Deciphering IGH rearrangement complexity and detection strategies in acute lymphoblastic leukaemia

Abstract

Acute lymphoblastic leukaemia is a highly heterogeneous malignancy characterised by various genomic alterations that influence disease progression and therapeutic outcomes. Gene fusions involving the immunoglobulin heavy chain gene represent a complex and diverse category. These fusions often result in enhancer hijacking, upregulation of partner proto-oncogenes and contribute to leukemogenesis. This review highlights the mechanisms underlying IGH gene fusions, the critical role they play in ALL pathogenesis, and current detection technologies.

Fig. 1. A schematic of the human IGH locus.

a Located at the sub telomeric region on chromosome 14q, b the IGH locus comprises a series of 123 -129 Variable (V_H) (number present varies depending on haplotype), 27 Diversity (D_H), 9 Joining (J_H) and 11 Constant (C_H) regions. In early and late pro-B cells, the V_H, D_H and J_H regions undergo somatic recombination in a 2-step process, which results in a functional V(D)J unit. This V(D)J unit along with the C_H regions are expressed, with the Enhancers (Eμ) driving transcription. c Due to aberrant D-J or V-DJ somatic recombination a gene from another chromosomal location can be translocated adjacent to the J or DJ region. This results in the deregulation of the translocated gene, driven by the transcriptional enhancers located within the IGH locus, which contributes to the pathogenesis of ALL.

Fig. 2. Gene fusion mechanism.

a Gene fusions normally arise through chromosomal structural alterations like translocations, inversions, deletions, and insertions. b In contrast, IGH fusions stem from aberrant V(D)J recombination resulting in the translocation or insertion of a gene downstream of the IGH enhancer (red star). Both mechanisms result in NTN (red hash) being inserted at the fusion breakpoint. However, the NTNs are spliced out of normal gene fusion events during transcription due to their intronic location, while they may be maintained in IGH fusions. Following translation of a normal fusion transcript, a chimeric protein is produced, while the translocated gene in IGH fusions is overexpressed, due to its proximity to the enhancer.

Fig. 3. Schematic representation illustrating the identification of gene fusion events through sequencing read alignment across the fusion breakpoint.

Paired-end sequencing reads are aligned, where each end of the paired read maps entirely to two different genomic regions (Spanning Reads), or when one end of the read overlaps the fusion breakpoint (Chimeric). However, due to the presence of NTNs between IGH and fusion partner (in red), chimeric reads overlapping the fusion breakpoint may exhibit suboptimal or no mapping (unmapped read portion shown with dotted outline).