Integrated single-cell and bulk RNA-Seq analysis enhances prognostic accuracy of PD-1/PD-L1 immunotherapy response in lung adenocarcinoma through necroptotic anoikis gene signatures

Abstract

In addition to presenting significant diagnostic and treatment challenges, lung adenocarcinoma (LUAD) is the most common form of lung cancer. Using scRNA-Seq and bulk RNA-Seq data, we identify three genes referred to as HMR, FAM83A, and KRT6A these genes are related to necroptotic anoikis-related gene expression. Initial validation, conducted on the GSE50081 dataset, demonstrated the model's ability to categorize LUAD patients into high-risk and low-risk groups with significant survival differences. This model was further applied to predict responses to PD-1/PD-L1 blockade therapies, utilizing the IMvigor210 and GSE78220 cohorts, and showed strong correlation with patient outcomes, highlighting its potential in personalized immunotherapy. Further, LUAD cell lines were analyzed using quantitative PCR (qPCR) and Western blot analysis to confirm their expression levels, further corroborating the model's relevance in LUAD pathophysiology. The mutation landscape of these genes was also explored, revealing their broad implication in various cancer types through a pan-cancer analysis. The study also delved into molecular subclustering, revealing distinct expression profiles and associations with different survival outcomes, emphasizing the model’s utility in precision oncology. Moreover, the diversity of immune cell infiltration, analyzed in relation to the necroptotic anoikis signature, suggested significant implications for immune evasion mechanisms in LUAD. While the findings present a promising stride towards personalized LUAD treatment, especially in immunotherapy, limitations such as the retrospective nature of the datasets and the need for larger sample sizes are acknowledged. Prospective clinical trials and further experimental research are essential to validate these findings and enhance the clinical applicability of our prognostic model.

Elucidating the role of angiogenesis-related genes in colorectal cancer: a multi-omics analysis

“…We also evaluated the immunotherapeutic response of cluster I and cluster II using the IMvigor210 and GSE78220 datasets, as done in previous studies ( 29 , 30 ). Although we identified an association between the ARC and the TME, our analysis did not reveal a significant correlation between these subtypes and immunotherapy response or patient survival.…”

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“…Exploration of four ARC-related genes at scRNA-seq level. We also evaluated the immunotherapeutic response of cluster I and cluster II using the IMvigor210 and GSE78220 datasets, as done in previous studies (29,30). Although we identified an association between the ARC and the TME, our analysis did not reveal a significant correlation between these subtypes and immunotherapy response or patient survival.…”