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* Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110; and
Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Childrens Hospital of Philadelphia, University of Pennsylvania School of Medicine and
Abramson Family Cancer Research Institute, Philadelphia, PA 19104
| Abstract |
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| Introduction |
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Signal ends and coding ends can also be joined aberrantly in ways that cannot lead to the formation of a functional Ag receptor gene. In this regard, the originally appended coding end and signal end can be rejoined, generating an open-and-shut joint, or a coding end can be joined to the signal end generated by cleavage at the other gene segment, generating a hybrid joint (6, 7). Although hybrid joints can form through classical NHEJ, these joints can also be formed in ways that bypass the requirement for classical NHEJ factors (8, 9, 10, 11, 12). For example, the truncated "core" Rags can catalyze hybrid joint formation through a transposition-like reaction (11, 12, 13). However, full-length Rag proteins do not efficiently catalyze hybrid joint formation in vivo, suggesting that the non-core regions of the Rag proteins inhibit this transposition activity (11). Whether the non-core regions have intrinsic activities that inhibit transposition or whether they serve as targets for trans-acting factors that promote this inhibitory function is not known. Moreover, hybrid joint formation could also be catalyzed through alternative end-joining pathways of DNA DSB repair (14, 15, 16, 17, 18). Importantly, in wild-type developing lymphocytes, the formation of these nonfunctional hybrid joints, through either NHEJ-dependent or NHEJ-independent pathways, occurs at very low levels.
Deficiency in the ataxia telangiectasia mutated (Atm) serine threonine kinase leads to lymphopenia and lymphoid malignancies with chromosomal translocations involving Ag receptor genes (19, 20). This is due, in part, to the function of Atm in the repair of Rag-mediated DSBs (21, 22, 23, 24). In this regard, we have previously shown that, in Atm-deficient lymphocytes undergoing V(D)J recombination, there is an accumulation of unrepaired coding ends that are frequently resolved aberrantly as chromosomal translocations or large chromosomal deletions or inversions (22). In addition, there is a marked increase in hybrid joint formation during inversional rearrangements (22). We have proposed that the accumulation of unrepaired coding ends and the increase in hybrid joint formation could both be explained by a requirement for Atm to stabilize DNA DSB complexes generated after Rag-mediated DNA cleavage (22). These defects, however, could also reflect distinct requirements for Atm in promoting the NHEJ-dependent joining of coding ends and in prohibiting hybrid joint formation by NHEJ-independent pathways, such as Rag-mediated transposition. To distinguish between these possibilities, in this study, we determine whether hybrid joints generated in Atm-deficient cells form through NHEJ-dependent or NHEJ-independent joining pathways.
| Materials and Methods |
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All mice were bred and maintained under specific pathogen-free conditions at the Washington University School of Medicine and were handled in accordance to the guidelines set forth by the Division of Comparative Medicine of Washington University.
Cell lines and culture conditions
Artemis–/–, Artemis–/–:Atm–/–, and Ku70–/– v-abl-transformed pre-B cells were generated by culturing bone marrow of 3- to 5-wk-old mice with the pMSCV v-abl retrovirus, as described previously (22). Cells were generated from at least two mice of each genotype, which all expressed an Eµ-Bcl-2 transgene. These cells (106/ml) were transduced with the pMX-INV retrovirus by centrifugation at 1800 rpm for 90 min. Cells containing pMX-INV were isolated by fluorescence activated cell sorting based on expression of the human CD4 (hCD4). hCD4 expression was detected using PE-conjugated anti-hCD4 (BD Pharmingen). The wild type, Atm–/– and scid abl pre-B cell lines containing pMX-INV have been described previously (22). Cells were treated with 3 µM STI571 (Novartis) for the indicated times at 106 cells/ml. KU-55933 (Sigma-Aldrich) was used at 15 µM.
Southern blot and PCR analyses
Genomic DNA was isolated and Southern blot analyses were conducted using the indicated restriction enzymes and the C4 probe as previously described (22). PCR analyses for hybrid joint formation during pMX-INV rearrangement in abl pre-B cells, and during Vβ14 and V
5 rearrangement in thymocytes, were performed as previously described (22). IL2 gene PCR was conducted as a DNA loading control as previously described (22).
| Results |
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We have recently established an experimental approach whereby chromosomal V(D)J recombination can be analyzed in murine v-abl transformed pre-B cells, hereafter referred to as abl pre-B cells (22). Rag gene expression and G1 cell cycle arrest can be induced in these cells upon inhibition of v-abl kinase activity with STI571 (22, 25). This leads to robust rearrangement of the endogenous IgL
locus and introduced retroviral recombination substrates, such as pMX-INV (Fig. 1) (22). pMX-INV has a pair of RSs that are oriented such that normal rearrangement occurs by inversion, generating a signal joint and coding joint that remain in the chromosome (Fig. 1a). pMX-INV also has an IRES-human CD4 cDNA cassette that permits the flow cytometric purification of cells containing chromosomal pMX-INV integrants (22).
