Identification of Human Global, Tissue and Within-Tissue Cell-Specific Stably Expressed Genes at Single-Cell Resolution.

Stably Expressed Genes (SEGs) are a set of genes with invariant expression. Identification of SEGs, especially among both healthy and diseased tissues, is of clinical relevance to enable more accurate data integration, gene expression comparison and biomarker detection. However, it remains unclear how many global SEGs there are, whether there are development-, tissue- or cell-specific SEGs, and whether diseases can influence their expression. In this research, we systematically investigate human SEGs at single-cell level and observe their development-, tissue- and cell-specificity, and expression stability under various diseased states. A hierarchical strategy is proposed to identify a list of 408 spatial-temporal SEGs. Development-specific SEGs are also identified, with adult tissue-specific SEGs enriched with the function of immune processes and fetal tissue-specific SEGs enriched in RNA splicing activities. Cells of the same type within different tissues tend to show similar SEG composition profiles. Diseases or stresses do not show influence on the expression stableness of SEGs in various tissues. In addition to serving as markers and internal references for data normalization and integration, we examine another possible application of SEGs, i.e., being applied for cell decomposition. The deconvolution model could accurately predict the fractions of major immune cells in multiple independent testing datasets of peripheral blood samples. The study provides a reliable list of human SEGs at the single-cell level, facilitates the understanding on the property of SEGs, and extends their possible applications.

Mesenchymal Stem Cell-Loaded Hydrogel Improves Surgical Treatment for Chronic Cerebral Ischemia.

Chronic cerebral ischemia (CCI) results in a prolonged insufficient blood supply to the brain tissue, leading to impaired neuronal function and subsequent impairment of cognitive and motor abilities. Our previous research showed that in mice with bilateral carotid artery stenosis, the collateral neovascularization post Encephalo-myo-synangiosis (EMS) treatment could be facilitated by bone marrow mesenchymal stem cells (MSCs) transplantation. Considering the advantages of biomaterials, we synthesized and modified a gelatin hydrogel for MSCs encapsulation. We then applied this hydrogel on the brain surface during EMS operation in rats with CCI, and evaluated its impact on cognitive performance and collateral circulation. Consequently, MSCs encapsulated in hydrogel significantly augment the therapeutic effects of EMS, potentially by promoting neovascularization, facilitating neuronal differentiation, and suppressing neuroinflammation. Furthermore, taking advantage of multi-RNA-sequencing and in silico analysis, we revealed that MSCs loaded in hydrogel regulate PDCD4 and CASP2 through the overexpression of miR-183-5p and miR-96-5p, thereby downregulating the expression of apoptosis-related proteins and inhibiting early apoptosis. In conclusion, a gelatin hydrogel to enhance the functionality of MSCs has been developed, and its combination with EMS treatment can improve the therapeutic effect in rats with CCI, suggesting its potential clinical benefit.

A Multi-Gene Model Effectively Predicts the Overall Prognosis of Stomach Adenocarcinomas With Large Genetic Heterogeneity Using Somatic Mutation Features.

BACKGROUND: Stomach adenocarcinoma (STAD) is one of the most common malignancies worldwide with poor prognosis. It remains unclear whether the prognosis is associated with somatic gene mutations. METHODS: In this research, we collected two independent STAD cohorts with both genetic profiling and clinical follow-up data, systematically investigated the association between the prognosis and somatic mutations, and analyzed the influence of heterogeneity on the prognosis-genetics association. RESULTS: Typical association was identified between somatic mutations and overall prognosis for individual cohorts. In The Cancer Genome Atlas (TCGA) cohort, a list of 24 genes was also identified that tended to mutate within cases of the poorest prognosis. The association showed apparent heterogeneity between different cohorts, although common signatures could be identified. A machine-learning model was trained with 20 common genes that showed a similar mutation rate difference between prognostic groups in the two cohorts, and it classified the cases in each cohort into two groups with significantly different prognosis. The model outperformed both single-gene models and TNM-based staging system significantly. CONCLUSION: The study made a systematic analysis on the association between STAD prognosis and somatic mutations, identified signature genes that showed mutation preference in different prognostic groups, and developed an effective multi-gene model that can effectively predict the overall prognosis of STAD in different cohorts.