High LYRM4-AS1 predicts poor prognosis in patients with glioma and correlates with immune infiltration

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Biochemistry, Biophysics and Molecular Biology

Main article text

 

Introduction

Materials and Methods

Datasets

Differentially expressed genes (DEGs) analysis

GO and KEGG enrichment analysis

Gene set enrichment analysis

Immune infiltration analysis

Cell culture

Cell transfection

Cell viability assays

RT-qPCR

Morphological changes due to apoptosis

Flow cytometry detecting cell apoptosis

Wound healing assay

Statistical analysis

Results

LYRM4-AS1 was high expressed in glioma

LYRM4-AS1 expression correlated with clinical characteristics

High LYRM4-AS1 expression in glioma patients predicted worse prognosis

A high LYRM4-AS1 level was independent prognostic factor of OS in patients with glioma

Identifications of DEGs and functional enrichment analyses

The correlation between LYRM4-AS1 and immune infiltration

The relationship between LYRM4-AS1 and immune checkpoints

Inhibition of LYRM4-AS1 expression can inhibit glioma cell viability and migration

Discussion

Conclusions

Supplemental Information

The correlation analysis of LYRM4-AS1 expression and gender of glioma patients.

The RNA-seq data with clinical information were obtained from TCGA-GBM and TCGA-LGG projects, and correlation of LYRM4-AS1 expression and gender of glioma patients was analyzed.

DOI: 10.7717/peerj.16104/supp-1

Prognostic analysis of high LYRM4-AS1 expression in glioma patients.

Prognostic analysis of high LYRM4-AS1 expression in IDH status:Mut (A), WHO grade: G3 (B), 1p/19q codeletion: Non-codel (C), Age: ≤60 (D, Age: > 60 (E), Histological type: Astrocytoma (F), Primary therapy outcome: PD (G), Primary therapy outcome: SD&CR&PR (H) of glioma patients. SD, stable disease; PR, partial response; CR, complete response; PD, progressive disease. The RNA-seq data with clinical information were obtained from TCGA-GBM and TCGA-LGG projects.

DOI: 10.7717/peerj.16104/supp-2

Construction of an OS predictive nomogram based on LYRM4-AS1 expression and clinicopathological factors.

The OS nomogram based on WHO grade, IDH status, age and LYRM4-AS1 was constructed (A). The C-index of the nomograms was 0.843 (95% CI [0.832–0.854]). Drawing a vertical line from the total point axis straight downward to the outcome axis can pick up the probability of patients with glioma at 1,3,5-years. The calibration curve nomogram predicting 5-year OS (B). The horizontal coordinate was the survival probability predicted by the OS nomogram and the vertical coordinate is the actual survival probability. The 5-year survival predicted was indicated by the blue line and the gray line represented the ideal situation in which predicted and actual survival coincide. The closer the predicted line was to the diagonal line, the more accurate the model was.

DOI: 10.7717/peerj.16104/supp-3

LYRM4-AS1 related signaling pathways based on GSEA.

Pathways and biological processes were differentially enriched in LYRM4-AS1-related phenotype, including P53 signaling pathway (A), signaling by NOTCH (B), cell cycle (C), JAK_STAT signaling pathway (D), interferon signaling (E) and cytokine-cytokine receptor interaction (F). The top portion showed the enrichment scores. If the normalized enrichment score (NES) was positive, a peak appeared on the left side, indicating that the core molecules of the gene set were mainly concentrated in the high expression group on the left side. Each vertical line in the middle represented one molecule in the gene set. The lower part visualized the values after normalizing the gene set expression data. The RNA-seq data were obtained from TCGA-GBM and TCGA-LGG projects.

DOI: 10.7717/peerj.16104/supp-4

The infiltration levels of Th2 cells, Macrophages, aDCs and Neutrophils in high and low LYRM4-AS1 expression group.

The analysis of LYRM4-AS1 expression levels and immune cell infiltration levels of Th2 cells (A), Macrophages (B), aDCs (C) and Neutrophils (D) compared with low LYRM4-AS1 expression groups. RNA-seq data of glioma patients were from GBM and LGG projects of TCGA.

DOI: 10.7717/peerj.16104/supp-5

The identified DEGs between high and low LYRM4-AS1 expression group of glioma tissues.

DOI: 10.7717/peerj.16104/supp-6

The results of the GO enrichment analysis.

DOI: 10.7717/peerj.16104/supp-7

The results of the KEGG enrichment analysis.

DOI: 10.7717/peerj.16104/supp-8

The results of GSEA analysis.

DOI: 10.7717/peerj.16104/supp-10

Correlation of LYRM4-AS1 expression with immune checkpoints.

DOI: 10.7717/peerj.16104/supp-11

Raw data: wound healing assay.

DOI: 10.7717/peerj.16104/supp-15

Raw data: wound healing pictures.

DOI: 10.7717/peerj.16104/supp-16

Additional Information and Declarations

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Hai Yue Wang performed the experiments, analyzed the data, prepared figures and/or tables, and approved the final draft.

Ying Xie performed the experiments, prepared figures and/or tables, and approved the final draft.

Hongzhen Du analyzed the data, prepared figures and/or tables, and approved the final draft.

Bin Luo conceived and designed the experiments, authored or reviewed drafts of the article, and approved the final draft.

Zengning Li conceived and designed the experiments, authored or reviewed drafts of the article, and approved the final draft.

Data Availability

The following information was supplied regarding data availability:

The raw data and R code are available in the Supplemental Files.

Funding

This work was supported by the Research Projects of China Association for Geriatric Health Care (No. HZ202102), the Medical Science Research Projects in Hebei Province (No. 20190454) and the “Spark” Youth Research Project of the First Hospital of Hebei Medical University (No. XH201810). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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