Efficacy of Crizotinib for Advanced ALK-Rearranged Non-Small-Cell Lung Cancer Patients with Brain Metastasis: A Multicenter, Retrospective Study in China

NPM3 as an Unfavorable Prognostic Biomarker Involved in Oncogenic Pathways of Lung Adenocarcinoma via MYC Translational Activation

BACKGROUND

The nucleoplasmin/nucleophosmin (NPM) family was previously regarded as a critical regulator during disease development, and its mediation in carcinogenesis has achieved intensive attention recently. However, the clinical importance and functional mechanism of NPM3 in lung adenocarcinoma (LUAD) have not been reported yet.

OBJECTIVE

This study aimed to investigate the role and clinical significance of NPM3 in the development and progression of LUAD, including the underlying mechanisms.

METHODS

The expression of NPM3 in pan-cancer was analyzed via GEPIA. The effect of NPM3 on prognosis was analyzed by the Kaplan-Meier plotter and the PrognoScan database. In vitro, cell transfection, RT-qPCR, CCK-8 assay, and wound healing assay were employed to examine the role of NPM3 in A549 and H1299 cells. Gene set enrichment analysis (GSEA) was performed using the R software package to analyze the tumor hallmark pathway and KEGG pathway of NPM3. The transcription factors of NPM3 were predicted based on the ChIP-Atlas database. Dual-luciferase reporter assay was applied to verify the transcriptional regulatory factor of the NPM3 promoter region.

RESULTS

The NPM3 expression was found to be markedly higher in the LUAD tumor group than the normal group and to be positively correlated with poor prognosis, tumor stages, and radiation therapy. In vitro, the knockdown of NPM3 greatly inhibited the proliferation and migration of A549 and H1299 cells. Mechanistically, GSEA predicted that NPM3 activated the oncogenic pathways. Further, the NPM3 expression was found to be positively correlated with cell cycle, DNA replication, G2M checkpoint, HYPOXIA, MTORC1 signaling, glycolysis, and MYC targets. Besides, MYC targeted the promoter region of NPM3 and contributed to the enhanced expression of NPM3 in LUAD.

CONCLUSION

The overexpression of NPM3 is an unfavorable prognostic biomarker participating in oncogenic pathways of LUAD via MYC translational activation and it contributes to tumor progression. Thus, NPM3 could be a novel target for LUAD therapy.

A ferroptosis-related LncRNAs signature for predicting prognoses and screening potential therapeutic drugs in patients with lung adenocarcinoma: A retrospective study

BACKGROUND

Lung adenocarcinoma (LUAD) has a high mortality rate. Ferroptosis is linked to tumor initiation and progression.

AIMS

This study aims to develop prognostic models of ferroptosis-related lncRNAs, evaluate the correlation between differentially expressed genes and tumor microenvironment, and identify prospective drugs for managing LUAD.

METHODS AND RESULTS

In this study, transcriptomic and clinical data were downloaded from the TCGA database, and ferroptosis-related genes were obtained from the FerrDb database. Through correlation analysis, Cox analysis, and the LASSO algorithm for constructing a prognostic model, we found that ferroptosis-related lncRNA-based gene signatures (FLncSig) had a strong prognostic predicting ability in the LUAD patients. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichments reconfirmed that ferroptosis is related to receptor-ligand activity, enzyme inhibitor activity, and the IL-17 signaling pathway. Next, tumor mutation burden (TMB), tumor immune dysfunction and exclusion (TIDE) algorithms, and pRRophetic were used to predict immunotherapy response and chemotherapy sensitivity. The IMvigor210 cohort was also used to validate the prognostic model. In the tumor microenvironment, Type_II_IFN_Response and HLA were found to be a group of low-risk pathways, while MHC_class_I was a group of high-risk pathways. Patients in the high-risk subgroup had lower TIDE scores. Exclusion, MDSC, CAF, and TAMM2 were significantly and positively correlated with risk scores. In addition, we found 15 potential therapeutic drugs for LUAD. Finally, differential analysis of stemness index based on mRNA expression (mRNAsi) indicated that mRNAsi was correlated with gender, primary tumor (T), distant metastasis (M), and the tumor, node, and metastasis (TNM) stage in LUAD patients.

CONCLUSIONS

In conclusion, the prognostic model based on FLncSig can alleviate the difficulty in predicting the prognosis and immunotherapy of LUAD patients. The identified FLncSig and the screened drugs exhibit potential for clinical application and provide references for the treatment of LUAD.

Molecular subtypes of lung adenocarcinoma patients for prognosis and therapeutic response prediction with machine learning on 13 programmed cell death patterns

BACKGROUND

Lung adenocarcinoma (LUAD) seriously threatens people's health worldwide. Programmed cell death (PCD) plays a critical role in regulating LUAD growth and metastasis as well as in therapeutic response. However, currently, there is a lack of integrative analysis of PCD-related signatures of LUAD for accurate prediction of prognosis and therapeutic response.

