Comprehensive Molecular Characterizations of Chinese Patients With Different Subtypes of Lung Squamous Cell Carcinoma

Integrative machine learning model for subtype identification and prognostic prediction in lung squamous cell carcinoma

BACKGROUND

Lung squamous cell carcinoma (LUSC) is a leading cause of cancer-related mortality, and tumor heterogeneity could result in diverse prognostic subtypes. Traditional prognostic factors, like tumor, node, and metastasis (TNM) staging, offer limited predictive accuracy. This study aims to identify LUSC subtypes and develop predictive models that have the potential to improve prognosis prediction accuracy and support personalized treatment.

METHODS

Expression and clinical data were collected from three datasets. One dataset (TCGA-LUSC) was used as a training set, while the others (GSE30219 and GSE73403) were independent testing sets. Unsupervised clustering was applied to the training set to identify LUSC subtypes. The relationship between survival outcomes and these identified subtypes was validated in the testing sets using binary machine learning models and survival curve analysis. The impact of chemotherapy on the prognosis for subtypes was also presented. Subsequently, four survival machine learning models were developed to predict LUSC prognosis. These models were validated in the testing sets and integrated into an online tool to assist in survival prediction.

RESULTS

Two subtypes, C1 and C2, were identified in the training set. The C1 subtype was associated with poorer survival outcomes and was enriched in cancer-associated fibroblasts and macrophages. In contrast, the C2 subtype correlated with better outcomes and was enriched in CD8 + T cells. Regarding chemotherapy, the C2 subtype with chemotherapy showed the best survival outcomes compared to other groups. A 9-gene signature was derived from the model's importance values for subtype prediction and included TGM2, AOC3, TBXA2R, RGS3, DLC1, MMP19, ACVRL1, TCF21, and TIMP3. This signature outperformed 14 published signatures and clinical variables at survival prediction with the highest time-dependent AUC (tdAUC) and concordance index (C-index). Four machine learning models were developed using this signature, achieving tdAUC values of 0.712 and 0.684 and C-index values of 0.682 and 0.625 in the independent testing sets. An online tool for predicting survival probabilities for LUSC patients up to 10 years post-treatment is available at https://hznuduan.shinyapps.io/LCSP/ .

CONCLUSION

We identified two LUSC subtypes by unsupervised clustering and developed an online tool for prognosis prediction using supervised machine learning models.

SMO mutation predicts the effect of immune checkpoint inhibitor: From NSCLC to multiple cancers

Background

The emergence of immune checkpoint inhibitors (ICIs) is one of the most promising breakthroughs for the treatment of multiple cancer types, but responses vary. Growing evidence points to a link between developmental signaling pathway-related genes and antitumor immunity, but the association between the genomic alterations in these genes and the response to ICIs still needs to be elucidated.

Methods

Clinical data and sequencing data from published studies and our cohort were collected to analyze the association of the mutation status of SMO with the efficacy of ICI therapy in the non-small cell lung cancer (NSCLC) cohort and the pan-cancer cohort. Furthermore, the correlation between SMO mutation and immunotherapeutic biomarkers such as immune cell infiltration, immune-related genes, and underlying signaling pathways was analyzed. Three SMO mutant plasmids were transfected into cells to explore the SMO mutation status in the context of its expression and cell growth.

Result

In the NSCLC discovery cohort, the median progression-free survival in the SMO mutant (SMO_MUT) was longer than that in the wild type (SMO_WT) (23.0 vs. 3.8 months, adjusted p = 0.041). This finding was further confirmed in the NSCLC validation cohort (8.7 vs. 5.1 months, adjusted p = 0.013). In the pan-cancer cohort (n = 1,347), a significant overall survival advantage was observed in patients with SMO mutations [not reached (NR) vs. 18 months, adjusted p = 0.024]. In the subgroup analysis, the survival advantage of SMO_MUT against SMO_WT was prominent and consistent across genders, ages, treatment types, cancer types, and the tumor mutation burden (TMB) status (all pinteraction > 0.05). In an in vitro experiment, we found that both the mutant and wild-type plasmids can promote the expression of SMO, but the mutant plasmid had lower SMO mRNA and protein levels than the wild type. In CCK-8 experiments, we found that SMO_MUT plasmids can improve the growth of Calu-1 and PC-9 cells, but this capability varied between different mutations and cells. Upon further exploration, the SMO mutation status was found to be related to a higher TMB, more neoantigen load, more DNA damage repair (DDR) mutations, higher microsatellite instability (MSI) score, and higher CD8+ T-cell infiltration.