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Atm could prevent hybrid joint formation through either NHEJ-dependent or NHEJ-independent pathways. To determine whether NHEJ-independent pathways can mediate hybrid joining in abl pre-B cells, we generated abl pre-B cells deficient in both core (Ku70) and noncore (Artemis and DNA-PKcs) NHEJ proteins and transduced these cells with pMX-INV. The induction of Rag in Ku70–/–, Artemis–/–, and Scid abl pre-B cells led to DNA cleavage at pMX-INV and a marked accumulation of unrepaired coding ends, but low levels of coding joint formation, as would be expected given the NHEJ deficiencies (Figs. 2a, 3a, and 4a). Although pMX-INV hybrid joints also formed in Ku70–/–, Artemis–/–, and Scid abl pre-B cells, the level of hybrid joint formation was approximately 20-fold lower than that observed in Atm-deficient cells (Fig. 2). Thus, NHEJ-independent pathways do mediate hybrid joint formation, although at very low levels, in NHEJ-deficient abl pre-B cells.
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The low level of hybrid joint formation in NHEJ-deficient cells could be due to the suppression of NHEJ-independent pathways by Atm. In this regard, we reasoned that if Atm prevents hybrid joint formation primarily by modulating the function of NHEJ-independent pathways, then abl pre-B cells deficient in both Atm and the NHEJ protein Artemis (Artemis–/–:Atm–/–) should form hybrid joints at a level similar to that observed in Atm–/– cells. However, in striking contrast to Atm–/– cells, pMX-INV hybrid joints form at a very low level in Artemis–/–:Atm–/– abl pre-B cells (Fig. 3). Thus, the efficient formation of hybrid joints in Atm-deficient abl pre-B cells is dependent on the NHEJ protein Artemis.
To confirm that Artemis is also required for hybrid joint formation in developing Atm-deficient lymphocytes in vivo, we assayed rearrangements at the TCR β and
loci in developing thymocytes. To this end, CD4–/CD8–/CD25+ (CD25+ DN) thymocytes were purified by flow cytometric cell sorting from wild-type, Atm–/–, Artemis–/–, and Artemis–/–:Atm–/– mice. In wild-type CD25+ DN thymocytes, we find low levels of hybrid joint formation involving the Vβ14 and V
5 gene segments, which both rearrange by inversion (Fig. 5). In contrast, hybrid joints involving these V gene segments are readily detected in Atm–/– CD25+ DN thymocytes, reaching levels that are 20-fold higher than those observed in wild-type CD25+ DN thymocytes (Fig. 5). Importantly, these hybrid joints were not detected in Artemis–/–:Atm–/– CD25+ DN thymocytes (Fig. 5). Thus, as was observed in Atm–/– abl pre-B cells, the robust hybrid joint formation observed in developing Atm–/– lymphocytes is also dependent on Artemis.
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We wished to determine whether hybrid joint formation in Atm-deficient abl pre-B cells was dependent on NHEJ factors in addition to Artemis. Mice with combined deficiency in Atm and DNA-PKcs or Ku70 exhibit early embryonic lethality, precluding the generation of abl pre-B cells with combined deficiencies in Atm and either DNA-PKcs or Ku70 (26). Thus, an alternate approach was needed to determine whether DNA-PKcs and Ku70 are required for hybrid joint formation in cells deficient in Atm activity. In this regard, treatment of wild-type abl pre-B cells with the Atm kinase inhibitor, KU-55933, resulted in an increase in pMX-INV hybrid joint formation and an accumulation of unrepaired coding ends, demonstrating that inhibition of Atm kinase activity recapitulates the Atm–/– phenotype. (Fig. 4) (22). Induction of Rag expression in Scid or Ku70–/– abl pre-B cells leads to an accumulation of unrepaired coding ends and a low level of coding and hybrid joint formation (Figs. 2 and 4). Notably, treatment of Scid or Ku70–/– abl pre-B cells with KU-55933 leads to a slight increase in unrepaired coding ends, possibly due to the blunting of Atm-dependent pathways that mediate cell death in response to unrepaired DNA DSBs (Fig. 4a). However, treatment of Scid or Ku70–/– abl pre-B cells with KU-55933 did not lead to the increase in hybrid joint formation that was observed in wild-type abl pre-B cells (Fig. 4). Thus, formation of hybrid joints in abl pre-B cells deficient in Atm kinase activity is dependent on the DNA-PKcs and Ku70 NHEJ factors.
| Discussion |
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Furthermore, hybrid joints formed by Rag-mediated transposition usually exhibit minimal joint diversity consisting of the addition of, at most, two P-nucleotides (8, 29, 30). However, sequence analysis of hybrid joints generated in Atm-deficient cells reveals the full spectrum of joint diversity including nucleotide loss and N- and P-nucleotide addition (22). It is conceivable that NHEJ-independent hybrid joint formation could also occur through an alternative end-joining pathway (14, 15, 16, 17, 18). However, when active, this pathway can mediate the efficient repair of Rag-mediated DSBs in DNA-PKcs-deficient cells, yet we find that most hybrid joints that form in Atm-deficient cells are dependent on DNA-PKcs. Together, our data clearly demonstrate that the majority of hybrid joints that form during V(D)J recombination in Atm-deficient lymphocytes require NHEJ activity. Thus, Atm functions to modulate the NHEJ repair of Rag-mediated DSBs in a way that significantly limits the formation of hybrid joints during rearrangements that occur by inversion.
