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18 pages, 3429 KB  
Article
Loss of PTEN as an Independent Poor Prognosis Indicator in Lung Adenocarcinoma, but Not in Squamous Cell Carcinoma, Is Associated with an Immunosuppressive Tumor Microenvironment and Distinct Co-Mutational Profiles
by Maeva Houry, Shannon J. Silva, Maider Artola, Carmen Behrens, Katerina Politi, Ignacio Wistuba, Luis Montuenga, Francisco Exposito and Alfonso Calvo
Med. Sci. 2026, 14(2), 254; https://doi.org/10.3390/medsci14020254 - 14 May 2026
Abstract
Background/Objectives: Non-small cell lung cancer (NSCLC) comprises biologically heterogeneous tumors, primarily lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), which differ in genomic landscape and clinical behavior. The tumor suppressor PTEN is a key negative regulator of the PI3K/AKT/mTOR pathway and is [...] Read more.
Background/Objectives: Non-small cell lung cancer (NSCLC) comprises biologically heterogeneous tumors, primarily lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), which differ in genomic landscape and clinical behavior. The tumor suppressor PTEN is a key negative regulator of the PI3K/AKT/mTOR pathway and is frequently inactivated in NSCLC through genetic and non-genetic mechanisms. Although reduced PTEN expression has been associated with poor outcomes in lung cancer, its prognostic relevance across these histological subtypes remains unclear. Methods: Here, we investigated the prognostic significance of PTEN in NSCLC subtypes using a multi-level approach combining protein, transcriptomic, and genomic analyses. PTEN protein expression was evaluated by immunohistochemistry in a tissue microarray from resected NSCLC patients, and findings were validated using publicly available datasets including TCGA-RPPA, GEO/EGA-based transcriptomic cohorts, and large genomic resources. In parallel, mutational landscapes and co-mutation patterns were analyzed in several independent datasets, and tumor immune microenvironment composition was inferred using CIBERSORT deconvolution analysis. Results: Low PTEN protein and mRNA levels, as well as PTEN mutations, were consistently associated with significantly worse overall survival (OS) in LUAD but not in LUSC. Multivariable Cox regression analysis confirmed PTEN as an independent prognostic factor in LUAD. Although PTEN mutations were more frequent in LUSC, they showed no prognostic value in this subtype. Co-mutation analyses revealed recurrent PTEN partnerships with TP53, EGFR, and APC in LUAD, with PTEN-TP53 co-alterations enriched in metastatic disease. Immune deconvolution demonstrated that PTEN-low LUAD tumors were characterized by an immunosuppressive microenvironment, including increased T regulatory cells and reduced inflammatory immune populations. Notably, increased M2-like macrophages were associated with shorter OS in PTEN-low LUADs, whereas a high number of total macrophages (CD68+ cells) emerged as an independent predictor of more favorable OS. Conclusions: Collectively, these results identify PTEN loss as a subtype-specific prognostic biomarker in LUAD and link its deficiency to immunosuppressive tumor microenvironment remodeling. Full article
(This article belongs to the Special Issue Feature Papers in Section “Cancer and Cancer-Related Research”)
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32 pages, 10285 KB  
Article
A Zinc Finger Protein-Based Prognostic Model in Lung Adenocarcinoma Identifies FGD3 as a Marker Associated with Lorlatinib Resistance
by Jiayue Sun, Yue Yang, Xiaoyi Huang, Dinglong Xue, Jiazhuang Li, Yaru Huang and Qingwei Meng
Cancers 2026, 18(10), 1591; https://doi.org/10.3390/cancers18101591 - 14 May 2026
Abstract
Background: Lung adenocarcinoma (LUAD) is the most common type of lung cancer and a major cause of cancer death. Zinc finger proteins (ZNFs) have been implicated in LUAD progression, functioning either as oncogenes or tumor suppressors. Therefore, an in-depth investigation of ZNFs [...] Read more.
