International Journal of Molecular Sciences

The establishment and development of single-cell RNA-sequencing (scRNA-seq) technology has accelerated the analysis of cell genome characteristics down to the single-cell level. Despite the rapid development of scRNA-seq technology, we cannot obtain a complete gene expression matrix in the biological experiments, and the scRNA-seq data obtained from experiments also have a high dropout rate. Unfortunately, gene expression analysis and clustering tools require a complete matrix of gene expression values for classification or clustering calculations. Most imputation methods focus on the impact of the imputed high-dimensional expression matrix on clustering and cannot obtain the low-dimensional representation matrix, which may have an even better guiding effect on clustering. To this end, we designed an iterative imputation pipeline called scIRT to estimate dropout events for scRNA-seq and achieve dimensionality reduction simultaneously by combining the synthetic minority over-sampling technique (SMOTE) and non-negative matrix factorization (NMF). The adaptation of SMOTE effectively imputes missing data, while NMF performs dimensionality reduction and feature extraction on high-dimensional data. Using several scRNA-seq datasets, we demonstrated that this new approach achieved better and more robust performance than the existing approaches. We also compared the different effects of the imputed matrix and the low-dimensional representation matrix on clustering. ScIRT is a tool that can be used to preprocess scRNA-seq data. It can effectively recover missing data from scRNA-seq to facilitate downstream analyses such as cell type clustering and visualization.

Calcium (Ca²⁺)signaling dysfunction is a central contributor to neuronal hyperexcitability and seizure propagation in epilepsy, yet the intracellular mechanisms underlying the actions of valproic acid (VPA) remain incompletely understood. In this study, we investigated whether VPA modulates Ca²⁺ homeostasis at the level of the endoplasmic reticulum (ER) and how this action influences cytosolic Ca²⁺ dynamics associated with epileptiform activity. ER Ca²⁺ levels were directly measured using ER-targeted aequorin in HeLa and PC12 cells, while cytosolic Ca²⁺ signals were monitored by fura-2 fluorescence imaging in bovine chromaffin cells exposed to veratridine, a model of sustained sodium channel activation and Ca²⁺ oscillations. VPA induced a concentration-dependent release of Ca²⁺ from the ER, with an IC₅₀ of approximately 17 µM. This effect was preserved in permeabilized cells and exhibited activation kinetics comparable to those elicited by inositol 1,4,5-trisphosphate (InsP₃). Pharmacological inhibition of InsP₃ receptors (InsP₃Rs), but not ryanodine receptors or SERCA, abolished VPA-induced ER Ca²⁺ release, supporting a selective InsP₃R-mediated mechanism. Functionally, VPA suppressed the repetitive cytosolic Ca²⁺ oscillations induced by veratridine, while simultaneously producing a sustained elevation of cytosolic Ca²⁺ originating from ER stores and facilitating depolarization-evoked catecholamine secretion. Together, these results support the conclusion that VPA induces InsP₃R-mediated Ca²⁺ mobilization from the endoplasmic reticulum and identify ER Ca²⁺ release as a previously unrecognized intracellular mechanism contributing to its modulatory effects on Ca²⁺ signaling and excitability in epilepsy.

With the progress of global aging, osteoporosis, as a systemic bone disease, has become an increasingly serious public health problem. Osteoporosis has an insidious onset, and the fractures it causes have a high rate of disability and mortality. Early diagnosis and intervention of the disease are particularly important. Currently, diagnostic methods for osteoporosis, such as dual-energy X-ray absorptiometry (DXA), quantitative computed tomography (QCT), and bone turnover markers (BTM), all have their limitations. miRNA is a type of non-coding RNA that plays a role in the epigenetic regulation of gene expression. A large number of studies have shown that miRNA is involved in the formation and functional execution of osteoblasts. The differential expression of miRNA levels can effectively distinguish osteoporosis patients from normal individuals, and miRNA detection has the advantages of simple sample collection, non-invasive measurement, specificity for bone metabolism, correct correlation with standard techniques for bone remodeling analysis, and the ability to respond to the treatment of diseases affecting bone metabolism. This makes miRNAs potentially effective diagnostic markers for osteoporosis. This article aims to summarize our current understanding of miRNA regulation of osteoblast generation and function, and we will also discuss the potential value of these miRNAs as biomarkers for the diagnosis of osteoporosis.