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Somatic Recombination Between an Ancient and a Recent NOTCH2 Gene Variant Is Associated with the NOTCH2

Rainer Hubmann1,2,3, Martin Hilgarth1, Tamara Löwenstern4

  • 1Department of Internal Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, 1090 Vienna, Austria.

International Journal of Molecular Sciences
|December 17, 2024
PubMed

Insights

Constitutively active NOTCH2 signaling in chronic lymphocytic leukemia (CLL) is linked to a deleted mRNA sequence. Inherited NOTCH2 variants recombine somatically, causing aberrant splicing and NOTCH2 gain-of-function, potentially explaining CLL

Area of Science:

  • Genetics and Molecular Biology
  • Oncology
  • Hematology

Background:

  • Constitutively active NOTCH2 signaling is a recognized characteristic of chronic lymphocytic leukemia (CLL).
  • The underlying genetic defect driving this aberrant signaling in CLL has remained largely unknown.
  • NOTCH2 signaling plays a critical role in various cellular processes, and its dysregulation is implicated in several diseases.

Purpose of the Study:

  • To elucidate the precise molecular defect responsible for constitutive NOTCH2 activation in CLL.
  • To investigate the role of genetic variations and somatic recombination in NOTCH2 aberrant signaling in CLL.
  • To explore the potential link between inherited NOTCH2 variants, their geographical distribution, and CLL incidence.

Main Methods:

  • Deletion analysis of the NOTCH2 mRNA sequence coding for the negative regulatory region (NRR) in CLL cells.
  • Identification and phylogenetic analysis of single nucleotide variations (SNVs) within intronic regions of NOTCH2.
  • Nanopore sequencing to detect somatic reciprocal crossing over between NOTCH2 variants.
  • Analysis of splicing branch point sequences (BPS) and their impact on pre-mRNA splicing.

Main Results:

  • A consistent deletion of the NOTCH2 NRR-coding mRNA sequence was observed in CLL cells.
  • The common NOTCH2ΔNRR-DEL2 deletion is associated with two intronic SNVs (rs2453058 and rs5025718) affecting BPS.
  • Phylogenetic analysis revealed ancient (rs2453058, *1A01) and recent (rs5025718, *1a4) NOTCH2 variants with differential geographical frequencies.
  • Somatic recombination between *1A01 and *1a4 variants in CLL cases leads to altered BPS patterns and aberrant splicing, resulting in NOTCH2 NRR deletion and gain-of-function.

Conclusions:

  • Somatic recombination of inherited NOTCH2 variants (*1A01 and *1a4) is a key mechanism leading to NOTCH2 gain-of-function in CLL.
  • This recombination event causes aberrant pre-mRNA splicing, resulting in the loss of the NOTCH2 NRR domain.
  • The findings suggest a potential role for somatic recombination of inherited NOTCH2 variants in CLL etiology and its geographical clustering.
Keywords:
CLLNOTCH2evolutiongain of functionhaplotypessomatic recombination

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