METHODS

The bulk transcriptome and clinical information of LUAD were obtained from TCGA and GEO databases. A total of 1382 genes involved in regulating 13 various PCD patterns (apoptosis, necroptosis, pyroptosis, ferroptosis, cuproptosis, netotic cell death, entotic cell death, lysosome-dependent cell death, parthanatos, autophagy-dependent cell death, oxeiptosis, alkaliptosis and disulfidptosis) were included in the study. Weighted gene co-expression network analysis (WGCNA) and differential expression analysis were performed to identify PCD-associated differential expression genes (DEGs). An unsupervised consensus clustering algorithm was used to explore the potential subtypes of LUAD based on the expression profiles of PCD-associated DEGs. Univariate Cox regression analysis, Least Absolute Shrinkage and Selection Operator (LASSO) regression, Random Forest (RF) analysis and stepwise multivariate Cox analysis were performed to construct a prognostic gene signature. The "oncoPredict" algorithm was utilized for drug-sensitive analysis. GSVA and GSEA were utilized to perform function enrichment analysis. MCPcounter, quanTIseq, Xcell and ssGSEA algorithms were used for tumor immune microenvironment analysis. A nomogram incorporating PCDI and clinicopathological characteristics was established to predict the prognosis of LUAD patients.

RESULTS

Forty PCD-associated DEGs related to LUAD were obtained by WGCNA analysis and differential expression analysis, followed by unsupervised clustering to identify two LUAD molecular subtypes. A programmed cell death index (PCDI) with a five-gene signature was established by machine learning algorithms. LUAD patients were then divided into a high PCDI group and a low PCDI group using the median PCDI as a cutoff. Survival and therapeutic analysis revealed that the high PCDI group had a poor prognosis and was more sensitive to targeted drugs but less sensitive to immunotherapy compared to the low PCDI group. Further enrichment analysis showed that B cell-related pathways were significantly downregulated in the high PCDI group. Accordingly, the decreased tumor immune cell infiltration and the lower tumor tertiary lymphoid structure (TLS) scores were also found in the high PCDI group. Finally, a nomogram with reliable predictive performance PCDI was constructed by incorporating PCDI and clinicopathological characteristics, and a user-friendly online website was established for clinical reference ( https://nomogramiv.shinyapps.io/NomogramPCDI/ ).

CONCLUSION

We performed the first comprehensive analysis of the clinical relevance of genes regulating 13 PCD patterns in LUAD and identified two LUAD molecular subtypes with distinct PCD-related gene signature which indicated differential prognosis and treatment sensitivity. Our study provided a new index to predict the efficacy of therapeutic interventions and the prognosis of LUAD patients for guiding personalized treatments.

Molecular Characterization and Prognosis of Lactate-Related Genes in Lung Adenocarcinoma

Objective: To explore the lactate-related genes (LRGs) in lung adenocarcinoma (LUAD) by various methods, construct a prognostic model, and explore the relationship between lactate subtypes and the immune tumor microenvironment (TME). Methods: 24 LRGs were collected. The mutation landscape and the prognosis value of LRGs were explored by using The Cancer Genome Atlas (TCGA) data. Consensus clustering analysis was used for different lactate subtype identification. Based on the lactate subtypes, we explore the landscape of TME cell infiltration. A risk-score was calculated by using the LASSO-Cox analysis. A quantitative real-time PCR assay was utilized to validate the expression of characteristic genes in clinical cancer tissues and paracarinoma tissues from LUAD patients. Results: Comparing the normal samples, 18 LRGs were differentially expressed in tumor samples, which revealed that the differential expression of LRGs may be related to Copy Number Variation (CNV) alterations. The two distinct lactate subtypes were defined. Compared to patients in the LRGcluster A group, LUAD patients in the LRGcluster B group achieved better survival. The prognostic model was constructed based on differentially expressed genes (DEGs) via the LASSO-Cox analysis, which showed the accuracy of predicting the prognosis of LUAD patients using the ROC curve. A high-risk score was related to a high immune score, stromal score, and tumor mutation burden (TMB). Patients had better OS with low risk compared with those with high risk. The sensitivities of different risk groups to chemotherapeutic drugs were explored. Finally, the expression of characteristic genes in clinical cancer tissues and paracarinoma tissues from LUAD patients was verified via qRT-PCR. Conclusions: The lactate subtypes were independent prognostic biomarkers in LUAD. Additionally, the difference in the lactate subtypes was an indispensable feature for the individual TME. The comprehensive evaluation of the lactate subtypes in the single tumor would help us to understand the infiltration characteristics of TME and guide immunotherapy strategies.

