Oligo-CALL: A next-generation barcoding platform for studying resistance to targeted therapy.

Area of Science:

• Molecular Biology
• Genetics
• Cancer Research

Background:

• Therapy resistance in cancer is driven by heterogeneous cell populations and clonal evolution.
• Existing CRISPR-based lineage tracing methods often lack efficiency and integration with single-cell transcriptomics.

Purpose of the Study:

• To develop an advanced barcoding system for precise lineage tracing and integration with single-cell RNA sequencing.
• To investigate clonal evolution and molecular mechanisms underlying resistance to KRAS^G12C inhibitors in lung cancer.

Main Methods:

• Development and application of Oligo-CALL (Oligonucleotide-inducible CRISPR transcriptional activator-Assisted Lineage Labeling).
• Integration of Oligo-CALL with single-cell RNA sequencing for simultaneous lineage and transcriptome analysis.
• Treatment of lung cancer cells with a KRAS^G12C inhibitor and subsequent clonal analysis.

Main Results:

• Oligo-CALL demonstrated >95% efficiency in linking lineage identity to transcriptomes.
• Identified consistently enriched clones posttreatment, supporting a predestined resistance model.
• Uncovered clone-specific pathways, highlighting recurrent alterations in DNA repair pathways in resistant clones.
• Demonstrated synergistic effects of poly(adenosine 5'-diphosphate-ribose) polymerase inhibition with KRAS^G12C inhibition.

Conclusions:

• Oligo-CALL is a versatile platform for dissecting lineage evolution and molecular dynamics of targeted therapy resistance.
• DNA repair pathways are critical targets for overcoming KRAS^G12C inhibitor resistance in lung cancer.
• Combined inhibition of KRAS^G12C and poly(adenosine 5'-diphosphate-ribose) polymerase shows promise for enhanced cancer therapy.