1-phenyl 2-thiourea (PTU) activates autophagy in zebrafish embryos

A Novel Lysosome-Related Gene Signature Predicts Lung Cancer Prognosis: A Bioinformatics-Driven Study

Background and Aims

The biological function of lysosomes has been increasingly appreciated in cancer. However, the relationship between lysosome and lung adenocarcinoma (LUAD) was not well understood. In this study, a lysosome-related signature was developed for LUAD risk stratification and prognosis prediction.

Methods

Download RNA-seq data of LUAD and clinical information of corresponding samples from the UCSC-Xena platform. GSE31210 databases is used as a validation cohort. The lysosome-related genes was obtained from molecular signature database. The differentially expressed genes (DEGs) as well as lysosome-associated prognosis signatures were identified by using univariate, multivariate cox, and Lasso regression. A nomogram was constructed and evaluated using ROC and DCA.

Results

A total of 109 lysosome-related DEGs were identified and 30 prognostic related DEGs were subsequently screened. Cluster analysis further divides the TCGA cohort into clusters 1 and 2. Patients in cluster 2 had a worse prognosis (p = 0.016), lower LYSOSOME score. Enrichment analysis showed that 21 significantly enriched gene sets in the cluster 2 were activated. And 10 pathways, such as E2F_TARGETS, G2M_CHECKPOINT were upregulated. Multivariate Cox regression analysis identified 17 best prognostic genes as risk signature. An independent prognostic factor, the risk signature, was identified. A prognostic nomogram including risk signature, age, TNM stage, and gender was constructed, and ROC and DCA curves proved its excellent performance. We examined CTSZ and AP3S2 protein expression in 48 stage 3-4 NSCLC samples. Low AP3S2 expression was associated with better prognosis (median overall survival: 37.87 vs. 8.53 months, p = 0.0211). Increased CTSZ expression also indicated better prognosis (median overall survival: 6.77 vs. 30.50 months, p = 0.0306).

Conclusion

We identified molecular subtypes and lysosomal-based prognostic signatures for LUAD patients, as well as 17 genes that serve as a biomarker for evaluating the prognosis of LUAD patients.

Autophagic stress activates distinct compensatory secretory pathways in neurons

Autophagic dysfunction is a hallmark of neurodegenerative disease, leaving neurons vulnerable to the accumulation of damaged organelles and proteins. However, the late onset of diseases suggests that compensatory quality control mechanisms may be engaged to delay the deleterious effects induced by compromised autophagy. Neurons expressing common familial Parkinson's disease (PD)-associated mutations in LRRK2 kinase exhibit defective autophagy. Here, we demonstrate that both primary murine neurons and human iPSC-derived neurons harboring pathogenic LRRK2 upregulate the secretion of extracellular vesicles. We used unbiased proteomics to characterize the secretome of LRRK2G2019S neurons and found that autophagic cargos including mitochondrial proteins were enriched. Based on these observations, we hypothesized that autophagosomes are rerouted toward secretion when cell-autonomous degradation is compromised, likely to mediate clearance of undegraded cellular waste. Immunoblotting confirmed the release of autophagic cargos and immunocytochemistry demonstrated that secretory autophagy was upregulated in LRRK2G2019S neurons. We also found that LRRK2G2019S neurons upregulate the release of exosomes containing miRNAs. Live-cell imaging confirmed that this upregulation of exosomal release was dependent on hyperactive LRRK2 activity, while pharmacological experiments indicate that this release staves off apoptosis. Finally, we show that markers of both vesicle populations are upregulated in plasma from mice expressing pathogenic LRRK2. In sum, we find that neurons expressing pathogenic LRRK2 upregulate the compensatory release of secreted autophagosomes and exosomes, to mediate waste disposal and transcellular communication, respectively. We propose that this increased secretion contributes to the maintenance of cellular homeostasis, delaying neurodegenerative disease progression over the short term while potentially contributing to increased neuroinflammation over the longer term.

Single-nucleus transcriptome profiling of prefrontal cortex induced by chronic methamphetamine treatment

Background

Methamphetamine (METH) addiction causes a huge burden on society. The prefrontal cortex (PFC), associated with emotion and cognitive behaviours, is also involved in addiction neurocircuitry. Although bulk RNA sequencing has shown METH-induced gene alterations in the mouse PFC, the impact on different cell types remains unknown.

Aims

To clarify the effects of METH treatment on different cell types of the PFC and the potential pathways involved in METH-related disorders.

Methods

We performed single-nucleus RNA sequencing (snRNA-seq) to examine the transcriptomes of 20 465 nuclei isolated from the PFC of chronic METH-treated and control mice. Main cell types and differentially expressed genes (DEGs) were identified and confirmed by RNA fluorescence in situ hybridization(FISH).

Results

Six main cell types were identified depending on the single-cell nucleus sequencing; of particular interest were the mature oligodendrocytes in the PFC. The DEGs of mature oligodendrocytes were enriched in the myelin sheath, adenosine triphosphate (ATP) metabolic process, mitochondrial function and components, and so on. The messenger RNA levels of Aldoc and Atp5l (FISH) and the protein level of the mitochondrial membrane pore subunit TOM40 (immunofluorescence) decreased in the mature oligodendrocytes. Fast blue staining and transmission electron microscopy image indicated myelin damage, and the myelin thickness decreased in METH brains.

Conclusions

snRNA-seq reveals altered transcriptomes of different cell types in mouse PFC induced by chronic METH treatment, underscoring potential relationships with psychiatric disorders.

Zebrafish as a Model Organism for Studying Pathologic Mechanisms of Neurodegenerative Diseases and other Neural Disorders

Zebrafish are widely considered an excellent vertebrate model for studying the pathogenesis of human diseases because of their transparency of embryonic development, easy breeding, high similarity with human genes, and easy gene manipulation. Previous studies have shown that zebrafish as a model organism provides an ideal operating platform for clarifying the pathological and molecular mechanisms of neurodegenerative diseases and related human diseases. This review mainly summarizes the achievements and prospects of zebrafish used as model organisms in the research of neurodegenerative diseases and other human diseases related to the nervous system in recent years. In the future study of human disease mechanisms, the application of the zebrafish model will continue to provide a valuable operating platform and technical support for investigating and finding better prevention and treatment of these diseases, which has broad application prospects and practical significance. Zebrafish models used in neurodegenerative diseases and other diseases related to the nervous system.