Background: Lung adenocarcinoma (LUAD) is the most common type of lung cancer and a major cause of cancer death. Zinc finger proteins (ZNFs) have been implicated in LUAD progression, functioning either as oncogenes or tumor suppressors. Therefore, an in-depth investigation of ZNFs may contribute to the development of novel diagnostic and therapeutic strategies for LUAD. Methods: Transcriptomic and clinical data were obtained from the TCGA and GEO databases. Prognosis-related ZNF genes were identified using univariate Cox, LASSO, and multivariate Cox regression analyses. An eight-gene ZNF-based prognostic signature was constructed and validated in two independent external cohorts (GSE50081 and GSE26939). A nomogram integrating independent prognostic factors was developed. Immune infiltration, somatic mutation profiles, and drug sensitivity were systematically analyzed. We further focused on FGD3, a key gene from the signature, examining its expression in LUAD cells and tissues, including lorlatinib-resistant models. Results: The prognostic signature comprising TRIM6, TRIM29, CTCFL, FGD3, GATA4, CASZ1, TRAF2, and ZNF322 effectively stratified patients into distinct risk groups with significantly different overall survival (p < 0.05). The risk score, together with T and N stage, served as independent prognostic predictors (n = 500, p < 0.05). High-risk patients exhibited an immune-desert phenotype, increased tumor mutational burden, and distinct drug sensitivity patterns. Notably, FGD3 expression was downregulated in LUAD tissues (n = 14, p < 0.0001) and lorlatinib-resistant cells, and its restoration suppressed resistant cell proliferation and partially reversed drug resistance. Conclusions: This study establishes a promising ZNF-based prognostic model for LUAD, providing a potential tool for risk stratification and individualized therapeutic decision-making. The identification of FGD3 as a potential mediator of drug resistance highlights its promise as a candidate biomarker and therapeutic target in LUAD. Full article
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16 pages, 5044 KB  
Article
Integrative In Silico Identification of TP53-Associated Drug Repurposing Candidates in Lung Adenocarcinoma
by Akile Tuncal and Rasime Kalkan
Pharmaceuticals 2026, 19(5), 761; https://doi.org/10.3390/ph19050761 (registering DOI) - 13 May 2026
Abstract
Background/Aim: Lung adenocarcinoma (LUAD) is the most common subtype of lung cancer and is characterized by high genetic heterogeneity and poor prognosis. TP53 is the most frequently mutated gene in LUAD and plays a critical role in tumor initiation, progression, and therapeutic resistance. [...] Read more.
Background/Aim: Lung adenocarcinoma (LUAD) is the most common subtype of lung cancer and is characterized by high genetic heterogeneity and poor prognosis. TP53 is the most frequently mutated gene in LUAD and plays a critical role in tumor initiation, progression, and therapeutic resistance. The present study aimed to prioritize TP53-associated drug repurposing candidates in LUAD using an integrative in silico approach. Materials and Methods: A total of 1309 TP53-associated compounds were retrieved from the Gene2Drug database. Drug sensitivity profiles of lung adenocarcinoma cell lines were evaluated using PRISM Repurposing Public 22Q2 viability data obtained from the DepMap platform. Candidate compounds were ranked according to Gene2Drug significance scores (p < 1 × 10−3), and compounds with concordant sensitivity patterns in PRISM data were prioritized. Results: LUAD cell lines showed the strongest sensitivity to atropine (p = 6.83 × 10−5). Additionally, LUAD cell lines displayed consistent sensitivity signals for dropropizine (p = 8.47 × 10−3), terazosin (p = 1.11 × 10−3), morantel (p = 9.05 × 10−3), netilmicin (p = 8.37 × 10−3), altretamine (p = 9.82 × 10−3), and perphenazine (p = 9.58 × 10−3). These findings indicate that several non-oncology drugs exhibit distinct and reproducible sensitivity profiles in LUAD cell lines. Conclusions: Based on TP53-associated drug sensitivity profiles, this in silico analysis identifies atropine among the prioritized candidates, showing the strongest TP53-associated sensitivity signal in LUAD cell lines. Although experimental validation is required, the integration of independent computational datasets provides a robust framework for candidate prioritization and our findings provide a rationale for further preclinical investigation of atropine and related compounds in LUAD. Full article
(This article belongs to the Special Issue Novel Anticancer Drug Development and Toxicity Reduction Strategies)
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40 pages, 2081 KB  
Article
AI-Driven Combination Therapy for Counteracting Dysregulated Genes in Lung Adenocarcinoma: Contribution-Aware Metaheuristic for Drug Repurposing
by Sajjad Nematzadeh and Arzu Karaul
Pharmaceuticals 2026, 19(5), 748; https://doi.org/10.3390/ph19050748 (registering DOI) - 9 May 2026
Viewed by 271
Abstract
Background/Objectives: Lung adenocarcinoma (LUAD) is molecularly heterogeneous and often requires rational drug combinations rather than single-agent therapy. Many computational repurposing methods use global signature matching or network scores, but they often treat dysregulated genes equally and optimize a single scalar objective. This [...] Read more.
