Single-cell RNA sequencing data analysis utilizing multi-type graph neural networks.

Single-cell RNA sequencing (scRNA-seq) is the sequencing technology of a single cell whose expression reflects the overall characteristics of the individual cell, facilitating the research of problems at the cellular level. However, the problems of scRNA-seq such as dimensionality reduction processing of massive data, technical noise in data, and visualization of single-cell type clustering cause great difficulties for analyzing and processing scRNA-seq data. In this paper, we propose a new single-cell data analysis model using denoising autoencoder and multi-type graph neural networks (scDMG), which learns cell-cell topology information and latent representation of scRNA-seq data. scDMG introduces the zero-inflated negative binomial (ZINB) model into a denoising autoencoder (DAE) to perform dimensionality reduction and denoising on the raw data. scDMG integrates multiple-type graph neural networks as the encoder to further train the preprocessed data, which better deals with various types of scRNA-seq datasets, resolves dropout events in scRNA-seq data, and enables preliminary classification of scRNA-seq data. By employing TSNE and PCA algorithms for the trained data and invoking Louvain algorithm, scDMG has better dimensionality reduction and clustering optimization. Compared with other mainstream scRNA-seq clustering algorithms, scDMG outperforms other state-of-the-art methods in various clustering performance metrics and shows better scalability, shorter runtime, and great clustering results.

RPL41 sensitizes retinoblastoma cells to chemotherapeutic drugs via ATF4 degradation.

Retinoblastoma is the most common intraocular cancer with metastatic potential affecting infants and children. Although chemotherapy is available for retinoblastoma, side effects and drug resistance are frequent. Rpl41, encoding ribosomal protein L41 (RPL41), has been identified as a tumor suppressor gene, and its targeted degradation of activating transcription factor 4 (ATF4) produces an antitumor effect. The goal of the present study is to provide experimental evidence for the clinical application of a small peptide regimen in combination with chemotherapy for the treatment of retinoblastoma and to investigate the mechanism of their combined cytotoxicity. It was observed that treatment with the RPL41 peptide alone decreased the viability, migration, and invasion of retinoblastoma Y79 and Weri-Rb1 cells, in addition to promoting cell apoptosis and cell cycle arrest. Furthermore, RPL41 protein levels showed a significantly decreased trend in retinoblastoma specimens, whereas ATF4 protein levels tended to be increased. Mechanistically, ATF4 degradation as a result of RPL41 peptide treatment was observed in retinoblastoma Y79 and Weri-Rb1 cells. Most important, low-dose administration of the RPL41 peptide significantly enhanced the antitumor effect of carboplatin, and further analysis confirmed their synergistic effect as anti-retinoblastoma therapy, indicating that RPL41 sensitized Y79 and Weri-Rb1 retinoblastoma cells to carboplatin. Thus, our data provide a preclinical rationale for the exploration of the RPL41 peptide as a potential adjuvant to carboplatin treatment in retinoblastoma.

Mini-peptide RPL41 attenuated retinal neovascularization by inducing degradation of ATF4 in oxygen-induced retinopathy mice.

Endoplasmic reticulum (ER) stress signaling is activated in retinal degeneration disease. Activating transcription factor 4 (ATF4), an important mediator of the unfolded protein response (UPR), is a key element that maintains cell survival and proliferation in hypoxic conditions. Our previous studies showed that a small ribosomal protein L41 (RPL41) inhibits ATF4 by inducing its phosphorylation and degradation. In the present study, the effects of mini-peptide RPL41 on retinal neovascularization (RNV) in oxygen-induced retinopathy (OIR) mice was investigated. We induced OIR in C57BL/6 mice and obtained retinas from normoxia, OIR, OIR control (treated with PBS), and OIR treated (treated with RPL41) mice. Our results showed that ER stress signaling was activated and ATF4 was overexpressed in the retinas of OIR mice. After intravitreal injection of RPL41, the size of RNV and vaso-obliteration, and the number of preretinal neovascular cell nuclei in the retinas of OIR mice were significantly decreased. Western blot analysis and quantitative real-time polymerase chain reaction (qPCR) showed ATF4 and VEGF expression decreased after intravitreal injection of RPL41. Furthermore, the expression levels of inflammatory genes including TNF-α, IL-1ß, and IL-6 were significantly decreased compared with the OIR control mice. In conclusion, RPL41 prevented pathologic neovascularization and exerted anti-inflammatory effects by degrading the important ER stress factor ATF4, thus, RPL41 could be a promising therapeutic agent for the treatment of neovascular eye diseases, especially retinopathy of prematurity (ROP).