Combining autophagy and immune characterizations to predict prognosis and therapeutic response in lung adenocarcinoma

Identification of C4BPA as biomarker associated with immune infiltration and prognosis in breast cancer

Background

C4BPA is a gene that encodes the C4BP protein α chain and is involved in the complement system. C4BPA is regarded as a new biomarker for cancer, especially for non-small cell lung cancer and ovarian cancer. However, its role in breast cancer (BC) has not yet been determined.

Methods

In this research, we used a bioinformatics approach to assess the prognostic significance of C4BPA in BC. Utilizing a variety of databases and analysis tools, including The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), R, STRING, and the Kaplan-Meier plotter, we specifically assessed the connection between C4BPA and BC.

Results

C4BPA expression was markedly decreased in BC tissues compared to its expression in normal breast tissues (P<0.05). Additionally, a receiver operating characteristic (ROC) curve revealed that C4BPA has a significant capacity for prognostication and diagnostics. Additionally, C4BPA expression was linked to some immune infiltrating cells' functionality, according to gene set enrichment analysis (GSEA) and immune infiltration analysis. Low C4BPA expression was additionally related to poor progression-free interval (PFI) and overall survival (OS), according to the Kaplan-Meier method. We also found that C4BPA expression was independently connected to PFI and OS through Cox regression analysis. Finally, prognostic analysis of the various subgroups of breast invasive carcinoma (BRCA/BIC) in TCGA showed that patients with low C4BPA expression might have worse PFI and OS in patients with Luminal A compared to other BC subtypes.

Conclusions

In conclusion, these results revealed that C4BPA could potentially act as a diagnostic biomarker for BC patients indicating unfavorable prognoses and offers valuable knowledge for creating therapeutics and prognostic indicators.

Immune, metabolic landscapes of prognostic signatures for lung adenocarcinoma based on a novel deep learning framework

Lung adenocarcinoma (LUAD) is a malignant tumor with high lethality, and the aim of this study was to identify promising biomarkers for LUAD. Using the TCGA-LUAD dataset as a discovery cohort, a novel joint framework VAEjMLP based on variational autoencoder (VAE) and multilayer perceptron (MLP) was proposed. And the Shapley Additive Explanations (SHAP) method was introduced to evaluate the contribution of feature genes to the classification decision, which helped us to develop a biologically meaningful biomarker potential scoring algorithm. Nineteen potential biomarkers for LUAD were identified, which were involved in the regulation of immune and metabolic functions in LUAD. A prognostic risk model for LUAD was constructed by the biomarkers HLA-DRB1, SCGB1A1, and HLA-DRB5 screened by Cox regression analysis, dividing the patients into high-risk and low-risk groups. The prognostic risk model was validated with external datasets. The low-risk group was characterized by enrichment of immune pathways and higher immune infiltration compared to the high-risk group. While, the high-risk group was accompanied by an increase in metabolic pathway activity. There were significant differences between the high- and low-risk groups in metabolic reprogramming of aerobic glycolysis, amino acids, and lipids, as well as in angiogenic activity, epithelial-mesenchymal transition, tumorigenic cytokines, and inflammatory response. Furthermore, high-risk patients were more sensitive to Afatinib, Gefitinib, and Gemcitabine as predicted by the pRRophetic algorithm. This study provides prognostic signatures capable of revealing the immune and metabolic landscapes for LUAD, and may shed light on the identification of other cancer biomarkers.

Identification and validation of eight lysosomes-related genes signatures and correlation with immune cell infiltration in lung adenocarcinoma

Lung cancer is the leading cause of cancer-related death. Lysosomes are key degradative compartments that maintain protein homeostasis. In current study, we aimed to construct a lysosomes-related genes signature to predict the overall survival (OS) of patients with Lung Adenocarcinoma (LUAD). Differentially expressed lysosomes-related genes (DELYs) were analyzed using The Cancer Genome Atlas (TCGA-LUAD cohort) database. The prognostic risk signature was identified by Least Absolute Shrinkage and Selection Operator (LASSO)-penalized Cox proportional hazards regression and multivariate Cox analysis. The predictive performance of the signature was assessed by Kaplan-Meier curves and Time-dependent receiver operating characteristic (ROC) curves. Gene set variant analysis (GSVA) was performed to explore the potential molecular biological function and signaling pathways. ESTIMATE and single sample gene set enrichment analysis (ssGSEA) were applied to estimate the difference of tumor microenvironment (TME) between the different risk subtypes. An eight prognostic genes (ACAP3, ATP8B3, BTK, CAV2, CDK5R1, GRIA1, PCSK9, and PLA2G3) signature was identified and divided patients into high-risk and low-risk groups. The prognostic signature was an independent prognostic factor for OS (HR > 1, p < 0.001). The molecular function analysis suggested that the signature was significantly correlated with cancer-associated pathways, including angiogenesis, epithelial mesenchymal transition, mTOR signaling, myc-targets. The low-risk patients had higher immune cell infiltration levels than high-risk group. We also evaluated the response to chemotherapeutic, targeted therapy and immunotherapy in high- and low-risk patients with LUAD. Furthermore, we validated the expression of the eight gene expression in LUAD tissues and cell lines by qRT-PCR. LYSscore signature provide a new modality for the accurate diagnosis and targeted treatment of LUAD and will help expand researchers' understanding of new prognostic models.

Identification of a coagulation-related signature correlated with immune infiltration and their prognostic implications in lung adenocarcinoma

BACKGROUND

Lung adenocarcinoma (LUAD) is a fatal form of lung cancer with a poor prognosis. Coagulation system had been confirmed closely related to tumor progression and the hypercoagulable state encouraged the immune infiltration and development of tumor cells, leading to a poor prognosis in cancer patients. However, the use of the coagulation-related genes (CRGs) for prognosis in LUAD has yet to be determined. In this study, we constructed an immune-related signature (CRRS) and identified a potential coagulation-related biomarker (P2RX1).

METHODS

We obtained a total of 209 CRGs based on two coagulation-related KEGG pathways, then developed the CRRS signature by using the TCGA-LUAD RNA-seq data via the procedure of LASSO-Cox regression, stepwise-Cox regression, univariate and multivariate Cox regression. Grouped by the CRRS, Kaplan-Meier survival curves and receiver operating characteristic curves were drawn for the training and validation sets, respectively. In addition, single-sample gene set enrichment analysis was exploited to explore immune infiltration level. Moreover, immunophenotypes and immunotherapy grouped by CRRS were further analyzed.

RESULTS

We developed an immune-related signature (CRRS) composed of COL1A2, F2, PLAUR, C4BPA, and P2RX1 in LUAD. CRRS was an independent risk factor for overall survival and displayed stable and powerful performance. Additionally, CRRS possessed distinctly superior accuracy than traditional clinical variables and molecular features. Functional analysis indicated that the differentially high expressed genes in the low-risk group significantly enriched in T cell and B cell receptor signaling pathways. The low-risk group was sensitive to anti-PD-1/PD-L1 immunotherapy and displayed abundant immune infiltration and immune checkpoint gene expression. Finally, we identified an independent prognostic gene P2RX1. Low expression of P2RX1 associated with poor overall survival and decreased immune infiltration.

CONCLUSIONS

Our study revealed a significant correlation between CRRS and immune infiltration. CRRS could serve as a promising tool to improve the clinical outcomes for individual LUAD patients.