Real-world treatment and prognostic factors for survival in ALK+ non-small cell lung cancer (NSCLC) patients with brain metastases in China

BACKGROUND

To explore the efficacy and prognostic factors of different treatment modalities on anaplastic lymphoma kinase (ALK)+ non-small cell lung cancer (NSCLC) patients with brain metastases (BMs).

METHODS

A total of 86 patients were enrolled into the study. They were divided into two cohorts based on their history of treatment with ALK tyrosine kinase inhibitors (ALK-TKIs) prior to the incidence of BMs. ALK-TKI-naïve patients with BMs were included in cohort 1 (n = 59); patients who developed BMs after ALK-TKIs treatment were enrolled in cohort 2 (n = 27). Prognostic factors related with overall survival (OS) when treated with ALK-TKIs were assessed in multivariable analysis.

RESULTS

With a median follow-up of 41.8 months, the median OS was 34.8 months. In cohort 1, the OS, intracranial progression-free survival (iPFS), and progression-free survival (PFS) were 38.7 months (95% CI: 23.3 to 54.1), 18.5 months (95% CI: 9.6 to 27.4), and 19.1 months (95% CI: 13.7 to 24.5), respectively. Significantly improved OS and iPFS were noted in those patients in which second-generation ALK-TKIs versus crizotinib were initiated (OS: not reached vs. 29.0 months, p = 0.040; iPFS: 22.8 vs. 11.9 months, p = 0.035). In cohort 2, patients who experienced BMs as a result of the treatment failure of ALK-TKIs had a median OS of 27.1 months. Considerable duration of stable disease in patients with measurable BMs was observed (iPFS: 11.5 months, 95% CI: 4.4 to 18.6; PFS: 12.2 months, 95% CI: 3.2 to 21.1).

CONCLUSION

Second-generation ALK-TKIs further improved the duration of intracranial response and survival in ALK+ NSCLC patients with BMs in a real-world setting. The potent intracranial efficacy of second-generation ALK-TKIs might generate the lowered urgency of local treatment.

Identification of cuproptosis-related gene signature to predict prognosis in lung adenocarcinoma

Background: Studies have reported that coppers are involved in the tumorigenesis and development of tumor. In herein, we aimed to construct a prognostic classification system for lung adenocarcinoma (LUAD) associated with cuproptosis.

Methods: Samples information of LUAD were acquired from The Cancer Genome Atlas (TCGA) and GSE31210 dataset. Cuproptosis-related genes were screened from previous research. ConsensusClusterPlus was applied to determine molecular subtypes, which evaluated by genome analysis, tumor immune microenvironment analysis, immunotherapy, functional enrichment analysis. Furthermore, univariate Cox analysis combined with Lasso analysis were employed to construct a cuproptosis-related risk model for LUAD.

Results: 14 genes related to cuproptosis phenotype were identified, and 2 clusters (C1 and C2) were determined. Among which, C1 had better survival outcome, less advanced stages, enhanced immune infiltration and enriched in TCA related pathways. A 7 cuproptosis-associated genes risk model was constructed, and the performance was verified in the GSE31210 dataset. A higher RiskScore was significantly correlated with worse overall survival, advanced stages. Cox survival analysis showed that RiskScore was an independent predictor. High-risk group patients had weakened immune infiltration, less likely to benefit from immunotherapy and was more sensitived to immunotherapy.

Conclusion: The cuproptosis-related gene signature could serve as potential prognostic predictors for LUAD patients and may provide clues for the intervention of cuproptosis induced harm and targeted anti-tumor application.

Mechanism of Shishiwei Wendan Decoction in the Prevention and Treatment of Lung Adenocarcinoma Using Network Pharmacology and Molecular Docking

Objective

This study used network pharmacology and molecular docking technology to elucidate the mechanism of action of Shishiwei Wendan Decoction against lung adenocarcinoma.

Methods

By using the world's largest TCM System Pharmacology Database and Analysis Technology Platform (TCMSP) system to conduct in-depth mining analysis and data collection of the main active components of the medicinal components in Shishiwei Wendan Decoction and using the human gene card database (GeneCards), Human Mendelian Inheritance Online System (OMIM), and Human Disease-Related Gene and Mutation Information Database (DisGeNET) to collect the pathogenic targets of lung adenocarcinoma and build a PPI network; for the core drug targets, use GO enrichment analysis and KEGG pathway analysis; use Cytoscape software to build relevant network maps; and use AutoDock to achieve molecular docking.

