A non-B DNA can replace heptamer of V(D)J recombination when present along with a nonamer: implications in chromosomal translocations and cancer

The RAG (recombination-activating gene) complex is responsible for the generation of antigen receptor diversity by acting as a sequence-specific nuclease. Recent studies have shown that it also acts as a structure-specific nuclease. However, little is known about the factors regulating this activity at the genomic level. We show in the present study that the proximity of a V(D)J nonamer to heteroduplex DNA significantly increases RAG cleavage and binding efficiencies at physiological concentrations of MgCl2. The position of the nonamer with respect to heteroduplex DNA was important, but not orientation. A spacer length of 18 bp between the nonamer and mismatch was optimal for RAG-mediated DNA cleavage. Mutations to the sequence of the nonamer and deletion of the nonamer-binding domain of RAG1 reinforced the role of the nonamer in the enhancement in RAG cleavage. Interestingly, partial mutation of the nonamer did not significantly reduce RAG cleavage on heteroduplex DNA, suggesting that even cryptic nonamers were sufficient to enhance RAG cleavage. More importantly, we show that the fragile region involved in chromosomal translocations associated with BCL2 (B-cell lymphoma 2) can be cleaved by RAGs following a nonamer-dependent mechanism. Hence our results from the present study suggest that a non-B DNA can replace the heptamer of RSS (recombination signal sequence) when present adjacent to nonamers, explaining the generation of certain chromosomal translocations in lymphoid malignancies.

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Role of the Bone Marrow Niche in Supporting the Pathogenesis of Lymphoid Malignancies

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.692320 ◽

2021 ◽

Vol 9 ◽

Author(s):

Shahrzad Jalali ◽

Stephen M. Ansell

Keyword(s):

Bone Marrow ◽

Cancer Cells ◽

Cell Lymphoma ◽

B Cell Lymphoma ◽

Bone Marrow Niche ◽

Hematopoietic Stem ◽

Lymphoid Malignancies ◽

Hematological Cancers ◽

Primary Location

While the bone marrow (BM) microenvironment is the primary location for nurturing the multipotent hematopoietic stem cells and developing the blood cells of either myeloid or lymphoid origin under normal physiological conditions, it could provide a supportive milieu for the proliferation of blood cancer cells. In fact, the multiple and complex direct cell-to-cell or indirect soluble factors-mediated interactions taking place among the BM cells of different origins are shown to play a significant role in tumorigenesis of hematological cancers. In the current review, we focus on lymphoid malignancies and highlight the novel insights surrounding the role of both cellular as well as non-cellular BM compartments in modulating hematopoiesis and promoting growth and proliferation of cancer cells across a variety of aggressive and indolent lymphoid malignancies, including diffuse large B-cell lymphoma, follicular lymphoma, mantle cell lymphoma, and Waldenstrom Macroglobulinemia. We also discuss the mechanisms of potential intervention and discuss their therapeutic impact in clinical settings.

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The phosphodiesterase PDE4B limits cAMP-associated PI3K/AKT–dependent apoptosis in diffuse large B-cell lymphoma

Blood ◽

10.1182/blood-2004-01-0240 ◽

2005 ◽

Vol 105 (1) ◽

pp. 308-316 ◽

Cited By ~ 90

Author(s):

Peter G. Smith ◽

Fengfei Wang ◽

Kathryn N. Wilkinson ◽

Kerry J. Savage ◽

Ulf Klein ◽

...

Keyword(s):

B Cell ◽

Cell Lymphoma ◽

B Cell Lymphoma ◽

Lymphoid Malignancies ◽

Large B Cell Lymphoma ◽

Constitutively Active Mutants ◽

B Lymphoid ◽

Induced Apoptosis ◽

Large B Cell

Abstract Diffuse large B-cell lymphoma (DLBCL) is a common and often fatal malignancy. Advances in the treatment of this disease will require the identification of novel therapeutic targets. We previously defined an expression signature of outcome in DLBCL and found that the phosphodiesterase PDE4B was overexpressed in fatal/refractory tumors. Phosphodiesterase 4B (PDE4B) inactivates the second messenger cyclic adenosine 3′,5′ monophosphate (cAMP) and abrogates its inhibitory effects in B lymphocytes. Hence, DLBCLs that express high PDE4B levels may be resistant to cAMP-induced apoptosis, contributing to their less favorable outcome. Herein, we confirmed the risk-related expression of PDE4B in an independent series of primary DLBCLs and defined the enzyme's role in modulating cAMP-induced apoptosis in parental DLBCL cell lines or those reconstituted with wild-type or mutant PDE4B. The cAMP-mediated apoptosis of DLBCLs was largely independent of the previously described cAMP effectors, protein kinase A (PKA) and exchange protein directly activated by cAMP (EPAC), but associated with inhibition of the phosphatidylinositol 3-kinase (PI3K)/AKT pathway. The central role of AKT in this process was confirmed by expressing constitutively active mutants of this kinase in DLBCL cells. Our findings highlight the important role of cAMP signaling in DLBCL and suggest that clinically relevant PDE4 and PI3K/AKT inhibitors might be useful in the treatment of DLBCL and additional B-lymphoid malignancies with increased PDE4B expression. (Blood. 2005;105:308-316)

