DFCI) ALL Consortium protocol 95-01. Institutional Review Board approval and informed consent were obtained for treatment and for procurement of the samples in all cases.

Mononuclear cells were isolated by Ficoll gradient centrifugation (Pharmacia, Uppsala, Sweden), lysed, and DNA extracted and purified according to the manufacturer's instructions using the NucleoSpin kit (BD Biosciences, Palo Alto, CA).

To identify patient leukemia-related IgH gene rearrangements, diagnostic BM and/or PB samples were polymerase chain reaction (PCR) amplified using a series of 7 V_H family FR1 consensus primers and a J_H consensus primer in a modification of a method previously described.³⁵  Primers were purchased from a commercial supplier (Invitrogen, Carlsbad, CA). The PCR conditions and methods used for detection of PCR products have been previously described.³⁶ 

Clonal PCR products were excised and purified using QIAquick gel extraction kits (QIAGEN, Valencia, CA). Purified PCR fragments were sequenced directly by the Dana-Farber/Harvard Cancer Center Core Sequencing Facility (Boston, MA). Sequence reactions were analyzed on an Applied Biosystems 3700 capillary sequencer using Big Dye Terminator Chemistry version 2 (Applied Biosystems, Foster City, CA). The relevant consensus forward and reverse primers were used as sequence primers to obtain the sequence of both strands. Nucleotide sequences were aligned using the DNAstar software (DNASTAR, Madison, WI).

V_H,D_H, and J_H segments were identified with a closest matching known human germ line genes using the ImMunoGeneTics (IMGT) Database (http://imgt.cines.fr, IMGT, European Bioinformatics Institute, Montepellier, France), the IGBlast search (http://www.ncbi.nlm.nih.gov/igblast/, National Center for Biotechnology Information, Bethesda, MD), or V BASE directory using DNAPLOT (http://www.mrc-cpe.cam.ac.uk/DNAPLOT.php?menu=901, Center for Protein Engineering, Cambridge, United Kingdom). The following criteria were used for D_H gene determination: a minimal homology of 6 matches in a row or 7 matches interrupted by 1 mismatch. The CDR3 length was calculated according to previously described criteria.⁶ 

Descriptive statistics (percentages, medians, and ranges) were used to describe VDJ gene utilization profiles. The χ² test was used to compare 2 categoric variables, and for 2 × 2 tables we used the Fisher exact test.³⁷  The Wilcoxon rank-sum and the Kruskal-Wallis tests were used to compare a continuous variable with a categoric variable with 2 or more categories, respectively.³⁸  The exact binomial distribution was used to assess differences between a specific observed percentage and an expected percentage. The Kaplan-Meier method and the log-rank test were used to estimate and compare time to relapse according to productivity of the rearrangements.^39,40  All tests were 2-sided except the exact binomial, which was 1-sided.

A total of 381 IgH sequences were identified at presentation from 317 children with B-lineage ALL enrolled in DFCI ALL Consortium protocol 95-01. A high identity (more than 98%) to the human germ line gene segments was found in 375 (98.4%) of the 381 sequences. We identified only 6 sequences (1.5%) with identity in a range of 86% to 96%. Of note, 4 of these cases used V3-11, raising the possibility of polymorphisms at this locus.

The frequency of the usage of the specific V_H segments is shown by their position on chromosome 14 in a telomeric-to-centromeric direction in Figure 1.

When this region was divided into 4 clusters each of approximately 200 kilobase (kb), we observed a privileged use of the D_HJ_H-proximal V_H segments in cluster D, with 47% versus expected 25% use (P < .001 using the binomial test). Fifty-two germ line V_H segments were used by the 381 IgH sequences. V_H6-1 (35, 9.19%), V_H3-13 (32, 8.4%), and V_H4-34 (22, 5.77%) were the 3 most overused V_H segments in pediatric B-ALL. Of the 52 V_H segments used, 9 were pseudogenes used by 24 sequences. In the D_HJ_H-proximal V_H segments, V_H6-1 segment was used in 35 of the 177 sequences, followed by V_H3-13 (n = 32), V_H3-11 (n = 19), V_H1-2 (n = 18), V_H2-5 (n = 16), V_H1-3 (n = 12), V_H3-9 (n = 12), and V_H3-15 (n = 10) segment. The rest of these V_H segments (V_H1-14, V_H5-a, V_H2-10, V_H1-8, V_H2-5, V_H3-7, and V_H4-4) in this region were used by fewer than 10 sequences.

