Mutations at <i>BCL11B</i> Exon 4 Associated with T Cell Acute Lymphoblastic Leukemia Are Facilitated by AID and Formation of Non-B DNA Conformations

One of the primary reasons behind the pathogenesis of T cell acute lymphoblastic leukemia (T-ALL) is the deregulation of the transcription factor <i>BCL11B</i>. The exon 4 of <i>BCL11B</i> harbors several driver mutations, which abolishes its DNA-binding ability. The high frequency of C > T or G > A conversion in close vicinity of AID (Activation-induced cytidine deaminase)-hotspot motifs in the deregulated gene prompted us to investigate the role of AID in <i>BCL11B</i> mutagenesis. Our results reveal that AID is expressed in T-ALL patient-derived cells, binds to <i>BCL11B</i> fragile region (FR) in exon 4 of T cells in vivo, and generates a signature mutation pattern in this region. The mutation frequency in <i>BCL11B FR</i> could be modulated upon overexpression of the AID gene in the knockout background, further suggesting the involvement of AID in <i>BCL11B</i> mutagenesis. Importantly, various lines of experimentation reveal that <i>BCL11B FR</i> could fold into parallel G-quadruplex, triplex, and hairpin structures, which could act as a replication/transcription block, causing mutagenesis. Thus, our results suggest that AID binds to <i>BCL11B</i> exon 4 due to non-B DNA formation, causing U:G mismatches or replication blocks, which, when repaired erroneously, generates deleterious mutations, resulting in loss of functionality of <i>BCL11B</i>, and thus becomes the cause of T-ALL.