What question did this study set out to answer?

The aim is to utilize structure-guided CRISPR-Cas9 to target the ABL1 gene, disrupting the BCR-ABL1 fusion involved in chronic myeloid leukaemia.

February 12, 2026Computational Biology and Bioinformatics1 citationsOpen Access

Structure-guided CRISPR CAS9 Targeting of ABL1 for Functional Disruption of BCR-ABL1 Fusion in Chronic Myeloid Leukaemia

SKSumita katalInstitute of Bioinformatics SKShivangi KoundalInstitute of Bioinformatics UKUma KumariInstitute of Bioinformatics

Key Points

The aim is to utilize structure-guided CRISPR-Cas9 to target the ABL1 gene, disrupting the BCR-ABL1 fusion involved in chronic myeloid leukaemia.
Applied a structure-guided CRISPR-Cas9 approach for genome editing.
Identified sgRNAs targeting ABL1 using the high-resolution crystal structure of ABL1 kinase.
Performed computational design and filtering of sgRNAs with tools like E-CRISP and CHOPCHOP.
Conducted in silico analyses for specificity and mismatch profiles.
Analyzed protein-protein interactions and signaling pathways related to ABL1.
Successfully identified highly specific sgRNAs capable of disrupting ABL1.
Confirmed precise targeting of exons important for kinase functions.
Showed strong interactions between ABL1 and oncogenic regulators.
Highlighted ABL1’s role in relevant cancer signaling pathways.
Provided a theoretical basis for future experimental validation of genome editing therapies.

Abstract

Chronic myeloid leukaemia (CML) is a clonal myeloproliferative cancer caused by the constant activity of the BCR–ABL 1 fusion protein s tyrosine kinase, resulting from the Philadelphia chromosome translocation, which leads to abnormal cell growth, survival, and disease progression. While tyrosine kinase inhibitors (TKIs) have greatly improved patient outcomes, issues like drug resistance and persistent leukemic stem cells highlight the need for alternative therapies. This study used a structure- guided CRISPR- Cas 9 genome editing approach to identify highly specific single- guide RNAs (sgRNAs) that can disrupt the human ABL 1 gene, a key part of the BCR–ABL 1 fusion. The high- resolution crystal structure of the ABL 1 kinase domain (PDB ID: 8 I 7 S) helped identify essential functional regions, including catalytic and ATP- binding sites, for precise CRISPR targeting. Computational design and filtering of sgrnas were performed using E- CRISP and CHOPCHOP, focusing on criteria like PAM site accessibility, targeting conserved kinase regions in exons, GC content, predicted efficiency, and low off- target risk. In silico analyses, including specificity scores, mismatch profiles, and sequence alignment across ABL 1 transcript variants, ensured high selectivity and broad coverage. Genomic visualization confirmed accurate targeting within exons encoding vital kinase functions. Protein–protein interaction analysis via STRING showed strong links between ABL 1 and key oncogenic regulators such as BCR, STAT 5, and MAPK pathway components. KEGG pathway analysis further indicated ABL 1 s involvement in chronic myeloid leukaemia, PI 3 K–AKT, MAPK signaling, and other cancer- related pathways, emphasising its importance in CML development. This combined computational approach demonstrates that structure- guided CRISPR- Cas 9 targeting of ABL 1 can effectively disrupt BCR–ABL 1 driven cancer signals. The results provide a strong theoretical basis for future experimental validation and genome editing therapies aimed at overcoming TKI resistance and achieving long- lasting molecular remission in CML.

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