The Journal of Immunology Ig Gene Rearrangement Steps Are Initiated in Early Human Precursor B Cell Subsets and Correlate with Specific Transcription Factor Expression1 Menno C. van Zelm,*† Mirjam van der Burg,* Dick de Ridder,*‡ Barbara H. Barendregt,*† Edwin F. E. de Haas,* Marcel J. T. Reinders,‡ Arjan C. Lankester,§ Tom Re´ve´sz,¶ Frank J. T. Staal,* and Jacques J. M. van Dongen2* The role of specific transcription factors in the initiation and regulation of Ig gene rearrangements has been studied extensively in mouse models, but data on normal human precursor B cell differentiation are limited. We purified five human precursor B cell subsets, and assessed and quantified their IGH, IGK, and IGL gene rearrangement patterns and gene expression profiles. Pro-B cells already massively initiate DH-JH rearrangements, which are completed with VH-DJH rearrangements in pre-B-I cells. Large cycling pre-B-II cells are selected for in-frame IGH gene rearrangements. The first IGK/IGL gene rearrangements were initiated in pre-B-I cells, but their frequency increased enormously in small pre-B-II cells, and in-frame selection was found in immature B cells. Transcripts of the RAG1 and RAG2 genes and earlier defined transcription factors, such as E2A, early B cell factor, E2-2, PAX5, and IRF4, were specifically up-regulated at stages undergoing Ig gene rearrangements. Based on the combined Ig gene rearrangement status and gene expression profiles of consecutive precursor B cell subsets, we identified 16 candidate genes involved in initiation and/or regulation of Ig gene rearrangements. These analyses provide new insights into early human pre- cursor B cell differentiation steps and represent an excellent template for studies on oncogenic transformation in precursor B acute lymphoblastic leukemia and B cell differentiation blocks in primary Ab deficiencies. The Journal of Immunology, 2005, 175: 5912–5922. recursor B cells develop from hemopoietic stem cells and group proteins HMGB1 and HMGB2 stimulate the RAG proteins differentiate through a number of stages in the bone mar- in DNA binding and the generation of the dsDNA breaks (4), P row (BM)3 before they migrate to the periphery as naive which are subsequently repaired via nonhomologous end joining mature B lymphocytes. The ultimate purpose of B cell differenti- (NHEJ) (5). In the next stage (pre-B-I), a VH segment is rearranged ation is to produce the broad repertoire of B cell Ag receptors, to the DJH element, and if an in-frame VDJH exon is formed, a which are composed of two identical Ig heavy chains and two pre-BCR is expressed, which is composed of IgH chains and sur- identical Ig light chains (reviewed in Ref. 1). Early in differenti- rogate light chains (VpreB and ␭14.1). The expression of this re- ation, V(D)J recombination is initiated in the Ig H chain (IGH) ceptor initiates several cycles of proliferation (large cycling pre- locus with DH to JH rearrangements in pro-B cells. The lympho- B-II cell stage). After this proliferation phase, Ig L chain cyte-specific RAG1 and RAG2 proteins introduce a single- rearrangements are initiated in the small pre-B-II cells. If a func- stranded nick between the recombination signal sequence (RSS) tional Ig L chain (Ig␬ or Ig␭) is expressed that is able to assemble and the flanking D or J gene segment, which results in the gener- with the Ig H chain, the cell becomes a surface membrane Igϩ ation of a dsDNA break (2, 3). The DNA-bending high mobility (SmIgϩ) immature B cell. If this cell is nonautoreactive, it mi- grates to the periphery as a naive mature B cell. *Department of Immunology and †Department of Pediatrics, Erasmus MC, Rotter- The differential expression of marker molecules is used to define dam, The Netherlands; ‡Information and Communication Theory Group, Faculty of the main stages of B cell differentiation. Five main human precur- Electrical Engineering, Mathematics and Computer Science, Delft University of § sor B cell differentiation stages can be recognized using the fol- Technology, Delft, The Netherlands; Department of Pediatrics, Leiden University ϩ Ϫ ϩ Medical Center, Leiden, The Netherlands; and ¶Hematology-Oncology Unit, Wil- lowing markers: 1) CD22 CD19 pro-B cells; 2) CD19 cyto- helmina Children’s Hospital, University Medical Center, Utrecht, The Netherlands plasmic Ig (CyIg)␮Ϫ pre-B-I cells; 3) CyIg␮ϩVpreBϩ pre-B-II Received for publication March 24, 2005. Accepted for publication August 1, 2005. large cells; 4) CyIg␮ϩVpreBϪ pre-B-II small cells; 5) SmIgMϩ The costs of publication of this article were defrayed in part by the payment of page immature B cells. Naive mature B lymphocytes in the periphery charges. This article must therefore be hereby marked advertisement in accordance ϩ ϩ with 18 U.S.C. Section 1734 solely to