Background/Objectives: Lung adenocarcinoma (LUAD) is molecularly heterogeneous and often requires rational drug combinations rather than single-agent therapy. Many computational repurposing methods use global signature matching or network scores, but they often treat dysregulated genes equally and optimize a single scalar objective. This study aimed to develop a contribution-aware computational framework for prioritizing repurposed multi-drug combinations that counteract LUAD driver modules; Methods: Ten LUAD driver scenarios were curated from the LUAD and non-small cell lung cancer literature and encoded as gene-level counteraction vectors across 44 unique genes. Direction-aware drug–gene interactions from the Comparative Toxicogenomics Database were processed into a weighted contribution matrix. A genetic algorithm was then used to search for small combinations of up to six drugs. The fitness function combined mean absolute error with terms for waste, mismatch, entropy, coverage, combination size, and optional cost. Orthogonal computational support was assessed using CLUE/Connectivity Map transcriptomic reversal analysis; Results: After filtering and optimization, 42 drugs and chemicals remained as candidate components across the scenarios. Increasing the combination size from one to three drugs usually reduced the mean absolute error, whereas larger combinations provided more limited gains. Compared with an MAE-only baseline, the full contribution-aware objective improved or preserved MAE in 54 of 60 scenario–drug-count comparisons. Drug and gene clustering identified interchangeable candidate groups and shared mechanisms across LUAD scenarios. CLUE-based analysis provided strong or moderate transcriptomic reversal support for several prioritized compounds; Conclusions: The proposed framework provides a transparent, scenario-based method for prioritizing repurposed drug combinations in LUAD. The results are computational and hypothesis-generating. They should guide future experimental testing, not clinical treatment decisions. Full article
(This article belongs to the Section AI in Drug Development)
21 pages, 4974 KB  
Article
TGBWDriver: A Cancer Driver Gene Identification Method Based on GraphSAGE and Bidirectional Weighted Feature Aggregation
by Jiaxin Chen, Yingzan Ren, Haihui Wang, Cong Zhan and Yusen Zhang
Int. J. Mol. Sci. 2026, 27(9), 4135; https://doi.org/10.3390/ijms27094135 - 5 May 2026
Viewed by 410
Abstract
Identifying cancer driver genes is fundamental for understanding tumor initiation and guiding therapeutic strategies. However, most existing methods assess gene importance from a global or static perspective, overlooking sample-specific functional differences in the same gene. To address this, we propose TGBWDriver, which integrates [...] Read more.
Identifying cancer driver genes is fundamental for understanding tumor initiation and guiding therapeutic strategies. However, most existing methods assess gene importance from a global or static perspective, overlooking sample-specific functional differences in the same gene. To address this, we propose TGBWDriver, which integrates a two-layer GraphSAGE with bidirectional weighted feature aggregation to capture structural characteristics while distinguishing context-dependent gene functions. An exponential pairwise voting strategy prioritizes candidate driver genes, improving ranking stability and accuracy. Systematic experiments on BRCA, LUAD, and PRAD datasets show that TGBWDriver outperforms five existing methods in precision, recall, and F1-score. Ablation studies confirm the critical role of each component. Moreover, TGBWDriver demonstrates strong capability in identifying potential novel cancer driver genes, with predictions showing significant biological relevance in GO enrichment and KEGG pathway analyses. The method provides an effective computational framework for cancer driver gene identification. The source code and datasets are freely available at https://github.com/SCSMDyeah/TGBW [Accessed on 4 May 2026]. Full article
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23 pages, 3895 KB  
Article
Methyltransferase SETD7 as a Regulator of STING-Dependent Cytokine Response in Lung Cancer Cells
by Ivan A. Nevzorov, Polina Korableva, Oleg Shuvalov, Sergey Parfenyev, Nickolai A. Barlev and Alexandra Daks
Int. J. Mol. Sci. 2026, 27(9), 4020; https://doi.org/10.3390/ijms27094020 - 30 Apr 2026
Viewed by 212
Abstract
The innate immune signaling pathway cGAS–STING plays an important role in the recognition of cytosolic nucleic acids and the induction of the interferon-dependent antiviral response. Despite the significant research interest in this cascade in the context of immune system function, the mechanisms regulating [...] Read more.
The innate immune signaling pathway cGAS–STING plays an important role in the recognition of cytosolic nucleic acids and the induction of the interferon-dependent antiviral response. Despite the significant research interest in this cascade in the context of immune system function, the mechanisms regulating cGAS–STING signaling and the switch between its pro-inflammatory and pro-apoptotic effects remain largely underexplored. According to publicly available RNA-seq data and microarray analyses, SETD7 lysine methyltransferase participates in interferon signaling in cancer cells. This study aims to elucidate the role of SETD7 in the regulation of the STING-dependent immune response in human lung adenocarcinoma (LUAD) cells. For this purpose, we developed a reproducible and cost-effective method for inducing the STING cascade by transfecting cells with salmon sperm DNA (sspDNA). We demonstrated that sspDNA efficiently induces phosphorylation of the key components of the STING–TBK1–IRF3 signaling pathway and activates the expression of interferons and pro-inflammatory cytokines. Using this approach, we further demonstrated that SETD7 is involved in the regulation of the IRF3-dependent transcriptional program. Suppression of SETD7 was associated with changes in the expression of genes related to innate immune response and apoptosis, including increased levels of IFNA1, IL1B, BAK1, BBC3 (PUMA), and BCL2. Furthermore, attenuation of SETD7 expression reduced the lentiviral transduction efficacy in H1299 cells. These results suggest that SETD7 may play a role in regulating the switch in STING signaling between pro-inflammatory and pro-apoptotic responses in LUAD cells. Full article
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16 pages, 3902 KB  
Article
Single-Cell Dissection Identifies METTL7B as Associated with Cell Adhesion-Mediated Tumor Invasion in Lung Adenocarcinoma and Glioblastoma
by Jie Mao, Jinquan Xia, Huibin Song, Fuhua Zhong, Huiyi Feng, Junhui Chen and Guangsuo Wang
Cancers 2026, 18(9), 1384; https://doi.org/10.3390/cancers18091384 - 27 Apr 2026
Viewed by 411
Abstract
Background: Tumor invasion is the central barrier to effective immunotherapy in lung adenocarcinoma (LUAD) and glioblastoma. Cell adhesion signaling critically shapes tumor–microenvironment interactions, yet the upstream regulators coordinating these invasive programs at single-cell resolution remain incompletely understood. Methyltransferase Like protein 7B (METTL7B) [...] Read more.