Of the 381 IgH sequences, V_H3 family gene segments were identified in 192 clones (50%), followed by V_H1 (62, 16%), V_H4 (60, 16%), V_H6 (35, 9%), V_H2 (22, 6%), and V_H5 (10, 3%). V_H3 is the largest family in children with B-lineage ALL, with its usage occurring at frequency commensurate with its germ line family size.¹⁰  We observed a privileged usage of V_H6 (9%) in children with B-lineage ALL compared with peripheral B lymphocytes (PBLs) (0.8%, P = .006 using the χ² test). Although murine data suggest that this gene segment is overused also in normal B cells in early life,³⁰  there are no published human studies to assess whether V_H6 use in ALL is different from what would be seen in fetal and childhood B cells.

Of the 381 IgH sequences, D_H segments could be identified in 304 sequences. For 77 (20%) of the 381 sequences insufficient D segment sequence was available for definitive identification of the D_H gene segment used, either because of aberrant VDJ recombinations or from exonuclease activity. A single D_H gene was identified in 301 sequences, and the unusual D_H-D_H joining sequences were found in only 3 sequences. For these 3 sequences using more than one D_H gene, the J_H-proximal D_H segment was considered for gene usage analysis to assess DJ recombination. The D_H2 gene family was used most frequently at 35% (105), followed by D_H3 (32%, 97), D_H6 (12%, 37), D_H1 (8%, 23), D_H5 (5%, 15), D_H7 (4%, 12), and D_H4 (4%, 12), respectively. The D_H2 and D_H7 genes were overrepresented whereas D_H4 and D_H5 gene segments were underrepresented in B-lineage ALL CDR3 regions compared with usage in PBLs¹² (P < .001 using χ² test) as shown in Figure 2.

Similar to the V_H gene families, assignment to D_H gene families is based upon sequence homology and not their chromosomal loci. The telomeric-to-centromeric position of these genes is shown in Figure 3 with the percentage of utilization of each gene. Four clusters were assigned, each of approximately 15 kb. A privileged usage of J_H-distal D_H segments was observed in cluster A (37%) and in cluster B (37%) versus expected 25% (P < .001 using the exact binomial test). Of 27 human germ line D_H gene segments, 26 were used by the B-ALL IgH sequences including 2 pseudogenes (D_H1-14 and D_H6-25). None of the sequences used D_H4-4 segment. Seven D_H segments (D_H2-2, D_H3-3, D_H2-8, D_H3-9, D_H3-10, D_H2-15, and D_H3-22) were overrepresented in comparison to individual family size as shown in Figure 3 (P < .001 using the exact binomial distribution).

Usage of the J_H4 gene family was 39% (148), followed by J_H6 (34%, 131), J_H5 (20%, 78), J_H2 (3%, 11), J_H3 (2%, 7), and J_H1 (2%, 6), respectively. The J_H gene usage in children with B-lineage ALL is significantly different from the J_H usage found in normal PBLs¹² where J_H4 is the most prominent J_H gene, used in 52.5%, versus J_H6, in 22.2% (P < .001 using the χ² test; Figure 4).

The CDR3 length was calculated in size of base pairs (bp) for 381 sequences showing a median of 30.0 bp. Excessively long CDR3 length (more than 100 bp) was found in 4 sequences, and by basic local alignment sequence tool (BLAST) search aberrant VDJ recombination was identified, including incorporation of D_H intron sequences in one case. For patients with multiple IgH sequences, the average of the CDR3 lengths was considered. We observed a significant association between CDR3 length and the V_H or D_H family utilization but not by their J_H genes (Table 1). A short CDR3 was correlated with utilization of V_H6 and D_H7-27 segments (P < .01 using the Kruskal-Wallis test).

A single IgH sequence was identified in 256 cases from diagnostic tumor samples, whereas 2 sequences were found in 58 cases and 3 sequences were found in 3 children. However, the technical approach we use identifies only major clonal rearrangements and does not detect small subclones. In this study we observed no correlation between biclonality or oligoclonality and clinical features except chromosome 9 deletions and in particular noted no association with relapse (Table 2).

In 52 (85%) of the 61 patients with more than one sequence at presentation, the IgH sequences were unrelated. Only 9 cases of the samples identified at presentation involved ongoing IgH rearrangement mechanisms, phenomena described previously to account for clonal evolution.^41-44  Sequence analyses demonstrated 2 cases showing V_H-V_H replacement (cases 99 and 177), 6 cases showing V_H to D_HJ_H joining (cases 190, 246, 266, 269, 392, and 400), and 1 case showing an “open-and-shut” mechanism (Table 3).Although any of these sequences identified at presentation could be used for MRD detection, no relapses have occurred in any of these 9 children.

