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Molecular subtypes of lung adenocarcinoma patients for prognosis and therapeutic response prediction with machine learning on 13 programmed cell death patterns

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Abstract

Background

Lung adenocarcinoma (LUAD) seriously threatens people’s health worldwide. Programmed cell death (PCD) plays a critical role in regulating LUAD growth and metastasis as well as in therapeutic response. However, currently, there is a lack of integrative analysis of PCD-related signatures of LUAD for accurate prediction of prognosis and therapeutic response.

Methods

The bulk transcriptome and clinical information of LUAD were obtained from TCGA and GEO databases. A total of 1382 genes involved in regulating 13 various PCD patterns (apoptosis, necroptosis, pyroptosis, ferroptosis, cuproptosis, netotic cell death, entotic cell death, lysosome-dependent cell death, parthanatos, autophagy-dependent cell death, oxeiptosis, alkaliptosis and disulfidptosis) were included in the study. Weighted gene co-expression network analysis (WGCNA) and differential expression analysis were performed to identify PCD-associated differential expression genes (DEGs). An unsupervised consensus clustering algorithm was used to explore the potential subtypes of LUAD based on the expression profiles of PCD-associated DEGs. Univariate Cox regression analysis, Least Absolute Shrinkage and Selection Operator (LASSO) regression, Random Forest (RF) analysis and stepwise multivariate Cox analysis were performed to construct a prognostic gene signature. The “oncoPredict” algorithm was utilized for drug-sensitive analysis. GSVA and GSEA were utilized to perform function enrichment analysis. MCPcounter, quanTIseq, Xcell and ssGSEA algorithms were used for tumor immune microenvironment analysis. A nomogram incorporating PCDI and clinicopathological characteristics was established to predict the prognosis of LUAD patients.

Results

Forty PCD-associated DEGs related to LUAD were obtained by WGCNA analysis and differential expression analysis, followed by unsupervised clustering to identify two LUAD molecular subtypes. A programmed cell death index (PCDI) with a five-gene signature was established by machine learning algorithms. LUAD patients were then divided into a high PCDI group and a low PCDI group using the median PCDI as a cutoff. Survival and therapeutic analysis revealed that the high PCDI group had a poor prognosis and was more sensitive to targeted drugs but less sensitive to immunotherapy compared to the low PCDI group. Further enrichment analysis showed that B cell-related pathways were significantly downregulated in the high PCDI group. Accordingly, the decreased tumor immune cell infiltration and the lower tumor tertiary lymphoid structure (TLS) scores were also found in the high PCDI group. Finally, a nomogram with reliable predictive performance PCDI was constructed by incorporating PCDI and clinicopathological characteristics, and a user-friendly online website was established for clinical reference (https://nomogramiv.shinyapps.io/NomogramPCDI/).

Conclusion

We performed the first comprehensive analysis of the clinical relevance of genes regulating 13 PCD patterns in LUAD and identified two LUAD molecular subtypes with distinct PCD-related gene signature which indicated differential prognosis and treatment sensitivity. Our study provided a new index to predict the efficacy of therapeutic interventions and the prognosis of LUAD patients for guiding personalized treatments.

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Data availability

Publicly available datasets were analyzed in this study. These data can be found here: https://portal.gdc.cancer.gov/ and https://www.ncbi.nlm.nih.gov/geo/.

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Funding

This work was supported by National Natural Science Foundation of China (Nos. 31870781, 81672858).

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Authors and Affiliations

  1. Key Laboratory Experimental Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China

    Qin Wei, Xiaoyu Jiang, Xinyi Miao, Yilin Zhang & Pengju Zhang

  2. Department of Infectious Disease, Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250013, China

    Fengzhe Chen

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  1. Qin Wei
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  4. Yilin Zhang
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Contributions

PZ, FC and QW designed the study. QW performed the acquisition and analysis of data. FC, XJ, XM and YZ collected clinical samples and performed IHC analysis. QW wrote the manuscript. PZ edited the manuscript. All authors read and approved the final manuscript.

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Correspondence to Fengzhe Chen or Pengju Zhang.

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Wei, Q., Jiang, X., Miao, X. et al. Molecular subtypes of lung adenocarcinoma patients for prognosis and therapeutic response prediction with machine learning on 13 programmed cell death patterns. J Cancer Res Clin Oncol 149, 11351–11368 (2023). https://doi.org/10.1007/s00432-023-05000-w

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