Immune and non-immune cell subtypes identify novel targets for prognostic and therapeutic strategy: A study based on intratumoral heterogenicity analysis of multicenter scRNA-seq datasets in lung adenocarcinoma

Unveiling the power of Treg.Sig: a novel machine-learning derived signature for predicting ICI response in melanoma

Background

Although immune checkpoint inhibitor (ICI) represents a significant breakthrough in cancer immunotherapy, only a few patients benefit from it. Given the critical role of Treg cells in ICI treatment resistance, we explored a Treg-associated signature in melanoma, which had never been elucidated yet.

Methods

A new Treg signature, Treg.Sig, was created using a computational framework guided by machine learning, utilizing transcriptome data from both single-cell RNA-sequencing (scRNA-seq) and bulk RNA-sequencing (bulk-seq). Among the 10 Treg.Sig genes, hub gene STAT1's function was further validated in ICI resistance in melanoma mice receiving anti-PD-1 treatment.

Results

Treg.Sig, based on machine learning, was able to forecast survival outcomes for melanoma across training dataset and external test dataset, and more importantly, showed superior predictive power than 51 previously established signatures. Analysis of the immune profile revealed that groups with high Treg.Sig levels exhibited immune-suppressive conditions, with inverse correlations observed between Treg.Sig and anti-cancer immune responses. Notably, among the 10 Treg.Sig genes, hub gene STAT1 mutation harbored lower response rate in ICIs-treated cohort. Mechanistically, STAT1 impinged on ICI resistances by modulating the phenotypic switch in N2 neutrophil polarization in melanoma mice receiving anti-PD-1 therapy, which affects overall survival.

Conclusion

The study developed a promising Treg.Sig signature that predicts ICI response of melanomas and could be used for selecting patients for immunotherapy. Meanwhile, our study potentially paves the way for overcoming immune resistance by targeting Treg-associated genes.

Lung adenocarcinoma size as a predictor of distant metastasis: A CT scan-based measurement

Previous studies have associated tumor size with metastasis and prognosis in lung carcinoma; however, a precise cut-off for predicting distant metastasis in lung adenocarcinoma remains unclear. The aim of this study was to determine the cut-off point for predicting distant metastasis in lung adenocarcinoma. A cross-sectional study was conducted at Dr. Moewardi Hospital, Surakarta, Indonesia, from January 2022 to September 2023. Total sampling was employed, involving patients over 18 years old with a confirmed diagnosis of lung adenocarcinoma based on lung computed tomography (CT) scan findings, who had not yet received chemotherapy and had confirmed metastasis outside the lung. The study's dependent variable was the incidence of distant metastasis, while the independent variable was lung adenocarcinoma size. Two experienced thoracic radiologists measured lung adenocarcinoma size by assessing the longest axis using chest multi-slice computed tomography (MSCT) in the lung window setting. Receiver operating characteristic (ROC) curve analysis determined the optimal tumor size cut-off for predicting distant metastasis. Of 956 thoracic cancer patients, 108 were diagnosed with lung adenocarcinoma. After applying the inclusion and exclusion criteria, 89 patients were eligible. In the present study, tumor size predicted 68.1% of distant metastasis cases, with a cut-off point of 7.25 cm, yielding a sensitivity of 61.9% and a specificity of 61.5%. Tumors >7.25 cm had a 2.60-fold higher risk of distant metastasis compared to smaller tumors, with larger tumors more likely to spread to various sites. In conclusion, lung adenocarcinomas larger than 7.25 cm have a 2.60-fold increased risk of distant metastasis, making tumor size a crucial predictive factor. The study provides valuable insights for radiologists and can improve diagnosis accuracy and treatment planning by emphasizing tumor size as a key factor in managing lung adenocarcinoma.

Construction of an immune-related gene prognostic model with experimental validation and analysis of immune cell infiltration in lung adenocarcinoma

There is a correlation between tumors and immunity with the degree of immune cell infiltration in tumors being closely related to tumor growth and progression. Therefore, the present study identified immune-related prognostic genes and evaluated the immune infiltration level in lung adenocarcinoma (LUAD). This study performed Kyoto Encyclopedia of Genes and Genomes, Gene Ontology, and Gene Set Enrichment Analysis (GSEA) enrichment analyses on differential immune-associated genes. A risk model was created and validated using six immune-related prognostic genes. Reverse transcription-quantitative PCR was used to assess the prognostic gene expression in non-small cell lung cancer cells. Immune cell infiltration in LUAD was analyzed using the CIBERSORT method. Single sample GSEA was used to compare Tumor Immune Dysfunction and Exclusion (TIDE) scores between high and low-risk groups and to assess the activation of thirteen immune-related pathways. Multifactor Cox proportional hazards model analysis identified six prognostic risk genes (S100A16, FURIN, FGF2, LGR4, TNFRSF11A and VIPR1) to construct a risk model. The survival and receiver operating characteristic curves indicated that patients with higher risk scores had lower overall survival rates. The expression levels of prognostic genes S100A16, FURIN, LGR4, TNFRSF11A and VIPR1 were significantly increased in LUAD. B cells naive, plasma cells, T cells CD4 memory activated, T cells follicular helper, T cells regulatory, NK cells activated, macrophages M1, macrophages M2, and Dendritic cells resting cells showed elevated expression in LUAD. The prognostic genes were differentially associated with individual immune cells. Immune-related function scores, such as those for antigen presenting cell (APC) co-stimulation, APC co-inhibition, check-point, Cytolytic-activity, chemokine receptor, parainflammation, major histocompatibility complex-class-I, type-I-IFN-reponse and T-cell-co-inhibition, were higher in the high-risk group compared with the low-risk group. Furthermore, the TIDE score of the high-risk group was significantly lower than the low-risk group. This immune-related gene prognostic model has the potential to predict the prognosis of LUAD patients, supporting the development of a personalized clinical diagnosis and treatment plan.

Unraveling the tumor immune microenvironment of lung adenocarcinoma using single-cell RNA sequencing

Tumor immune microenvironment (TIME) and its indications for lung cancer patient prognosis and therapeutic response have become new hotspots in cancer research in recent years. Tumor cells, immune cells, various regulatory factors, and their interactions in the TIME have been suggested to commonly influence lung cancer development and therapeutic outcome. The heterogeneity of TIME is composed of dynamic immune-related components, including various cancer cells, immune cells, cytokine/chemokine environments, cytotoxic activity, or immunosuppressive factors. The specific composition of cell subtypes may facilitate or hamper the response to immunotherapy and influence patient prognosis. Various markers have been found to stratify the patient prognosis or predict the therapeutic outcome. In this article, we systematically reviewed the recent advancement of TIME studies in lung adenocarcinoma (LUAD) using single-cell RNA sequencing (scRNA-seq) techniques, with specific focuses on the roles of TIME in LUAD development, TIME heterogeneity, indications of TIME in patient prognosis and therapeutic response during immunotherapy and drug resistance. The main findings in TIME heterogeneity and relevant markers or models for prognosis stratification and response prediction have been summarized. We hope that this review provides an overview of TIME status in LUAD and an inspiration for future development of strategies and biomarkers in LUAD treatment.