Transciptomic Profiling of CRISPR-Cas9 Mediated LEF1 Knockout in Chronic Lymphocytic Leukemia: Revealing Compensatory Survical Pathways

Abstract

Background: Chronic lymphocytic leukemia (CLL) remains a major clinical challenge, mainly due to the persistent drug resistance of leukemia- affected cells targeted therapies. The transcription factor gene LEF1, and its governing Wnt/β-catenin axis, is is a well-established driver as a fundamental driver promoting cellular growth and proliferation in this malignancy consequently that we designed this current study to identify the precise compensatory survival mechanism employed by CLL cells following successful disruption of LEF1 signaling.

Methods: Gene expression data were obtained from the GEO database (GSE299964) to study and analyzed LEF1inhibition in CLL cell. Differential expression analysis (DEA) and pathway enrichment analysis were used to identify inhibited and activated pathways also was designed a protein-protein interaction network (PPI) to identify and visualize the interaction. Statistical analyses were performed within the R environment (version 4.4.1).

Results: By used DEA, the results showed significant inhibition of the Wnt axis (LEF1, Log2FC: -6.22) and concurrent activation of the NF-κB/AP-1 pathway, particularly SLC3A2 (+3.59) and JUN (+3.10). And downregulation in key growth factors was observed specifically CCND1 and MYC. In contrast, the pathway enrichment analysis suggested strong statistical of the NF-kappa B, and an increase in the transcription factors was observed NFKB1 and JUN. It is important that the visualization of the PPI network provided visual evidence the existence of direct regulatory links connecting suppressed Wnt genes to activated NF-kappa B genes, this suggesting a potential emerging therapeutic dependency.

Conclusion: The study suggests that the inhibition of the Wnt/LEF1 axis is associated with the potential activation of a compensatory survival mechanism, involving the NF-kappa B/AP-1 pathway. These results indicate that chronic lymphocytic leukemia cells this reciprocal interaction may be used as an adaptive immune response to the disruption of the primary pathway. This aggregation strategy may represent a promising way to address anticipated resistance mechanisms, although further functional and laboratory studies are needed to validate them.