indicate this fact. are SmIgM SmIgD (6, 7). Although there is a common V(D)J recombinase machinery, Ig 1 This work was supported by Grant 349 from the foundation “Sophia Kinderziek- enhuis Fonds” (to M.C.v.Z. and J.J.M.v.D.) and Veni Grant 916.56.107 from ZonMw gene rearrangements are separated in time and restricted to one (M.v.d.B.). locus. Transcription factors PAX5, early B cell factor (EBF), and 2 Address correspondence and reprint requests to Dr. Jacques J. M. van Dongen, the E box proteins E2A, HEB, and E2-2 appear to act in a hier- Molecular Immunology Unit, Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 50, NL-3015 GE Rotterdam, the archical order for commitment to B cell fate and the initiation of Ig Netherlands. E-mail address: [email protected] gene rearrangements by opening Ig loci (8–12), and by inducing 3 Abbreviations used in this paper: BM, bone marrow; HMG, high mobility group; expression of recombination-related proteins (RAG1, RAG2, TdT) CyIg, cytoplasmic Ig; Kde, ␬-deleting element; LIG4, DNA ligase IV; NHEJ, non- (13) and (pre-) BCR proteins (VpreB, ␭14.1, CD79A) (14–16). homologous end joining; RQ-PCR, real-time quantitative PCR; RSS, recombination signal sequence; SmIg, surface membrane Ig; UCB, umbilical cord blood; GO, Gene The Ets transcription factor PU.1 is required for generation of lym- Ontology; KLF, Kru¨ppel-like family; EBF, early B cell factor. phoid as well as myeloid cells (17, 18), and is suggested to be the Copyright © 2005 by The American Association of Immunologists, Inc. 0022-1767/05/$02.00 The Journal of Immunology 5913 partner of IRF4 and IRF8 in large pre-B cells, where they inhibit RQ-PCR and GeneScan analysis of Ig gene rearrangements proliferation and initiate Ig L chain rearrangements (19, 20), In A multiplex TaqMan-based RQ-PCR was used to quantify IGH, IGK, and addition, histone-remodeling factors, EZH2 and BRG1, and DNA IGL gene rearrangements. Family-specific V and D segment forward prim- demethylases are likely to be involved in the induction of Ig gene ers, J segment-specific reverse primers, and J segment-specific probes were rearrangements (21–23). newly designed or adapted in such a way that Ͼ95% of all rearrangements could be detected (26–31). The RQ-PCR mixture of 25 ␮l contained Taq- The majority of our understanding of the initiation and regula- Man Universal MasterMix (Applied Biosystems), 900 nM concentrations tion of Ig gene rearrangements in precursor B cell differentiation of each primer (300 nM in case of multiplex mixtures), 100 nM concen- comes from studies in mouse models, and genome-wide gene ex- trations of each FAM-TAMRA-labeled probe, 50 ng of DNA, and 0.4 ng pression profiling has been performed exclusively in murine pre- of BSA, and was run on the ABIPRISM 7700 sequence detection system (Applied Biosystems) (32, 33). cursor B cells (24, 25). However, these studies did not show how An albumin RQ-PCR was used for quantification of the DNA input (34). V(D)J recombination is strictly regulated per locus in each specific For quantification of the Ig gene rearrangement, a standard curve was made stage of differentiation. on a 10-fold dilution series of DNA from one or more cell lines harboring Therefore, we aimed at purifying cells in the five main stages of monoallelic Ig gene rearrangements, diluted in a background of germline (unrearranged) DNA (total input, 50 ng). Each assay reproducibly reached human precursor B cell differentiation, thus creating the opportu- a sensitivity of at least 1% rearrangement in germline background and was nity to study the initiation of IGH and IGK/IGL rearrangements performed in duplicate on each DNA sample. The rearrangements were independently from each other and independently from the selec- quantified relative to the monoallelically rearranged control cell lines, tion processes. The precursor B cell subsets were purified with which were set at 100%. Consequently, it is possible to measure a level of 200% rearrangements in a cell population with all cells having biallelic membrane markers only, to allow both DNA extraction for anal- rearrangements. ysis of the Ig gene rearrangements using real-time quantitative To analyze the in-frame selection of Ig gene rearrangements in precursor PCR (RQ-PCR) and GeneScan assays, and RNA extraction for B cell subsets, complete IGH, IGK, and IGL rearrangements were ampli- genome-wide gene expression profiling using Affymetrix Gene- fied and subjected to GeneScan analysis with modified V segment forward primers, positioned in such a way that in-frame rearrangements result in Chip arrays. This approach enabled us for the first time to study the triplet spacing of the GeneScan peaks (primer sequences available on re- networks of factors that might be involved in the initiation and quest) (30).