Among the 381 sequences, 302 (79%) were joined in a potentially nonproductive rearrangement, including out-of-frame joinings or in-frame joinings containing a stop codon. Only 21% of the IgH rearrangements could potentially result in production of heavy chain protein, and these cases demonstrated an association with privileged usage of V_H segments with 36% of these sequences utilizing V_H4 (Table 4).

In-frame rearrangements only were detected in 59 patients, out-of-frame rearrangements only in 239, and in 19 patients both in-frame and out-of-frame rearrangements were detected in the same patient (Table 5). We noted an association between the presence of more than one sequence and whether the rearrangements were in frame or out of frame (Table 5).

Only 3% of patients with only in-frame rearrangements had more than one sequence detested, compared with 17% of the cases with only out-of-frame rearrangements (P = .006 by the Fisher exact test). A trend toward a higher probability of risk of relapse was observed in patients with only productive rearrangements (P = .08 by the log-rank test), compared with children in whom at least one nonproductive rearrangement was identified at presentation (Figure 5).

We assessed the V_HD_HJ_H gene usage profiles at presentation from 381 IgH sequences identified from 317 cases of B-lineage childhood ALL. This is the largest reported series of IgH sequences in childhood ALL and incorporates knowledge from the now complete map of the human IgH locus.

When V_H gene usage is analyzed by position on the chromosome rather than simply by V_H gene family, we observed a preferential usage of the D_HJ_H-proximal V_H segments including not only V_H6-1 segment, the closest segment to the D_HJ_H locus, but also other V_H family segments near the D_HJ_H locus, including V_H1-2, V_H1-3, V_H2-5, V_H3-7, V_H3-9, V_H3-11, V_H3-13, and V_H3-15 segments. The finding of position-dependent V_H gene utilization supports the hypothesis that chromosomal order might in part regulate the V_H sequences rearrangement.⁴⁵  V_H3 represents the largest gene family and was the most utilized family in children with B-lineage ALL, in keeping with the size of this V_H family in the germ line.^9,10  We observed a privileged usage of the V_H6 segment, previously identified as a component of the quite restricted human fetal antibody repertoire.^16,20  A privileged usage of V_H6 has also been reported in immature B cells.³⁰  Our observation is in line with previous reports from precursor B-ALL suggesting that ALL transformation arises at the early stage of B-cell development.^30,32,34 

The D_H2 and D_H7 segments were overrepresented and D_H4 and D_H5 segments underrepresented in childhood B-ALL compared with PBLs.¹¹  A privileged usage of D_H7 segments has been observed in both murine and human fetal cells (liver, spleen, and marrow B cells).^16,19,46-48  However, in the present study we observed a lower frequency (4%) of utilization of D_H7 in cases of ALL compared with those reported for use in nonmalignant B cells in fetal tissues by Sanz⁶  (14%) and by others (50%).^16,48  We also observed that J_H-distal D_H segments were overrepresented. Therefore, it is unlikely that this can be explained by proximal locus regulation of the recombination machinery at the D_HJ_H joining stage. In murine immature B-cell lines, a secondary D_HJ_H rearrangement has been suggested by the finding that an initial D_HJ_H rearrangement can be deleted and replaced by a more 5′ D_H gene.⁴⁹  Recent studies have shown that the specific recombination signal sequences (RSSs) and coding ends may play a role in the preferential joining of specific D_H to J_H genes,^50-52  and the more closely an RSS resembles the consensus (CACAGTG-spacer-ACAAAAACC), the more often it is recombined in extrachromosomal substrates.⁵³  Therefore, molecular mechanisms rather than location appear to govern the selection of D_H gene segment during early B-cell development.

A characteristic J_H gene usage pattern (J_H4 > J_H6 > J_H5 > > J_H3/2/1) has been reported for fetal, neonatal, childhood, and adult peripheral B-lymphocyte CDR3 regions.^12,46,54  The usage of the J_H genes in this study is in line with this order. It is likely that molecular mechanisms also govern the J_H gene usage, with J_H4 RSS more closely reassembling the consensus sequences followed by the RSSs of J_H6, J_H5, J_H3, J_H2, and J_H1.^12,54 