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Chromosomal reinsertion of broken RSS ends during T cell development

Journal of Experimental Medicine ◽

10.1084/jem.20070583 ◽

2007 ◽

Vol 204 (10) ◽

pp. 2293-2303 ◽

Cited By ~ 27

Author(s):

John D. Curry ◽

Danae Schulz ◽

Cynthia J. Guidos ◽

Jayne S. Danska ◽

Lauryl Nutter ◽

...

Keyword(s):

Signal Sequence ◽

T Cell Development ◽

Chromosomal Translocations ◽

Wild Type ◽

Lymphoid Malignancies ◽

Bona Fide ◽

Cryptic Rss ◽

Chromosomal Loci

The V(D)J recombinase catalyzes DNA transposition and translocation both in vitro and in vivo. Because lymphoid malignancies contain chromosomal translocations involving antigen receptor and protooncogene loci, it is critical to understand the types of “mistakes” made by the recombinase. Using a newly devised assay, we characterized 48 unique TCRβ recombination signal sequence (RSS) end insertions in murine thymocyte and splenocyte genomic DNA samples. Nearly half of these events targeted “cryptic” RSS-like elements. In no instance did we detect target-site duplications, which is a hallmark of recombinase-mediated transposition in vitro. Rather, these insertions were most likely caused by either V(D)J recombination between a bona fide RSS and a cryptic RSS or the insertion of signal circles into chromosomal loci via a V(D)J recombination-like mechanism. Although wild-type, p53, p53 x scid, H2Ax, and ATM mutant thymocytes all showed similar levels of RSS end insertions, core-RAG2 mutant thymocytes showed a sevenfold greater frequency of such events. Thus, the noncore domain of RAG2 serves to limit the extent to which the integrity of the genome is threatened by mistargeting of V(D)J recombination.

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Pharmacogenetic Approaches Identify ANTXR1 As a Potential Mediator of Response to Therapeutic NF-κB Inhibition in Diffuse Large B Cell Lymphoma

Blood ◽

10.1182/blood.v118.21.234.234 ◽

2011 ◽

Vol 118 (21) ◽

pp. 234-234

Author(s):

Soham D. Puvvada ◽

Cassandra L Love ◽

Vladimir Grubor ◽

Jenny Zhang ◽

Jason Smith ◽

...

Keyword(s):