Conclusions

The SMO mutation status is an independent prognostic factor that can be used to predict better clinical outcomes of ICI treatment across multiple cancer types.

A novel anti-lung cancer agent inhibits proliferation and epithelial-mesenchymal transition

OBJECTIVE

To synthesize a novel chalcone-1,3,4-thiadiazole hybrid and investigate its anticancer effects against NCI-H460 cells.

METHODS

(E)-3-(4-bromophenyl)-1-(4-hydroxyphenyl)prop-2-en-1-one, 1,3-dibromopropane and 1,3,4-thiadiazole-2-thiol were used as chemical materials to synthesize compound ZW97. The NCI-H460 lung cancer cell line was selected to explore the antitumor effects of compound ZW97 in vitro and in vivo.

RESULTS

Compound ZW97 selectively inhibited cell proliferation against lung cancer cell lines NCI-H460, HCC-44 and NCI-H3122 with IC₅₀ values of 0.15 μM, 2.06 μM and 1.17 μM, respectively. ZW97 suppressed migration and the epithelial-mesenchymal transition process in NCI-H460 cells in a concentration-dependent manner. Based on the kinase activity results and docking analysis, compound ZW97 is a novel tyrosine-protein kinase Met (c-Met kinase) inhibitor. It also inhibited NCI-H460 cell growth in xenograft models without obvious toxicity to normal tissues.

CONCLUSIONS

Compound ZW97 is a potential c-Met inhibitor that might be a promising agent to treat lung cancer by inhibiting the epithelial-mesenchymal transition process.

Case Report: A Novel Non-Reciprocal ALK Fusion: ALK-GCA and EML4-ALK Were Identified in Lung Adenocarcinoma, Which May Respond to Alectinib Adjuvant-Targeted Therapy

Anaplastic lymphoma kinase (ALK)-positive non-small-cell lung cancers (NSCLCs) have favorable and impressive response to ALK tyrosine kinase inhibitors (TKIs). However, ALK rearrangement had approximately 90 distinct fusion partners. Patients with different ALK fusions might have distinct responses to different-generation ALK-TKIs. In this case report, we identified a novel non-reciprocal ALK fusion: ALK-grancalcin (GCA) (A19: intragenic) and EML4-ALK (E20: A20) by next-generation sequencing (NGS) in a male lung adenocarcinoma patient who was staged as IIIB-N2 after surgery. After a multidisciplinary discussion, the patient received alectinib adjuvant targeted therapy and postoperative radiotherapy (PORT). He is currently in good condition, and disease-free survival (DFS) has been 20 months so far, which has been longer than the median survival time of IIIB NSCLC patients. Our study extended the spectrum of ALK fusion partners in ALK + NSCLC, and we reported a new ALK fusion: ALK-GCA and EML4-ALK and its sensitivity to alectinib firstly in lung cancer. It is vital for clinicians to detect fusion mutations of patients and report timely the newfound fusions and their response to guide treatment.

Coexpression of ΔNp63/p40 and TTF1 Within Most of the Same Individual Cells Identifies Life-Threatening NSCLC Featuring Squamous and Glandular Biphenotypic Differentiation: Clinicopathologic Correlations

Introduction

Double occurrence of TTF1 and ΔNp63/p40 (henceforth, p40) within the same individual cells is exceedingly rare in lung cancer. Little is known on their biological and clinical implications.

Methods

Two index cases immunoreactive for both p40 and TTF1 and nine tumors selected from The Cancer Genome Atlas (TCGA) according to the mRNA levels of the two relevant genes entered the study.