Background: Tumor invasion is the central barrier to effective immunotherapy in lung adenocarcinoma (LUAD) and glioblastoma. Cell adhesion signaling critically shapes tumor–microenvironment interactions, yet the upstream regulators coordinating these invasive programs at single-cell resolution remain incompletely understood. Methyltransferase Like protein 7B (METTL7B) has recently emerged as a candidate oncogenic regulator, but its lineage-specific functions and the potential downstream effectors are unclear. Methods: We integrated publicly available single-cell RNA sequencing datasets from LUAD and glioblastoma with The Cancer Genome Atlas (TCGA) transcriptomic analyses to resolve METTL7B-associated malignant cell states and microenvironmental interactions. Functional enrichment analyses identified invasion- and focal adhesion pathways linked to METTL7B expression. Gain- and loss-of-function experiments were conducted in LUAD and glioblastoma cell lines to validate downstream cell adhesion effectors. Spatial expression patterns were examined using immunofluorescence, and transwell assays were used to assess migratory and invasive phenotypes. Results: Single-cell analyses revealed that METTL7B was selectively enriched in malignant epithelial cells in LUAD and glioblastoma and defined a transcriptional program characterized by cell adhesion signaling. Integrin Alpha 3 (ITGA3) emerged as a conserved downstream effector of METTL7B, with progressive upregulation from minimally invasive to invasive LUAD and glioblastoma. Functional perturbation confirmed that METTL7B enhances tumor cell migration and invasion through integrin-associated pathways. Conclusions: METTL7B acts as a potential lineage-enriched regulator of invasive tumor states by activating cell adhesion signaling in LUAD and glioblastoma. These findings position METTL7B as a putative prognostic factor for strategies aimed at limiting invasion in lung cancer and glioblastoma. Full article
(This article belongs to the Special Issue Single-Cell Biology of Cancer)
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15 pages, 3054 KB  
Article
Upregulation of miR-589-3p Contributes to Lung Adenocarcinoma Progression Through Inhibition of WWC2
by Sultan F. Kadasah
Cancers 2026, 18(9), 1349; https://doi.org/10.3390/cancers18091349 - 23 Apr 2026
Viewed by 345
Abstract
Lung adenocarcinoma (LUAD) is the most common subtype of non-small cell lung cancer and remains a leading cause of cancer-related mortality worldwide. MicroRNAs (miRNAs) are critical regulators of tumor progression; however, the biological role and molecular mechanisms of miR-589-3p in LUAD remain unclear. [...] Read more.
Lung adenocarcinoma (LUAD) is the most common subtype of non-small cell lung cancer and remains a leading cause of cancer-related mortality worldwide. MicroRNAs (miRNAs) are critical regulators of tumor progression; however, the biological role and molecular mechanisms of miR-589-3p in LUAD remain unclear. In this study, the expression levels of miR-589-3p and WWC2 were analyzed using The Cancer Genome Atlas lung adenocarcinoma (TCGA-LUAD) datasets via the UALCAN platform. Flow cytometric apoptosis analysis and functional assays including CCK-8, colony formation, AO/EB staining, and Transwell invasion assays were performed in LUAD cell lines. The interaction between miR-589-3p and WWC2 was validated using dual-luciferase reporter assays, Western blotting, and rescue experiments. miR-589-3p expression was significantly elevated in LUAD tissues compared with normal lung tissues (p < 0.05) and was positively associated with an advanced tumor stage and lymph node metastasis (p < 0.05). Inhibition of miR-589-3p significantly suppressed proliferation and colony formation (p < 0.05), reduced invasive capacity (p < 0.05), and markedly increased apoptosis (p < 0.01) in LUAD cells. Dual-luciferase reporter assays confirmed WWC2 as a direct target of miR-589-3p, with miR-589-3p mimics significantly reducing WWC2 wild-type reporter activity (p < 0.05). WWC2 expression was significantly downregulated in LUAD tissues (p < 0.05), and WWC2 knockdown reversed the anti-proliferative, pro-apoptotic, and anti-invasive effects induced by miR-589-3p inhibition (p < 0.01). These findings demonstrate that miR-589-3p promotes lung adenocarcinoma progression by directly suppressing WWC2. The miR-589-3p/WWC2 axis represents a novel molecular mechanism contributing to LUAD malignancy and may provide a foundation for future mechanistic and translational studies. Full article
(This article belongs to the Section Cancer Biomarkers)
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11 pages, 972 KB  
Article
Immune Aging Within the Tumor Microenvironment Predicts Survival in Lung Adenocarcinoma
by Taeyun Kim, Hyunji Choi, Tae Won Jang and Chul-Ho Oak
Cancers 2026, 18(9), 1343; https://doi.org/10.3390/cancers18091343 - 23 Apr 2026
Viewed by 394
Abstract
Background/Objectives: Immune aging has been associated with survival outcomes in patients with lung adenocarcinoma (LUAD), but its relevance within the tumor microenvironment (TME) remains unclear. Methods: Clinical, RNA-sequencing, and somatic mutation data from the TCGA LUAD cohort were analyzed. Immune aging [...] Read more.