Results

Shishiwei Wendan Decoction screened 144 active ingredients and 384 drug targets; 7680 lung adenocarcinoma disease targets were obtained, including 380 targets for Shishiwei Wendan Decoction in the treatment of lung adenocarcinoma. GO enrichment analysis demonstrated 2,299 downstream genes, and key target genes were closely related to nutrient levels, membrane rafts, and protein serine/threonine kinase activity; KEGG functional enrichment analysis yielded 179 related pathways, including tumor necrosis factor signaling pathway which is related to the target gene. Molecular docking showed that the core active ingredients and key targets could be well combined.

Conclusion

Through the network pharmacology analysis and molecular docking experiments of Shishiwei Wendan Decoction against lung adenocarcinoma, it is found that Shishiwei Wendan Decoction has multidimensional effects on the treatment of lung adenocarcinoma, and it is the first Shiwei Wendan Decoction to treat lung adenocarcinoma. Decoction in the treatment of lung adenocarcinoma provides biointellectual support and the oretical support.

Construction of a lung adenocarcinoma prognostic model based on N6-methyl-adenosine-related long noncoding RNA and screening of potential drugs based on this model

Lung adenocarcinoma (LUAD) has a high mortality rate. N6-methyl-adenosine (m6A)-related long noncoding RNA (lncRNA) is associated with tumor prognosis. Our objective was to construct an m6A-related lncRNA prognostic model and screen potential drugs for the treatment of LUAD. The LUAD sequencing data were randomly divided into Train and Test cohorts. In the Train group, the LASSO Cox regression was used to construct the m6A-related lncRNA prognostic model. The LUAD tumor immune dysfunction and exclusion model was used to evaluate immunotherapy efficacy in LUAD. The 'pRRophetic' package was utilized to screen potential drugs for the treatment of LUAD. Eleven m6A-related lncRNAs were identified by LASSO Cox regression and were used to construct the risk model to calculate sample risk scores. Patients were divided into high- and low-risk groups based on their median risk scores. The LUAD data of The Cancer Genome Atlas database showed that the overall survival (OS) of the high-risk group was significantly lower than that of the low-risk group in both cohorts. Multivariate Cox regression analysis showed that this risk model could serve as an independent prognostic factor of LUAD, and receiver operating characteristic curves suggested that m6A-related lncRNA prognostic signature has a good ability in predicting OS. Finally, nine potential drugs for LUAD treatment were screened based on this prognostic model. The prognostic model constructed based on the m6A-related lncRNAs facilitated prognosis prediction in LUAD patients. The screened therapeutic agents have potential application values and provide a reference for the clinical treatment of LUAD.

Real World Experience of Crizotinib in 104 Patients With ALK Rearrangement Non-small-cell Lung Cancer in a Single Chinese Cancer Center

Purpose: Our study aimed to provide data on effectiveness, safety of crizotinib treatment, brain metastases, progression patterns, and sequential therapy beyond crizotinib treatment in patients with advanced ALK-positive NSCLC in China.

Methods: We reviewed the medical records of crizotinib-treated NSCLC patients with ALK-rearrangement between May 2014 and May 2018 at Fudan University Shanghai Cancer Center. All patients received crizotinib with 250 mg twice daily. Main outcome measures were progression-free survival (PFS), objective response rate (ORR), disease control rate (DCR), the second PFS (PFS2), overall survival (OS), and adverse events.

Results: One hundred and four patients with ALK-positive NSCLC were included in this retrospective study. ORR and DCR were 82.7 and 98.1%, respectively. The estimated PFS and OS were 13.0 months (95% CI 9.0–17.0 months) and 36.0 months (95% CI 31.0–41.0 months), respectively. Multivariable analysis showed that young age, presence of baseline adrenal gland metastases and non-adenocarcinoma were independent predictive factors for poorer PFS. Presence of baseline adrenal gland metastases, non-adenocarcinoma, intrathoracic progression and shorter crizotinib treatment time were associated with worse OS. Patients without baseline brain metastases (BBM) who were administered with crizotinib as first-line therapy can achieve a significantly longer PFS than those who received crizotinib as second or later line therapy (p = 0.006). For patients with BBM receiving sequential therapy beyond the first disease progression after crizotinib treatment (1st PD), crizotinib beyond progressive disease (CBPD) plus local therapy can lead to a significantly longer PFS2 (67.0 vs. 21.0 weeks; p = 0.046). Additionally, the OS was significantly longer in patients achieving 1st PD who received CBPD plus local therapy than those who did not receive CBPD or local therapy (35.0 vs. 24.0 months, p = 0.041). Presence of brain metastases at any time was in association with worse PFS. No unexpected adverse effects were reported.

Conclusions: Crizotinib was effective and well tolerated in Chinese patients with ALK-positive, advanced NSCLC in real-world clinical practice. For patients without BBM, crizotinib as first-line therapy can lead to a longer PFS than second-or later line therapy. CBPD plus local therapy after 1st PD beyond crizotinib is feasible and effective in clinical routine practice.