During the repair of genotoxic DSBs, NHEJ generally rejoins the two DNA ends generated at a single DSB. However, during V(D)J recombination, NHEJ must join DNA ends that are generated at two distinct DSBs. In this regard, the coding ends from two distinct DSBs are joined to generate a coding joint, and the signal ends from these two breaks are joined to generate a signal joint. Atm could function in a way that directs the correct joining of DNA ends generated by Rag during lymphocyte Ag receptor gene assembly. However, the increased hybrid joint formation in Atm-deficient cells is only observed during rearrangements that occur by inversion, not during those that occur by deletion (22). Thus, if Atm directs the appropriate joining of DNA ends during V(D)J recombination, the requirement for this function is restricted to rearrangements that occur by inversion.
Rather than invoke distinct Atm-regulated pathways that prevent the accumulation of unrepaired coding ends and the formation of hybrid joints exclusively during inversional rearrangements, we have proposed that both of these defects are due to a requirement for Atm to promote stability of DNA end complexes generated after Rag-mediated cleavage (22). Cleavage by the Rag proteins generates two DNA DSBs that divide the chromosome into three non-continuous segments: the centromeric chromosomal end, the telomeric chromosomal end and an intervening chromosomal segment. Signal ends flank the intervening chromosomal segment when the rearrangement occurs by deletion, whereas this segment is flanked by a coding end and a signal end when the rearrangement occurs by inversion. Loss of the intervening chromosomal segment during inversional rearrangements would leave chromosomal coding and signal ends that, upon joining, would form a hybrid joint. In contrast, during rearrangements by deletion, loss of the signal end flanked intervening chromosomal segment would leave chromosomal coding ends that, upon joining, would form a coding joint.
In addition, defects in the stability of postcleavage complexes in Atm-deficient cells would also lead to the loss of chromosomal coding ends. These coding ends could persist unrepaired or be resolved aberrantly as chromosomal translocations and large chromosomal deletions and inversions. Thus, a requirement for Atm to stabilize DSB complexes in a way that facilitates their repair through the NHEJ pathway could explain both the accumulation of unrepaired coding ends and the increase in hybrid joint formation observed in Atm-deficient lymphocytes. This notion is supported by our current data demonstrating that hybrid joint formation in Atm-deficient cells is dependent on classical NHEJ. Atm could function directly to stabilize DNA DSB complexes after Rag-mediated DNA cleavage; however, it seems more likely that Atm promotes stability by activating downstream proteins that perform this function. In this regard, it is notable that inhibition of Atm kinase activity, with KU-55933, is sufficient to recapitulate the defects in V(D)J recombination observed in Atm–/– cells.
The inhibition of hybrid joint formation during inversional rearrangements has important implications for efficient Ag receptor gene assembly. In this regard, inversional rearrangements involving V gene segments occur in the TCRβ and TCR
loci. Moreover, in the IgL
locus, half of the V
to J
rearrangements occur by inversion. Hybrid joint formation during these rearrangements would result in large deletions of the TCR or IgL
loci that could severely limit, or even prevent, subsequent rearrangements that would generate functional Ag receptor genes. Thus, by inhibiting hybrid joint formation during inversional rearrangements, Atm functions to preserve the integrity of Ag receptor loci in a manner that optimizes the generation of functional Ag receptor genes.
| Disclosures |
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| Footnotes |
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1 This work was supported by the National Institutes of Health grants AI47829 and AI1074953 and American Cancer Society grant RSG-05–070-01-LIB (to B.P.S.). ![]()
2 Address correspondence and reprint requests to Dr. Barry P. Sleckman, Department of Pathology and Immunology, 660 S. Euclid Avenue, Campus Box 8118, Washington University School of Medicine, St. Louis, MO 63110. E-mail address: Sleckman{at}immunology.wustl.edu ![]()
3 Abbreviations used in this paper: DSB, double strand break, NHEJ, non-homologous end joining; RS, recombination signal; Atm, ataxia telangiectasia mutated; hCD4, human CD4. ![]()
Received for publication May 27, 2008. Accepted for publication June 12, 2008.
| References |
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locus coding end breaks. Proc. Natl. Acad. Sci. USA 104: 6323-6328.
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