In normal B cells, previous studies have demonstrated shorter CDR3 in preterm infants than in term infants and adults.⁵⁵  In immature B cells, a recent study demonstrated that lack of expression of TdT was associated with the absence of shorter N sequences, which contributed to shorter CDR3 regions, especially at D_HJ_H joining.⁵⁶  TdT interacts with the DNA-dependent protein kinase (DNA-PK), particularly with the Ku proteins, suggesting that TdT expression may modulate gene segment recombination at the ligation step.⁵⁷  Most cases of ALL presenting within the first 3 years of age have been suggested to arise from in utero transformation events by the finding of a high frequency (87.5%) of absence of N sequences at D_HJ_H joining, similar to that found in human fetal life.^31,33  This high frequency of absence of N sequences at D_HJ_H joining was not observed in our study (data not shown). However, we observed that a short CDR3 was correlated with utilization of V_H6 and D_H7-27. This observation might be explained by developmental regulation of the recombination machinery with favored selection of J_H-proximal V_H and D_H gene segments and by influence of TdT expression at an earlier stage of B-cell development.^17,57 

The overall incidence of cases with more than one IgH sequence in the present study was 19%. Although this is lower than in some reported studies (30% to 60%) using PCR fingerprinting or cloning strategies that may be better suited to find a minor subclone(s),^44,58,59  our findings are in keeping with previous studies using Southern blot analysis.^60-62  Some studies have shown an association between oligoclonality at presentation and poor prognosis in ALL patients.^63,64  We did not observe an association between biclonality or oligoclonality and relapse or with any other clinical characteristic except for the presence of chromosome 9p deletion. The correlation between chromosome 9p deletion and more than one IgH sequence might be partly explained by the recent finding that illegitimate VDJ recombinations involved in chromosome 9p21 deletion in lymphoid leukemia are targeted at RSS-like sequences widely distributed in 9p21.⁶⁵  Detailed sequence analysis showed that among the cases with more than one sequence, most sequences were unrelated with ongoing rearrangements found in only 15% of cases.

Similar to the findings previously reported for immature B cells,⁶⁶  and in keeping with a previous study in ALL,³³  only 21% of V_H-J_H rearrangements detected were potentially productive. Unlike normal B cells, this does not lead to loss of leukemic clone, demonstrating that ALL does not require signals mediated by Ig signaling for survival. Of note, a trend toward a higher probability of risk of relapse was found in patients with only productive rearrangements compared with children in whom at least one nonproductive rearrangement was identified at presentation. The reason potentially productive rearrangement would be relevant to clinical outcome is unclear. We did note an association between detection of more than one sequence and functional IgH rearrangement. Whether this relates to the stage of differentiation of the B cell at which malignant transformation occurs, or to lack of allelic exclusion by nonfunctional VDJ recombination, is currently unknown. In productive rearrangements we observed a privileged usage of V_H4 segments. Of note, V_H4-34 was found to be the third most overused V_H segment (22 of 381, 5.8%) and the most frequently overrepresented V_H4 family segment (22 of 60, 36.7%). The V_H4-34 gene segment is located 500 kb upstream of the D gene locus and is markedly overrepresented in the normal B-cell repertoire.⁶⁷  A biased usage of the V_H4-34 segment in rearranged V_H4 family genes has been reported in immature B cells.¹⁷  Increased usage of this gene segment also occurred in pathologic states including autoimmune disease and B-cell malignancies associated with autoimmune phenomena.^68,69  The relevance of these findings to ALL is not clear, because ALL is not thought to be an antigen-driven process, although it is possible that this may be important in the subset of cases with potentially productive Ig gene rearrangements.

In summary, this study describes the V_HD_HJ_H gene utilization profile from 317 children with B-lineage ALL. A biased usage of V_H6, and a shift from J_H4 to J_H6, was observed, similar to the patterns of immature B cells, in keeping with the widely held views that leukemic transformation occurs at the early stage of B-cell differentiation. The preferential usage of D_HJ_H-proximal V_H gene segments suggests that V to DJ recombination is somewhat dependent on physical location at the V_H locus. However, D_H and J_H segment utilization is position independent and more likely governed by molecular mechanisms. Moreover, patients with only productive rearrangement demonstrated a trend toward an increased risk of relapse, suggesting that molecular pathophysiology might be relevant to clinical outcome.

The members of the DFCI/ALL consortium are: Dana-Farber Cancer Institute, Children's Hospital, Boston, MA; St Justine Children's Hospital, Montreal, QC, Canada; San Jorge Children's Hospital, San Truce, Puerto Rico; University of Rochester Medical Center, Rochester, NY; Mount Sinai Medical Center, New York, NY; McMaster University Medical Center, Hamilton, ON, Canada; Maine Children's Cancer Program, Scarborough, ME; Centre Hospitalier de l'Universite Laval du CHUQ, Ste Foy, QC, Canada; and Tulane University, New Orleans, LA

We thank Peter Varney for help in the preparation of the manuscript and all members of the DFCI ALL Consortium for providing samples for this study.