ATG16L1 is a Potential Prognostic Biomarker and Immune Signature for Osteosarcoma: A Study Based on Bulk RNA and Single-Cell RNA-Sequencing

Abstract

Background Osteosarcoma is a common solid malignancy of the bone in children and adolescents, and its metastasis and recurrence are the principal causes of poor treatment outcomes. Methods Autophagy-related genes were used to cluster osteosarcoma patients by consensus clustering analysis using the GSE21257 database. Differentially expressed genes (DEGs) were identified by limma package. Multiple-gene risk signature was constructed using least absolute shrinkage and selection operator (LASSO) analysis and Cox regression analyses. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to determine gene expression levels. Then, single-cell RNA-sequencing dataset GSE152048 were used to identify the correlation between the DEGs and effector molecules expressed in specific tumor-infiltrating immune cells. Results Two clusters were identified in the consensus clustering analysis, which were confirmed by principal component analysis. Limma analysis revealed that 15 genes were related, and 9 genes were screened using protein-protein interaction network and LASSO regression analysis. Cox regression analyses identified 5 genes. Combined with survival analysis, only the autophagy related 16 like 1 gene ( ATG16L1 ) was significant. The results of qRT-PCR showed low expression levels of ATG16L1 in tumor cells group. Immune infiltration analysis revealed significantly lower expression of CD8 + T cells in the high ATG16L1 gene expression group. ScRNA-seq revealed that in the ATG16L1 + CD8 + T cell group, the expression of GZMB was lower, whereas the expression of ITGA1 was higher. These results showed that ATG16L 1 is an immune-related gene, which is associated with poor prognosis in patients with osteosarcoma. Conclusion ATG16L1 is a potential prognostic biomarker and immune signature and may be a therapeutic target for osteosarcoma.

The heterogeneity and drug resistance of malignant cells and intercellular communication of microenvironment in osteosarcoma: Based on single‐cell analysis

“…Despite these limitations, scRNA‐seq has great potential for identifying new therapeutic targets and refining tumour classifications to tailor patient therapeutic regimens. Future research on OS scRNA‐seq should address the limitations of the technique, such as its inability to distinguish minute transcriptional variations between cells, the difficulty in identifying uncommon immune cell populations, 37 and the limitation of detecting poly(A)‐RNAs 131 . The use of single‐cell universal poly(A)‐independent RNA sequencing and spatially resolved single‐cell RNA sequencing can provide more accurate data and a better understanding of the function and interactions of individual cells in anatomical space 132 …”

Carboxypeptidase E is a prognostic biomarker co-expressed with osteoblastic genes in osteosarcoma

“…Both Zhou et al (2020) and Liu et al (2021) reported on the single-sell transcriptomics landscape in OS. Additionally, the survival-related genes and a highly invasive cell population have been identified using previous data ( Feleke et al, 2022 ; Qin et al, 2022 ; Guo et al, 2022 ). One of the key findings in this work was that CPE was upregulated in the OS samples.…”

“… Feleke et al (2022) identified four differentially expressed survival-related genes (MUC1, COL13A1, JAG2, and KAZALD1) using the Therapeutically Applicable Research to Generate Effective Treatments dataset ( Feleke et al, 2022 ; Liu et al, 2021 ). Furthermore, Qin et al (2022) reported the potential prognostic value of ATG16L1 in OS using conventional bulk RNA sequencing and scRNA-Seq. Therefore, integrating bulk RNASeq and scRNA-Seq analyses is a prospective method for characterizing the composition of the tumor microenvironment and screening new biomarkers.…”

Detection of Genetic Markers Involved in Metastatic Colorectal Carcinoma to Lymph Nodes

“…Autophagy related 16 like 1 gene (ATG16L1) an autophagy related gene [40]. Qin et al showed that ATG16L1 is an immune-related gene, which is associated with poor prognosis in patients with osteosarcoma [41]. Thus defects in this gene might contribute to metastasis.…”