Development and validation of a novel epigenetic-related prognostic signature and candidate drugs for patients with lung adenocarcinoma

Comprehensive Analysis Reveals the Potential Roles of Transcription Factor Dp-1 in Lung Adenocarcinoma

Background

Transcription factor Dp-1 (TFDP1) was overexpressed and interacted with other genes to impact multiple signaling pathways in various human cancers. However, there is less research about the TFDP1 specific roles in lung adenocarcinoma (LUAD).

Methods

We first explored TFDP1 expression levels and relative diseases from a pan-cancer perspective using the ONCOMINE, TIMER, and Open Targets Platform databases. Then, we used UALCAN, GEPIA 2, TCGA-LUAD data, and Kaplan-Meier plotter to examine TFDP1 clinicopathological features and prognosis in LUAD patients. Genomic alterations and DNA methylation analysis were performed by cBioPortal and MethSurv, respectively. Then, we used a cancer single-cell state atlas (CancerSEA) to find TFDP1 functions at a single-cell resolution. LinkedOmics was used to find TFDP1 coexpressed genes, biological processes, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Then, Gene Set Cancer Analysis (GSCA) was used to examine the drug resistence of TFDP1 in LUAD.

Results

We found that TFDP1 was overexpressed in most human cancers and related to various diseases, including LUAD. Moreover, LUAD patients with high TFDP1 expression levels might be significantly associated with individual cancer stages and have a poor prognosis. Multivariate analysis revealed that the American Joint Committee on Cancer (AJCC) pathologic stage, AJCC stage T, and AJCC stage N were the independent prognostic factors. LUAD patients with TFDP1 alterations suggested poor overall survival (OS), and disease-free survival (DFS), while hypermethylation might lead to a good prognosis. TFDP1 and its coexpressed genes were enriched in multiple signaling pathways and biological processes involved in the cell cycle, spliceosome, and DNA replication. Furthermore, TFDP1 was strongly positively related to the half-maximal inhibitory concentration (IC50) values of multiple drugs.

Conclusions

In summary, TFDP1 was a possible biomarker and potential therapeutic target for LUAD patients.

Identification of N7-methylguanosine related signature for prognosis and immunotherapy efficacy prediction in lung adenocarcinoma

Background

Lung adenocarcinoma (LUAD) is one of the most frequent causes of tumor-related mortality worldwide. Recently, the role of N7-methylguanosine (m7G) in tumors has begun to receive attention, but no investigation on the impact of m7G on LUAD. This study aims to elucidate the significance of m7G on the prognosis and immunotherapy in LUAD.

Methods

Consensus clustering was employed to determine the molecular subtype according to m7G-related regulators extracted from The Cancer Genome Atlas (TCGA) database. Survival, clinicopathological features and tumor mutational burden (TMB) analysis were applied to research molecular characteristics of each subtype. Subsequently, “limma” package was used to screen differentially expressed genes (DEGs) between subtypes. In the TCGA train cohort (n = 245), a prognostic signature was established by univariate Cox regression, lasso regression and multivariate Cox regression analysis according to DEGs and survival analysis was employed to assess the prognosis. Then the prognostic value of the signature was verified by TCGA test cohort (n = 245), TCGA entire cohort (n = 490) and GSE31210 cohort (n = 226). Moreover, the association among immune infiltration, clinical features and the signature was investigated. The immune checkpoints, TMB and tumor immune dysfunction and exclusion (TIDE) were applied to predict the immunotherapy response.

Results

Two novel molecular subtypes (C1 and C2) of LUAD were identified. Compared to C2 subtype, C1 subtype had poorer prognosis and higher TMB. Subsequently, the signature (called the “m7G score”) was constructed according to four key genes (E2F7, FAM83A, PITX3, and HOXA13). The distribution of m7G score were significantly different between two molecular subtypes. The patients with lower m7G score had better prognosis in TCGA train cohort and three verification cohort. The m7G score was intensively related to immune infiltration. Compared with the lower score, the higher m7G score was related to remarkable upregulation of the PD-1 and PD-L1, the higher TMB and the lower TIDE score.

Conclusion

This study established a m7G-related signature for predicting prognosis and immunotherapy in LUAD, which may contribute to the development of new therapeutic strategies for LUAD.

A novel prognostic signature of metastasis-associated genes and personalized therapeutic strategy for lung adenocarcinoma patients

Lung adenocarcinoma (LUAD) is a highly invasive and metastatic malignant tumor with high morbidity and mortality. This study aimed to construct a prognostic signature for LUAD patients based on metastasis-associated genes (MAGs). RNA expression profiles were downloaded from the Cancer Genome Atlas (TCGA) database. RRA method was applied to identify differentially expressed MAGs. A total of 192 significantly robust MAGs were determined among seven GEO datasets. MAGs were initially selected through the Lasso Cox regression analysis and 6 MAGs were included to construct a prognostic signature model. Transcriptome profile, patient prognosis, correlation between the risk score and clinicopathological features, immune cell infiltration characteristics, immunotherapy sensitivity and chemotherapy sensitivity differed between low- and high-risk groups after grouping according to median risk score. The reliability and applicability of the signature were further validated in the GSE31210, GSE50081 and GSE68465 cohort. CMap predicted 62 small molecule drugs on the base of the prognostic MAGs. Targeted drug staurosporine had hydrogen bonding with Gln-172 of SLC2A1, which is one of MAGs. Staurosporine could inhibit cell migration in A549 and H1299. We further verified mRNA and protein expression of 6 MAGs in A549 and H1299. The signature can serve as a promising prognostic tool and may provide a novel personalized therapeutic strategy for LUAD patients.