Exploration of the Molecular Mechanism of Intercellular Communication in Paediatric Neuroblastoma by Single-cell Sequencing

Overview

Journal Sci Rep

Specialty Science

Date 2023 Nov 22

PMID 37990103

Authors

Jing Chu

Affiliations

Soon will be listed here.

Abstract

Neuroblastoma (NB) is an embryonic tumour that originates in the sympathetic nervous system and occurs most often in infants and children under 2 years of age. Moreover, it is the most common extracranial solid tumour in children. Increasing studies suggest that intercellular communication within the tumour microenvironment is closely related to tumour development. This study aimed to construct a prognosis-related intercellular communication-associated genes model by single-cell sequencing and transcriptome sequencing to predict the prognosis of patients with NB for precise management. Single-cell data from patients with NB were downloaded from the gene expression omnibus database for comprehensive analysis. Furthermore, prognosis-related genes were screened in the TARGET database based on epithelial cell marker genes through a combination of Cox regression and Lasso regression analyses, using GSE62564 and GSE85047 for external validation. The patients' risk scores were calculated, followed by immune infiltration analysis, drug sensitivity analysis, and enrichment analysis of risk scores, which were conducted for the prognostic model. I used the Lasso regression feature selection algorithm to screen characteristic genes in NB and developed a 21-gene prognostic model. The risk scores were highly correlated with multiple immune cells and common anti-tumour drugs. Furthermore, the risk score was identified as an independent prognostic factor for NB. In this study, I constructed and validated a prognostic signature based on epithelial marker genes, which may provide useful information on the development and prognosis of NB.

Citing Articles

Validation of the biological function and prognostic significance of AURKA in neuroblastoma.

Chu J PLoS One. 2024; 19(11):e0313939.

PMID: 39585848 PMC: 11588284. DOI: 10.1371/journal.pone.0313939.

References

Friedman J, Hastie T, Tibshirani R . Regularization Paths for Generalized Linear Models via Coordinate Descent. J Stat Softw. 2010; 33(1):1-22. PMC: 2929880. View

Pont F, Tosolini M, Fournie J . Single-Cell Signature Explorer for comprehensive visualization of single cell signatures across scRNA-seq datasets. Nucleic Acids Res. 2019; 47(21):e133. PMC: 6868346. DOI: 10.1093/nar/gkz601. View

Hou R, Denisenko E, Ong H, Ramilowski J, Forrest A . Predicting cell-to-cell communication networks using NATMI. Nat Commun. 2020; 11(1):5011. PMC: 7538930. DOI: 10.1038/s41467-020-18873-z. View

Ma X, Zhu H, Cheng L, Chen X, Shu K, Zhang S . Targeting FGL2 in glioma immunosuppression and malignant progression. Front Oncol. 2022; 12:1004700. PMC: 9606621. DOI: 10.3389/fonc.2022.1004700. View

Subramanian A, Tamayo P, Mootha V, Mukherjee S, Ebert B, Gillette M . Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005; 102(43):15545-50. PMC: 1239896. DOI: 10.1073/pnas.0506580102. View

Kanehisa M . Toward understanding the origin and evolution of cellular organisms. Protein Sci. 2019; 28(11):1947-1951. PMC: 6798127. DOI: 10.1002/pro.3715. View

Pan J, Zhu J, Wang M, Yang T, Hu C, Yang J . Association of MYC gene polymorphisms with neuroblastoma risk in Chinese children: A four-center case-control study. J Gene Med. 2020; 22(8):e3190. DOI: 10.1002/jgm.3190. View

Gao Y, Qi W, Sun L, Lv J, Qiu W, Liu S . FOXO3 Inhibits Human Gastric Adenocarcinoma (AGS) Cell Growth by Promoting Autophagy in an Acidic Microenvironment. Cell Physiol Biochem. 2018; 49(1):335-348. DOI: 10.1159/000492884. View

Zhao H, Li Z, Gao Y, Li J, Zhao X, Yue W . Single-Cell RNA-Sequencing Portraying Functional Diversity and Clinical Implications of IFI6 in Ovarian Cancer. Front Cell Dev Biol. 2021; 9:677697. PMC: 8425592. DOI: 10.3389/fcell.2021.677697. View

10.

Rouhimoghadam M, Safarian S, Carroll J, Sheibani N, Bidkhori G . Tamoxifen-Induced Apoptosis of MCF-7 Cells via GPR30/PI3K/MAPKs Interactions: Verification by ODE Modeling and RNA Sequencing. Front Physiol. 2018; 9:907. PMC: 6050429. DOI: 10.3389/fphys.2018.00907. View

11.

Ma B, Wen S, Luo Y, Zhang T, Yang Y, Shen C . Targeting Tumor Hypoxia Inhibits Aggressive Phenotype of Dedifferentiated Thyroid Cancer. J Clin Endocrinol Metab. 2022; 108(2):368-384. DOI: 10.1210/clinem/dgac548. View

12.

Binlateh T, Reudhabibadh R, Prommeenate P, Hutamekalin P . Investigation of mechanisms underlying the inhibitory effects of metformin against proliferation and growth of neuroblastoma SH-SY5Y cells. Toxicol In Vitro. 2022; 83:105410. DOI: 10.1016/j.tiv.2022.105410. View

13.

Li J, Chen S, Pan X, Yuan Y, Shen H . Cell clustering for spatial transcriptomics data with graph neural networks. Nat Comput Sci. 2024; 2(6):399-408. DOI: 10.1038/s43588-022-00266-5. View

14.

Nakagawara A, Li Y, Izumi H, Muramori K, Inada H, Nishi M . Neuroblastoma. Jpn J Clin Oncol. 2018; 48(3):214-241. DOI: 10.1093/jjco/hyx176. View

15.

Peng L, Yuan R, Han C, Han G, Tan J, Wang Z . CellEnBoost: A Boosting-Based Ligand-Receptor Interaction Identification Model for Cell-to-Cell Communication Inference. IEEE Trans Nanobioscience. 2023; 22(4):705-715. DOI: 10.1109/TNB.2023.3278685. View

16.

Keyel M, Reynolds C . Spotlight on dinutuximab in the treatment of high-risk neuroblastoma: development and place in therapy. Biologics. 2019; 13:1-12. PMC: 6306059. DOI: 10.2147/BTT.S114530. View

17.

Wang T, Sun J, Zhao Q . Investigating cardiotoxicity related with hERG channel blockers using molecular fingerprints and graph attention mechanism. Comput Biol Med. 2022; 153:106464. DOI: 10.1016/j.compbiomed.2022.106464. View

18.

Liu X, Wang Q, Yang D, Fu M, Yang M, Bi Y . Association between Gastrointestinal Dysfunction Score (GIDS) and disease severity and prognosis in critically ill patients: A prospective, observational study. Clin Nutr. 2023; 42(5):700-705. DOI: 10.1016/j.clnu.2023.03.004. View

19.

Parihar R, Rivas C, Huynh M, Omer B, Lapteva N, Metelitsa L . NK Cells Expressing a Chimeric Activating Receptor Eliminate MDSCs and Rescue Impaired CAR-T Cell Activity against Solid Tumors. Cancer Immunol Res. 2019; 7(3):363-375. PMC: 7906796. DOI: 10.1158/2326-6066.CIR-18-0572. View

20.

Kanehisa M, Furumichi M, Sato Y, Kawashima M, Ishiguro-Watanabe M . KEGG for taxonomy-based analysis of pathways and genomes. Nucleic Acids Res. 2022; 51(D1):D587-D592. PMC: 9825424. DOI: 10.1093/nar/gkac963. View