Machine-learning-assisted multi-omics profiling identifies CALB1 as a subtype-associated regulator of PI3K/AKT signaling and malignant progression in non-small cell lung cancer.
- 1Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- 2Department of Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
Abstract
Non-small cell lung cancer (NSCLC) is molecularly heterogeneous, and computationally nominated biomarkers often lack sufficient functional validation. CALB1 is a calcium-binding protein, but its clinical relevance, cellular source, and signaling role in NSCLC remain unclear. This study aimed to identify subtype-associated regulators in NSCLC through a machine-learning-assisted multi-omics framework and to characterize the functional and signaling relevance of CALB1 in malignant progression. NSCLC transcriptomic cohorts were used to define metabolic-epigenetic remodeling (MER) subtypes. Machine-learning-assisted Cox modeling was then applied to identify subtype-associated prognostic regulators. CALB1 was selected for further validation using public cohorts, in-house NSCLC specimens, quantitative real-time polymerase chain reaction (qRT-PCR), western blotting, immunohistochemistry, single-cell RNA sequencing, proteomic and phosphoproteomic profiling, and functional assays. CALB1 was silenced in A549 and PC9 cells to assess its effects on PI3K/AKT activation, proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT)-associated phenotypes. Alpelisib was used as a PI3Kα inhibitor to examine the pathway-level involvement of PI3K/AKT signaling in CALB1-associated phenotypes. In vivo relevance and alpelisib responsiveness were further evaluated using a four-group subcutaneous A549 xenograft model comprising sh-Control + vehicle, sh-CALB1 + vehicle, sh-Control + alpelisib, and sh-CALB1 + alpelisib groups. Three MER subtypes were identified, with MER2 showing the poorest prognosis and distinct immune-metabolic features. CALB1 was retained in the prognostic model and positively correlated with model-derived risk scores. CALB1 was upregulated in NSCLC tissues, associated with advanced clinicopathological features and unfavorable prognosis, and mainly enriched in malignant epithelial cells. CALB1-high tumors showed enrichment of proliferative, metabolic, DNA repair, and PI3K/AKT-related programs. CALB1 knockdown induced coordinated proteomic and phosphoproteomic changes involving proliferation, migration, extracellular matrix organization, secretory trafficking, and PI3K/AKT signaling. Functionally, CALB1 silencing reduced p-PI3K and p-AKT levels and suppressed proliferation, migration, invasion, and EMT-associated phenotypes. PI3Kα inhibition with alpelisib attenuated CALB1 overexpression-associated malignant phenotypes in vitro. In vivo, stable CALB1 knockdown suppressed xenograft growth and enhanced the antitumor response to alpelisib, with the sh-CALB1 + alpelisib group showing the greatest reductions in tumor volume and tumor weight. This study identifies CALB1 as a subtype-associated regulator in NSCLC through a machine-learning-assisted multi-omics framework. CALB1 may promote malignant progression partly through PI3K/AKT-related signaling. Stable CALB1 knockdown increased the in vivo antitumor response to alpelisib, supporting CALB1 as a potential modulator of PI3Kα inhibitor sensitivity.
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BibTeX
@article{mao2026machinelearningassisted,
title = {{Machine-learning-assisted multi-omics profiling identifies CALB1 as a subtype-associated regulator of PI3K/AKT signaling and malignant progression in non-small cell lung cancer.}},
author = {Feng Mao and Ning Wang and Yuming Wang and Ziang Wang and Hui Zhang and Qingquan Luo},
journal = {Translational lung cancer research},
year = {2026},
month = sep,
doi = {10.21037/tlcr-2026-0576},
url = {https://europepmc.org/article/MED/42999431},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - Machine-learning-assisted multi-omics profiling identifies CALB1 as a subtype-associated regulator of PI3K/AKT signaling and malignant progression in non-small cell lung cancer.
AU - Feng Mao
AU - Ning Wang
AU - Yuming Wang
AU - Ziang Wang
AU - Hui Zhang
AU - Qingquan Luo
PY - 2026
DA - 2026/09/29
JO - Translational lung cancer research
DO - 10.21037/tlcr-2026-0576
UR - https://europepmc.org/article/MED/42999431
AB - Non-small cell lung cancer (NSCLC) is molecularly heterogeneous, and computationally nominated biomarkers often lack sufficient functional validation. CALB1 is a calcium-binding protein, but its clinical relevance, cellular source, and signaling role in NSCLC remain unclear. This study aimed to identify subtype-associated regulators in NSCLC through a machine-learning-assisted multi-omics framework and to characterize the functional and signaling relevance of CALB1 in malignant progression. NSCLC transcriptomic cohorts were used to define metabolic-epigenetic remodeling (MER) subtypes. Machine-learning-assisted Cox modeling was then applied to identify subtype-associated prognostic regulators. CALB1 was selected for further validation using public cohorts, in-house NSCLC specimens, quantitative real-time polymerase chain reaction (qRT-PCR), western blotting, immunohistochemistry, single-cell RNA sequencing, proteomic and phosphoproteomic profiling, and functional assays. CALB1 was silenced in A549 and PC9 cells to assess its effects on PI3K/AKT activation, proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT)-associated phenotypes. Alpelisib was used as a PI3Kα inhibitor to examine the pathway-level involvement of PI3K/AKT signaling in CALB1-associated phenotypes. In vivo relevance and alpelisib responsiveness were further evaluated using a four-group subcutaneous A549 xenograft model comprising sh-Control + vehicle, sh-CALB1 + vehicle, sh-Control + alpelisib, and sh-CALB1 + alpelisib groups. Three MER subtypes were identified, with MER2 showing the poorest prognosis and distinct immune-metabolic features. CALB1 was retained in the prognostic model and positively correlated with model-derived risk scores. CALB1 was upregulated in NSCLC tissues, associated with advanced clinicopathological features and unfavorable prognosis, and mainly enriched in malignant epithelial cells. CALB1-high tumors showed enrichment of proliferative, metabolic, DNA repair, and PI3K/AKT-related programs. CALB1 knockdown induced coordinated proteomic and phosphoproteomic changes involving proliferation, migration, extracellular matrix organization, secretory trafficking, and PI3K/AKT signaling. Functionally, CALB1 silencing reduced p-PI3K and p-AKT levels and suppressed proliferation, migration, invasion, and EMT-associated phenotypes. PI3Kα inhibition with alpelisib attenuated CALB1 overexpression-associated malignant phenotypes in vitro. In vivo, stable CALB1 knockdown suppressed xenograft growth and enhanced the antitumor response to alpelisib, with the sh-CALB1 + alpelisib group showing the greatest reductions in tumor volume and tumor weight. This study identifies CALB1 as a subtype-associated regulator in NSCLC through a machine-learning-assisted multi-omics framework. CALB1 may promote malignant progression partly through PI3K/AKT-related signaling. Stable CALB1 knockdown increased the in vivo antitumor response to alpelisib, supporting CALB1 as a potential modulator of PI3Kα inhibitor sensitivity.
SN - 2218-6751
SN - 2226-4477
ER -