Background/Objectives: Immune aging has been associated with survival outcomes in patients with lung adenocarcinoma (LUAD), but its relevance within the tumor microenvironment (TME) remains unclear. Methods: Clinical, RNA-sequencing, and somatic mutation data from the TCGA LUAD cohort were analyzed. Immune aging score within the TME was quantified using a predefined blood-driven 121-gene immune aging signature (IAS-121), and patients were categorized into the lowest versus the highest IAS-121 tertiles. Immune cell composition in the TME was inferred using xCell. Overall survival (OS) was evaluated using Kaplan–Meier analysis, Cox proportional hazards models adjusted for age, sex, tumor stage, smoking status, and EGFR mutation status, and restricted cubic spline analysis to examine the dose–response relationship between IAS-121 and mortality risk. Sensitivity analyses comparing the highest versus lowest quartiles or higher than median versus lower than median of IAS-121 were performed. Two independent LUAD cohorts (GSE68465 and GSE50081) were employed for validation. Results: A total of 518 patients with LUAD from the TCGA cohort were analyzed. Restricted cubic spline analysis showed a linear association between IAS-121 and OS. Patients in the highest IAS-121 tertile showed significantly better survival than those in the lowest tertile in both the TCGA cohort (p < 0.001) and the external validation cohorts (p = 0.003). In multivariable-adjusted Cox models, the lowest IAS-121 tertile was associated with worse survival in TCGA (adjusted HR 1.87, 95% CI 1.20–2.92) and in the pooled external cohorts (adjusted HR 1.57, 95% CI 1.02–2.43). Subgroup analyses showed generally consistent associations across clinical strata. Tumors with higher IAS-121 exhibited lower CD8+ and CD4+ naïve T-cell enrichment but higher neutrophil infiltration. Conclusions: Immune aging within TME is associated with poorer survival in LUAD. Given this study is hypothesis-generating, further investigations integrating tissue- and blood-based measures of immune aging are warranted to clarify its clinical and biological implications. Full article
(This article belongs to the Special Issue Lung Cancer: Diagnosis and Targeted Therapy)
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26 pages, 6646 KB  
Article
Comprehensive Pan-Cancer Analysis Identifies POFUT1 as a Prognostic Biomarker and Potential Therapeutic Target Associated with Immune Evasions
by Zakir Ullah, Xiaosong Pei, Perbhat Ali, Ikram Ullah, Yaqi Li and Shuai Liu
Cancers 2026, 18(9), 1342; https://doi.org/10.3390/cancers18091342 - 23 Apr 2026
Viewed by 499
Abstract
Background: Aberrant protein O-fucosylation mediated by protein O-fucosyltransferase 1 (POFUT1), has emerged as a hallmark of tumorigenesis that regulates key signaling pathways, including Notch, which is frequently dysregulated in cancers. Protein O-fucosylation, catalyzed by POFUT1, regulates Notch signaling and has been implicated in [...] Read more.
