Method Profile
Combine clinically annotated EGFR-mutant lung organoids with lineage profiling, gene perturbation and CDK4/6 inhibitor response comparisons.
Investigate non-genetic EGFR-inhibitor resistance and context-dependent drug vulnerabilities.
ELCOL contains 39 lines from 31 patients, including serial samples; selected basal-shift and non-basal-shift lung adenocarcinoma organoids are compared. Separate engineered normal alveolar lines from two donors supply functional evidence.
Matrigel-based cultures; 1,500 cells per well for seven-day ATP-based viability. The initial 54-compound screen uses three basal-shift and two non-basal-shift lines in triplicate; secondary IC50 comparisons use four technical replicates.
Lineage and genetics
Exome sequencing of EGFR/resistance lesions, RNA/chromatin profiles, NKX2-1, TAp63/ΔNp63 and AQP5 staining, NKX2-1 knockout and TP63 overexpression.
Drug comparisons
Osimertinib, palbociclib, abemaciclib and DMSO controls; cell-cycle analysis. Separate palbociclib xenograft comparison at 150 mg/kg/day orally for three weeks.
Keep source-patient response, established organoid phenotype, gene-perturbation evidence and mouse efficacy distinct. Compare CDK4/6 effects within EGFR/KRAS and CDKN2A/B contexts rather than using basal-shift alone.
39 organoid lines from 31 patients; initial drug panel five lines; single-cell profiling eight selected lines. Four xenograft lines with five tumors per condition. Clinical marker evaluation uses 53 re-biopsy samples.
Basal-shift versus non-basal-shift; CDKN2A/B loss versus wild type; EGFR versus KRAS backgrounds; NKX2-1-edited versus control models; pre/post-treatment patient pairs.
NKX2-1 loss with EGFR inhibition promoted basal-shift and resistance; CDKN2A/B loss or TP63 overexpression alone was insufficient. CDK4/6 responses were largely cytostatic and associated with CDKN2A/B loss in the tested EGFR-mutant models. Two of three KRAS-mutant lines carrying the loss resisted palbociclib.
Primary study comparisons of the named models, exposures and measured outcomes.
A 39-line EGFR-mutant lung-cancer organoid library identified resistant tumors with mixed adenocarcinoma and squamous features. NKX2-1 loss supported that shift experimentally, while CDK4/6 responses were associated with CDKN2A/B loss in the tested EGFR-mutant background.