Results

The two index cases were peripherally located, poorly differentiated, and behaviorally unfavorable carcinomas, which shared widespread p40 and TTF1 decoration within the same individual tumor cells. They also retained SMARCA2 and SMARCA4 expression, while variably stained for p53, cytokeratin 5, and programmed death-ligand 1. A subset of basal cells p40+/TTF1+ could be found in normal distal airways. Biphenotypic glandular and squamous differentiation was unveiled by electron microscopy, along with EGFR, RAD51B, CCND3, or NF1 mutations and IGF1R, MYC, CCND1, or CDK2 copy number variations on next-generation sequencing analysis. The nine tumors from TCGA (0.88% of 1018 tumors) shared the same poor prognosis, clinical presentation, and challenging histology and had activated pathways of enhanced angiogenesis and epithelial-mesenchymal transition. Mutation and copy number variation profiles did not differ from the other TCGA tumors.

Conclusions

Double p40+/TTF1+ lung carcinomas are aggressive and likely underrecognized non-small cell carcinomas, whose origin could reside in double-positive distal airway stem-like basal cells through either de novo-basal-like or differentiating cell mechanisms according to a model of epithelial renewal.

Use of cucurbitacins for lung cancer research and therapy

As the main substance in some traditional Chinese medicines, cucurbitacins have been used to treat hepatitis for decades in China. Currently, the use of cucurbitacins against cancer and other diseases has achieved towering popularity among researchers worldwide, as detailed in this review with summarized tables. Numerous studies have reported the potential tumor-killing activities of cucurbitacins in multiple aspects of human malignancies. Continuous research on its anticancer activity mechanisms also brings a glimmer of light to the treatment of patients with lung cancer. In line with the promising roles of cucurbitacins against cancer, through various molecular signaling pathways, it is justifiable to propose the use of cucurbitacins as a potential mainline chemotherapy before the onset and after the diagnosis of lung cancers. Here, this article mainly summarized the findings about the biological functions and underlying mechanisms of cucurbitacins on lung cancer pathogenesis and treatment. In addition, we also discussed the safety and efficacy of their application for further research and even clinical practice.

EGFR-Mutated Squamous Cell Lung Cancer and Its Association With Outcomes

Background

The therapeutic efficacy of epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) in advanced EGFR-mutant lung squamous cell carcinoma (SCC) patients remains uncertain. Furthermore, the factors underlying the responsiveness have not been fully investigated. We therefore investigated the link between genomic profiles and EGFR-TKI efficacy.

Material and Methods

We consecutively enrolled stage IV, EGFR-mutant, and EGFR-TKI–treated patients with SCC. Patients with EGFR wild-type lung SCC and EGFR-mutant lung adenocarcinoma were consecutively enrolled as controls, and next-generation sequencing (NGS) was performed.

Results

In total, 28 EGFR-mutant lung SCC, 41 EGFR-mutant lung adenocarcinoma, and 40 EGFR wild-type lung SCC patients were included. Among the patients with EGFR mutations, shorter progression-free survival (PFS) was observed in SCC compared to adenocarcinoma (4.6 vs. 11.0 months, P<0.001). Comparison of the genomic profiles revealed that EGFR-mutant SCC patients had similar mutation characteristics to EGFR-mutant adenocarcinoma patients, but differed from those with EGFR wild-type SCC. Further exploration of EGFR-mutant SCC revealed that mutations in CREBBP (P = 0.005), ZNF217 (P = 0.016), and the Wnt (P = 0.027) pathway were negatively associated with PFS. Mutations in GRM8 (P = 0.025) were associated with improved PFS.

Conclusions

EGFR-mutant lung SCC has a worse prognosis than EGFR-mutant adenocarcinoma. Mutations in other genes, such as CREBBP, ZNF217, GRM8, or Wnt that had implications on PFS raise the possibility of understanding mechanisms of resistance to EGFR-TKI in lung SCC, which will aid identification of potential beneficial subgroups of patients with EGFR-mutant SCCs receiving EGFR-TKIs.