TET deficiency perturbs mature B cell homeostasis and promotes oncogenesis associated with accumulation of G-quadruplex and R-loop structures

Abstract

Enzymes of the TET family are methylcytosine dioxygenases that undergo frequent mutational or functional inactivation in human cancers. Recurrent loss-of-function mutations in TET proteins are frequent in human Diffuse Large B-Cell Lymphoma (DLBCL). Here we investigate the role of TET proteins in B-cell homeostasis and development of B cell lymphomas with features of DLBCL. We show that deletion of Tet2 and Tet3 genes in mature B cells in mice perturbs B-cell homeostasis and results in spontaneous development of germinal center-derived B cell lymphomas with increased G-quadruplexes and R-loops. At a genome-wide level, G-quadruplexes and R-loops were associated with increased DNA double strand breaks at immunoglobulin switch regions. Deletion of the DNA methyltransferase DNMT1 in TET-deficient B cells prevented expansion of germinal center B cells, diminished the accumulation of G-quadruplexes and R-loops, and delayed B lymphoma development, consistent with the opposing functions of DNMT and TET enzymes in DNA methylation and demethylation. CRISPR-mediated depletion of nucleases and helicases that regulate G-quadruplexes and R-loops decreased the viability of TET-deficient B cells. Our studies suggest a molecular mechanism by which TET loss-of-function might predispose to development of B cell malignancies.

Accelerating the Alignment Processing Speed of the Comprehensive End-to-End Whole-Genome Bisulfite Sequencing Pipeline, wg-blimp

“…To further assess the accuracy of these aligners in a biological context we obtained publicly available mouse WGBS data from CD19 + B-cells [22] and spermatocytes [23] and used each aligner to analyze DNA methylation patterns in each dataset. We found both bwa-meth and gemBS aligners were able to accurately map reads (Fig.…”

Ligands stimulating antitumour immunity as the next G-quadruplex challenge

“…Structural features that favour G4 folding (GC-richness, strand separation, negative supercoils) also favour the formation of R-loops, another non-B structure [ 20 , 24 , 63 ]. R-loops, commonly occurring co-transcriptionally, are three-strand nucleic acid structures, wherein the nascent RNA strand is annealed to the template DNA strand forming a hybrid duplex, while the non-template DNA strand is displaced out.…”

“…They are key players in many biological processes such as replication, transcription activation and termination, and are crucial for immunoglobulin class-switch recombination (CSR) in activated B lymphocytes [ 66 ]. G4 and R-loop co-existence has been disclosed in human cells by the overlapping of nuclear foci of these two non-B DNA structures visualized with specific antibodies (BG4 and S9.6, respectively) [ 20 , 24 , 50 ]. In particular, kinetics of G4 and R-loop formation by cell treatments with G4 binders are very similar in human U2OS cells [ 20 ].…”

“…More recently, several structurally-diverse G4 binders were shown to inhibit and arrest DNA replication leading to DNA damage and genome instability [ 19 – 22 ]. In addition, as nuclear levels of G4 structures can be higher in cancer than normal cells [ 14 , 23 , 24 ], published data converge on G4s as potentially-effective pharmacological targets for cancer treatment. Therefore, past research in the field focused on developing more cytotoxic ligands, some of which have shown antitumour activity in human tumour xenograft models, in particular in combination regimen or in homologous recombination (HR) repair-deficient tumours [ 25 , 26 ].…”

Indoloquinoline-Mediated Targeted Downregulation of KRAS through Selective Stabilization of the Mid-Promoter G-Quadruplex Structure

“…Thus, genes with higher transcription rates have greater potential for promoter G4 formation, underscoring the apparent role of most promoter G4s as negative regulators of gene expression. G4 formation is inducible by small molecules, endogenous levels of G4s can predict tumor sensitivity to G4-targeted ligands, the structures occur more frequently in human tumors, and were recently described to correlate with oncogenesis of B-cells [ 29 , 30 ].…”