Background: Aberrant protein O-fucosylation mediated by protein O-fucosyltransferase 1 (POFUT1), has emerged as a hallmark of tumorigenesis that regulates key signaling pathways, including Notch, which is frequently dysregulated in cancers. Protein O-fucosylation, catalyzed by POFUT1, regulates Notch signaling and has been implicated in individual cancers, but its pan-cancer expression patterns, clinical significance, and relationship to tumor immunity remain incompletely characterized. Methodology: We conducted a multi-omics bioinformatics analysis using TCGA and other public datasets to evaluate POFUT1 expression across 33 cancer types (n > 10,000). Differential expressions, tumor stage correlations, and survival outcomes were assessed. Immune cell infiltration was estimated using SangerBox and TIMER algorithms, while promoter methylation patterns were analyzed through UALCAN. Functional enrichment and protein–protein interaction networks were constructed to elucidate functional mechanism. Western blot validation in prostate and ovarian cancer cell lines confirmed our computational analysis. Results: POFUT1 showed significant overexpression in 16 of 33 cancer types (FDR-adjusted p < 0.05), with the highest elevation in BRCA (breast invasive carcinoma; log2FC = 2.31) and LUAD (lung adenocarcinoma; log2FC = 2.1). A high POFUT1 expression correlated with poor overall survival in eight cancer types (HR range: 1.8–3.2, p < 0.01) and disease-free survival in seven cancers. POFUT1 levels positively correlated with myeloid-derived suppressor cells (MDSCs) infiltrating in 15 cancer types, while inversely correlated with natural killer T (NKT) cells presence in 15 cancers (mean R = −0.34, p < 0.05), indicating an association with immunosuppressive microenvironments. Promoter hypomethylation in tumors suggested epigenetic dysregulation as a potential driver of its overexpression. Western blot analysis confirmed POFUT1 protein upregulations in prostate and ovarian cancer cell lines (1.7–2.1-fold. p < 0.01), corroborating transcriptomic findings. Conclusion: This pan-cancer study establishes POFUT1 as a critical oncogenic factor linked to aggressive disease, immune evasion, and poor prognosis. Its consistent overexpression and functional impact highlight its potential as a biomarker and target for anticancer therapy. While these computational findings require experimental validation, POFUT1 emerges as a candidate biomarker warranting functional studies and potential therapeutic targeting. Full article
(This article belongs to the Special Issue Advancements in “Cancer Biomarkers” for 2025–2026)
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22 pages, 12097 KB  
Article
Integrative Analysis of Cellular Senescence-Related Genes Identifies FOLR1 as a Novel Tumor Suppressor and a Potential Therapeutic Target in Lung Adenocarcinoma
by Fei Wang, Chang Xie, Min Zhang, Xiangyang Wu, Xinqi Sun, Yan Li and Zhibing Ming
Cancers 2026, 18(9), 1330; https://doi.org/10.3390/cancers18091330 - 22 Apr 2026
Viewed by 250
Abstract
Background: Cellular senescence is a key regulatory mechanism in tumor initiation and progression, influencing cancer development through modulation of the cell cycle, the immune microenvironment, and inflammatory responses. However, the molecular characteristics and potential clinical value of senescence-related genes in lung adenocarcinoma (LUAD) [...] Read more.
Background: Cellular senescence is a key regulatory mechanism in tumor initiation and progression, influencing cancer development through modulation of the cell cycle, the immune microenvironment, and inflammatory responses. However, the molecular characteristics and potential clinical value of senescence-related genes in lung adenocarcinoma (LUAD) have not been systematically elucidated. This study aimed to comprehensively characterize the expression patterns, molecular subtypes, and prognostic significance of cellular senescence-related genes in LUAD, and to identify key regulatory determinants. Methods: Transcriptomic data of cellular senescence-related genes were obtained from The Cancer Genome Atlas (TCGA) cohort, and integrated analyses were performed to characterize their mutational landscape, copy number variations, and differential expression profiles. Senescence-related molecular subtypes were established using consensus clustering, followed by gene set variation analysis (GSVA) for pathway enrichment and immune infiltration analyses. A prognostic risk model was subsequently constructed using LASSO-penalized Cox regression, and its predictive performance was systematically evaluated. Candidate key regulators were further prioritized through bioinformatic screening, identifying FOLR1 as a hub gene. The biological function of FOLR1 was validated by qRT–PCR, Western blotting, assessment in clinical specimens, and a subcutaneous xenograft tumor model in mice. Results: Cellular senescence-related genes in LUAD exhibited a high frequency of somatic mutations and copy number alterations, accompanied by marked transcriptional dysregulation. Based on the expression profiles of these genes, LUAD patients could be stratified into three distinct molecular subtypes with significantly different clinical outcomes. These subtypes displayed pronounced heterogeneity in pathway enrichment patterns and immune cell infiltration. The subsequently developed prognostic signature demonstrated robust predictive performance in both the training and validation cohorts. Functional assays showed that FOLR1 was significantly downregulated in LUAD tissues and cell lines; FOLR1 knockdown promoted tumor cell proliferation, whereas restoration of its expression or pharmacological intervention markedly suppressed tumor progression. Consistently, in vivo xenograft experiments further corroborated the tumor-suppressive role of FOLR1 in lung adenocarcinoma. Conclusions: This study systematically delineated the molecular landscape of cellular senescence-related genes in LUAD and elucidated their associations with the tumor immune microenvironment and patient prognosis. Moreover, FOLR1 was identified as a potential tumor suppressor and therapeutic target. These findings provide a theoretical basis for senescence-informed molecular stratification and the development of precision treatment strategies in lung adenocarcinoma. Full article
(This article belongs to the Section Molecular Cancer Biology)
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27 pages, 6337 KB  
Article
Integrated Characterization of AP-2δ Reveals Distinct Regulatory Architecture in Lung Adenocarcinoma and Lung Squamous Cell Carcinoma
by Damian Kołat, Weronika Kruczkowska, Żaneta Kałuzińska-Kołat, Cromwel Tepap Zemnou, Mateusz Kciuk, Lin-Yong Zhao, Renata Kontek and Elżbieta Płuciennik
Cancers 2026, 18(8), 1278; https://doi.org/10.3390/cancers18081278 - 17 Apr 2026
Viewed by 384
Abstract
Background/Objectives: AP-2δ, encoded by TFAP2D, is one of the least characterized members of the AP-2 transcription factor family, although available evidence suggests biologically relevant roles in lung cancer that have not yet been thoroughly examined. The aim of the present study [...] Read more.