Gene Expression ◽

B Cell ◽

Gene Expression Profiling ◽

Exome Sequencing ◽

Cell Lines ◽

Expression Profiling ◽

B Cell Lymphoma ◽

Lymphoid Malignancies ◽

Whole Exome

Abstract Abstract 234 Background: NF-κB is a family of transcription factors known to play an essential role in the development & survival of lymphocytes. In recent years, it has been clear that aberrant NF-κB activation is a hallmark of various lymphoid malignancies and appears to be associated with chemotherapy resistance and adverse prognosis. The canonical NF-κB pathway is frequently engaged in lymphoid malignancies wherein activated IKK phosphorylates IκB proteins inducing IκB polyubiquination and subsequent proteasomal proteolytic degradation; this allows for release and nuclear translocation of NF-κB dimers to activate target gene transcription. Gene Expression Profiling (GEP) has identified two distinct sub groups of Diffuse Large B cell Lymphoma (DLBCL). While the Activated B cell (ABC) type shows constitutive activation of NF-κB, the role for NF-κB activation in Germinal Center B Cell (GCB) DLBCL is currently unclear. Since NF-κB inhibition has been identified as a therapeutic possibility in DLBCLs, it is important to define the role of this pathway and its modulators. In this study, we sought to investigate key regulators of the NF-κB pathway that might mediate a therapeutic response to IKKβ inhibition of NF-κB in DLBCL including the GCB subtype. Through GEP and Exome Sequencing, we demonstrate that ANTXR1 is a key mediator of response to IKKβ inhibition in DLBCL. Methods/Results: We obtained a novel selective inhibitor of IKKβ, TLX-2001 that has been found to be safe in animal models. IC50 were obtained on 61 cell lines representing various lymphomas including DLBCL (N=25) using cell viability MTT assays. The drug showed efficacy in both ABC and GCB DLBCL cell lines at physiologically achievable concentrations. These results were unsurprising in ABC DLBCLs which are known to depend on NF-κB activation, but the lethality of this selective drug in GCB DLBCLs was unexpected. To better understand the role of individual genes in the response in GCB DLBCLs, gene expression profiling was performed on 61 cell lines using Human Gene 1.0 ST Array. We found that ANTXR1 expression significantly correlated with NF-κB resistance (p = 0.035). Additionally, we sequenced the exomes of DLBCL tumors (N=95) and matched normal tissue (N=34). 95 cases of DLBCLs consisted of 73 cases of primary human DLBCLs and 22 DLBCL cell lines. Whole exome sequencing was performed using the Agilent solution-based system of exon capture to sequence all protein coding exons in the CCDS database. We identified 465 recurrently somatically mutated genes in these DLBCL cases, and found that mutation status of ANTXR1 was associated with high sensitivity to IKKβ inhibition (p =0.015) of NF-κB. Cell lines with non-synonymous mutations in ANTXR1 had over 3-fold lower IC50 (mean= 2.39 μM) compared to cell lines with no mutation in ANTXR1 (mean IC50 = 8.72μM). Discussion/Conclusion: ANTXR1 is the docking receptor for bacillus anthracis toxin, and anti-tumor responses have been observed in mice injected with recombinant engineered anthrax toxin. It is also known as TEM8 and maps to chromosome 2p13.1. Increased levels of TEM8 (tumor endothelial marker 8) have been noted in various malignancies including melanoma. Our data suggest that pharmacogenetic approaches that combine gene expression profiling and whole exome sequencing are useful tools for identifying novel genes that modulate therapeutic responses in lymphoma. Disclosures: No relevant conflicts of interest to declare.

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Enhancer control of local accessibility to V(D)J recombinase.

Molecular and Cellular Biology ◽

10.1128/mcb.17.8.4553 ◽

1997 ◽

Vol 17 (8) ◽

pp. 4553-4561 ◽

Cited By ~ 47

Author(s):

M T McMurry ◽

C Hernandez-Munain ◽

P Lauzurica ◽

M S Krangel

Keyword(s):

Signal Sequence ◽

Cell Receptor ◽

Single Copy ◽

Strand Breaks ◽

Cis Acting ◽

Human T Cell ◽

In The Wild ◽

Recombination Activating Gene

We have studied the role of transcriptional enhancers in providing recombination signal sequence (RSS) accessibility to V(D)J recombinase by examining mice carrying a transgenic human T-cell receptor (TCR) delta gene minilocus. This transgene is composed of unrearranged variable (Vdelta and Vdelta2), diversity (Ddelta3), joining (Jdelta1 and Jdelta3), and constant (Cdelta) gene segments. Previous data indicated that with the TCR delta enhancer (Edelta) present in the Jdelta3-Cdelta intron, V(D)J recombination proceeds stepwise, first V to D and then VD to J. With the enhancer deleted or mutated, V-to-D rearrangement is intact, but VD-to-J rearrangement is inhibited. We proposed that Edelta is necessary for J segment but not D segment accessibility and that J segment inaccessibility in the enhancerless minilocus resulted in the observed V(D)J recombination phenotype. In this study, we tested this notion by using ligation-mediated PCR to assess the formation of recombination-activating gene (RAG)-dependent double-strand breaks (DSBs) at RSSs 3' of Ddelta3 and 5' of Jdelta1. In five lines of mice carrying multicopy integrants of constructs that either lacked Edelta or carried an inactivated Edelta, the frequency of DSBs 5' of Jdelta1 was dramatically reduced relative to that in the wild type, whereas the frequency of DSBs 3' of Ddelta3 was unaffected. We interpret these results to indicate that Edelta is required for Jdelta1 but not Ddelta3 accessibility within the minilocus, and we conclude that enhancers regulate V(D)J recombination by providing local accessibility to the recombinase. cis-acting elements other than Edelta must maintain Ddelta3 in an accessible state in the absence of Edelta. The analysis of DSB formation in a single-copy minilocus integrant indicates that efficient DSB formation at the accessible RSS 3' of Ddelta3 requires an accessible partner RSS, arguing that RSS synapsis is required for DSB formation in chromosomal substrates in vivo.

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