NKX3-1 Deletion as a Potential Driver of Metastatic Lung Adenocarcinoma: Evidence from Genomic Data and Functional Validation
Woojin Lee
Thornhill Secondary School, Markham, Canada
Publication date: November 20, 2025
Thornhill Secondary School, Markham, Canada
Publication date: November 20, 2025
DOI: http://doi.org/10.34614/JIYRC2025II41
ABSTRACT
Metastatic progression drives poor outcomes in lung adenocarcinoma, yet the genomic alterations and lineage programs that modulate this process remain incompletely defined. In this study, we reanalyzed 2,653 tumor–normal pairs from the MSK “Lung Adenocarcinoma Met Organotropism” cohort using cBioPortal and identified eight genes with significantly enriched deletions in metastatic tumors, including a focal 8p loss harboring the homeobox transcription factor NKX3-1. NKX3-1 deletions were rare in primary tumors (0.12%) but increased in metastases (2.44%), prompting functional evaluation. To test whether restoring lineage transcriptional control constrains growth, we overexpressed NKX3-1 in A549 lung adenocarcinoma cells via Lipofectamine-based transfection at two plasmid: reagent dose pairs (3 μL:7 μL and 6 μL:14 μL). Cell morphology and confluency were assessed at 2 and 7 days, and viability was quantified at 3 days using a LUNA-FL automated counter. NKX3-1 overexpression reduced confluency in a dose- and time-dependent manner. Cultures became less compact by day 2 and exhibited a marked density loss by day 7, with rounded/contracted cells at the higher dose. At day 3, overall viability remained high (Lipofectamine-only 94.0%, low dose 92.4%, high dose 91.7%), but the total live-cell number dropped sharply (2.26×10^6 vs. 1.50×10^5 and 9.84×10^4), indicating a primarily cytostatic effect early after transfection. These findings support a tumor-suppressive role for NKX3-1 in lung adenocarcinoma, where restoring lineage factor activity restrains proliferation and progressively alters cell phenotype. The convergence of metastatic-enriched NKX3-1 loss and cytostatic rescue by NKX3-1 overexpression suggests that lineage reinforcement may be a potential therapeutic strategy and motivates in-depth, multi-model studies of NKX3-1 function in tumors with 8p deletions.
Metastatic progression drives poor outcomes in lung adenocarcinoma, yet the genomic alterations and lineage programs that modulate this process remain incompletely defined. In this study, we reanalyzed 2,653 tumor–normal pairs from the MSK “Lung Adenocarcinoma Met Organotropism” cohort using cBioPortal and identified eight genes with significantly enriched deletions in metastatic tumors, including a focal 8p loss harboring the homeobox transcription factor NKX3-1. NKX3-1 deletions were rare in primary tumors (0.12%) but increased in metastases (2.44%), prompting functional evaluation. To test whether restoring lineage transcriptional control constrains growth, we overexpressed NKX3-1 in A549 lung adenocarcinoma cells via Lipofectamine-based transfection at two plasmid: reagent dose pairs (3 μL:7 μL and 6 μL:14 μL). Cell morphology and confluency were assessed at 2 and 7 days, and viability was quantified at 3 days using a LUNA-FL automated counter. NKX3-1 overexpression reduced confluency in a dose- and time-dependent manner. Cultures became less compact by day 2 and exhibited a marked density loss by day 7, with rounded/contracted cells at the higher dose. At day 3, overall viability remained high (Lipofectamine-only 94.0%, low dose 92.4%, high dose 91.7%), but the total live-cell number dropped sharply (2.26×10^6 vs. 1.50×10^5 and 9.84×10^4), indicating a primarily cytostatic effect early after transfection. These findings support a tumor-suppressive role for NKX3-1 in lung adenocarcinoma, where restoring lineage factor activity restrains proliferation and progressively alters cell phenotype. The convergence of metastatic-enriched NKX3-1 loss and cytostatic rescue by NKX3-1 overexpression suggests that lineage reinforcement may be a potential therapeutic strategy and motivates in-depth, multi-model studies of NKX3-1 function in tumors with 8p deletions.