Background/Objectives: AP-2δ, encoded by TFAP2D, is one of the least characterized members of the AP-2 transcription factor family, although available evidence suggests biologically relevant roles in lung cancer that have not yet been thoroughly examined. The aim of the present study was to provide an integrated characterization of AP-2δ/TFAP2D in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). Methods: LUAD and LUSC data were obtained from The Cancer Genome Atlas. The analysis comprised the expression profiling of AP-2δ target genes, survival-guided TFAP2D stratification, clinical profiling, differential expression and intersection analyses, methylation-derived chromatin compartment profiling, TFAP2D-associated cofactor rewiring, and genome-wide enrichment of AP-2δ targets. In parallel, pocket prioritization was performed using an AlphaFold model of AP-2δ with cross-tool consensus mapping. Results: TFAP2D stratification delineated biologically-distinct states in both histological subtypes (LUAD and LUSC). AP-2δ target genes showed subtype-specific expression patterns and functional organization. The consistent survival association was observed for progression-free interval rather than uniformly across all endpoints. Clinical profiling was more closely associated with molecular subtype composition than broad clinicopathological differences. Differential expression analyses identified both shared and histology-dependent programs associated with TFAP2D. In the chromatin-compartment analysis, LUSC showed a broader and more coherent footprint, whereas LUAD displayed more selective cofactor rewiring. Structure-based analysis prioritized a small set of reproducible candidate pockets concentrated within ordered regions of the TF_AP-2 domain. Conclusions: AP-2δ marks biologically meaningful but histologically non-uniform regulatory states in lung cancer. These findings provide an integrated framework for understanding TFAP2D-dependent regulation in LUAD and LUSC, highlighting AP-2δ as a candidate for future mechanistic and translational investigation. Full article
(This article belongs to the Special Issue Computational Methods for Integrative Cancer Data Analysis)
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24 pages, 3150 KB  
Article
Molecular Links Between Smoking, COPD, and Lung Cancer: A DNA Methylation Perspective
by Camila Bernal Forigua, Litzy Gisella Bermúdez, Alejandra Cañas Arboleda, Rafael R. Ariza, Maria Teresa Roldán, Maria Teresa Morales, Daniel Mauricio González Cubides and Adriana Rojas
Cancers 2026, 18(8), 1273; https://doi.org/10.3390/cancers18081273 - 17 Apr 2026
Viewed by 621
Abstract
Background: DNA methylation alterations represent a key epigenetic mechanism linking environmental exposures to disease pathogenesis. The present study aimed to identify differentially methylated genes and shared biological processes associated with lung cancer (LuCa), chronic obstructive pulmonary disease (COPD) and tobacco exposure. Methods: A [...] Read more.
Background: DNA methylation alterations represent a key epigenetic mechanism linking environmental exposures to disease pathogenesis. The present study aimed to identify differentially methylated genes and shared biological processes associated with lung cancer (LuCa), chronic obstructive pulmonary disease (COPD) and tobacco exposure. Methods: A comprehensive literature search was performed in PubMed to identify studies evaluating DNA methylation in LuCa, COPD and smoking-related models. A total of 117 articles were selected, including 83 studies on lung cancer, 18 on COPD and 16 on smoking exposure. Genes exhibiting statistically significant methylation changes relative to controls were extracted from each study. To provide additional support for these findings, differential methylation signatures were further evaluated using The Cancer Genome Atlas (TCGA) lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) datasets. Functional and transcription factor motif enrichment analyses were subsequently conducted to identify shared biological pathways and regulatory mechanisms. Results: In total, 324 genes displaying altered methylation patterns across these conditions were identified. Seven tumor suppressor genes (CDKN2A, CDH13, MGMT, MIR137, DAPK1, RARB, and RASSF1A) consistently exhibited hypermethylation in both lung cancer and in association with smoking exposure. In addition, AHRR hypomethylation emerged as a shared epigenetic hallmark across all three conditions. TCGA-based analyses confirmed several of these methylation patterns and revealed subtype-specific methylation profiles associated with smoking history. Functional enrichment highlighted common biological processes and signaling pathways, particularly those related to transcriptional regulation, apoptosis and cancer-associated pathways. Conclusions: These results provide an integrative overview of shared DNA methylation alterations associated with smoking exposure, COPD, and lung cancer, and suggest potential DNA methylation candidates that may be relevant for future biomarker development and mechanistic studies. Full article
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8 pages, 766 KB  
Case Report
Acquired Resistance to Afatinib Mediated by EGFR T790M in Lung Adenocarcinoma Patients Harboring EGFR-KDD: A Case Report and Literature Review
by Qian Liu, Lu Lv, Guanchao Pang and Pingli Wang
Curr. Oncol. 2026, 33(4), 214; https://doi.org/10.3390/curroncol33040214 - 14 Apr 2026
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Abstract
Epidermal growth factor receptor (EGFR)-kinase domain duplication (KDD) represents an atypical mutation distinct from classical EGFR mutations in lung adenocarcinoma (LUAD). Although first- and second-generation EGFR-tyrosine kinase inhibitors (TKIs) have demonstrated clinical activity in EGFR-KDD, the mechanisms of acquired resistance in this setting [...] Read more.
Epidermal growth factor receptor (EGFR)-kinase domain duplication (KDD) represents an atypical mutation distinct from classical EGFR mutations in lung adenocarcinoma (LUAD). Although first- and second-generation EGFR-tyrosine kinase inhibitors (TKIs) have demonstrated clinical activity in EGFR-KDD, the mechanisms of acquired resistance in this setting remain poorly characterized. Herein, we present a LUAD patient with EGFR-KDD who achieved a sustained initial response to afatinib lasting 67 months before developing acquired resistance. Re-biopsy with next-generation sequencing (NGS) uncovered EGFR T790M, accompanied by EGFR amplification and EGFR M766T. The patient was switched to firmonertinib, with subsequent tumor regression. We reviewed published EGFR-KDD cases that had both acquired resistance to first- or second-generation EGFR-TKIs and corresponding repeat biopsy findings. Five of the eleven cases harbored EGFR T790M, yielding a prevalence of 45%, which is similar to that seen in classical EGFR mutations. This case suggests that EGFR T790M mediates acquired resistance to first- and second-generation EGFR-TKIs in EGFR-KDD, mirroring the resistance pattern observed in classical EGFR mutations. Full article
(This article belongs to the Section Thoracic Oncology)
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Article
Segmentectomy Versus Lobectomy in Patients with Stage IA Lung Adenocarcinoma: Long-Term Survival in a Propensity Score-Matched Cohort
by Zhangfeng Huang, Tenglong Luo, Zuhan Geng, Qi Gao and Yongde Liao
Cancers 2026, 18(8), 1202; https://doi.org/10.3390/cancers18081202 - 9 Apr 2026
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Abstract
Background: Whether there are differences in clinical outcomes between segmentectomy and lobectomy in patients with early-stage lung adenocarcinoma (LUAD) remains uncertain. This study aimed to compare all-cause mortality and lung cancer-specific mortality in patients with lung tumors ≤ 20 mm undergoing these [...] Read more.
Background: Whether there are differences in clinical outcomes between segmentectomy and lobectomy in patients with early-stage lung adenocarcinoma (LUAD) remains uncertain. This study aimed to compare all-cause mortality and lung cancer-specific mortality in patients with lung tumors ≤ 20 mm undergoing these two procedures. Methods: Patients with stage IA lung adenocarcinoma (≤20 mm) who underwent segmentectomy or lobectomy were identified from the SEER database (2008–2022). Propensity score matching (PSM) was applied to balance baseline characteristics. Kaplan–Meier curves depicted overall survival and lung cancer-specific survival. Multivariable Cox proportional hazards models were used to evaluate associations between surgical procedures and mortality, reporting hazard ratios (HRs) with 95% confidence intervals (CIs). Results: Among 9641 patients, 1065 (11.0%) underwent segmentectomy. After 1:1 PSM, 2028 patients had well-balanced covariates. The median follow-up was 43.0 months. In the lobectomy group, 158 all-cause deaths (35.1 per 1000 person-years) and 66 lung cancer-specific deaths (14.7 per 1000 person-years) occurred, compared with 176 and 80 events in the segmentectomy group (39.9 and 18.1 per 1000 person-years, respectively). Multivariable Cox regression demonstrated that segmentectomy, compared with lobectomy, was not associated with a higher risk of all-cause mortality (adjusted HR [aHR], 1.07, 95% CI 0.86–1.34) or lung cancer-specific mortality (aHR, 1.18, 95% CI 0.84–1.64). The results were consistent across tumor differentiation subgroups. Conclusions: Among patients with early-stage (≤20 mm) LUAD, segmentectomy was not associated with an increased risk of all-cause or lung cancer-specific mortality compared with lobectomy. Further studies with larger sample sizes are warranted to validate these findings. Full article
(This article belongs to the Special Issue Advances in Thoracic Oncology Research)
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