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Abstract Background Glioblastoma (GBM) is more difficult to treat than other intractable adult tumors. The main reason that GBM is so difficult to treat is that it is highly infiltrative. Migrasomes are newly discovered membrane structures observed in migrating cells. Thus, they can be generated from GBM cells that have the ability to migrate along the brain parenchyma. However, the function of migrasomes has not yet been elucidated in GBM cells. Results Here, we describe the composition and function of migrasomes generated along with GBM cell migration. Proteomic analysis revealed that LC3B-positive autophagosomes were abundant in the migrasomes of GBM cells. An increased number of migrasomes was observed following treatment with chloroquine (CQ) or inhibition of the expression of STX17 and SNAP29, which are involved in autophagosome/lysosome fusion. Furthermore, depletion of ITGA5 or TSPAN4 did not relieve endoplasmic reticulum (ER) stress in cells, resulting in cell death. Conclusions Taken together, our study suggests that increasing the number of autophagosomes, through inhibition of autophagosome/lysosome fusion, generates migrasomes that have the capacity to alleviate cellular stress.

Abstract Capicua (CIC) is an important downstream molecule of RTK/RAS/MAPK pathway. The regulatory mechanism of CIC underlying tumorigenesis in oligodendroglioma, where CIC is frequently mutated, has yet to be fully elucidated. Using patient-derived glioma lines, RNA-sequencing and bioinformatic analysis of publicly available databases, we investigated how CIC loss- or gain-of-function regulates its downstream targets, cell proliferation and glutamate release. Our results indicate an increased frequency of CIC truncating mutations in oligodendroglioma during progression. In vitro, CIC modulation had a modest effect on cell proliferation in glioma lines, and no significant changes in the expression of ETV1, ETV4 and ETV5. Transcriptional repression of known CIC targets was observed in gliomas expressing non-phosphorylatable CIC variant on Ser173 which was unable to interact with 14-3-3. These data outline a mechanism by which the repressor function of CIC is inhibited by 14-3-3 in gliomas. Using transcriptional profiling, we found that genes related to glutamate release were upregulated because of CIC depletion. In addition, loss of CIC leads to increased extracellular glutamate. Consistent with this, CIC restoration in an oligodendroglioma line reduced the levels of extracellular glutamate, neuronal toxicity and xCT/SLC7A11 expression. Our findings may provide a molecular basis for the prevention of glioma-associated seizures.

Abstract Background Gene expression data is widely used for identifying subtypes of diseases such as cancer. Differentially expressed gene analysis and gene set enrichment analysis are widely used for identifying biological mechanisms at the gene level and gene set level, respectively. However, the results of differentially expressed gene analysis are difficult to interpret and gene set enrichment analysis does not consider the interactions among genes in a gene set. Results We present CONFIGURE, a pipeline that identifies context specific regulatory modules from gene expression data. First, CONFIGURE takes gene expression data and context label information as inputs and constructs regulatory modules. Then, CONFIGURE makes a regulatory module enrichment score (RMES) matrix of enrichment scores of the regulatory modules on samples using the single-sample GSEA method. CONFIGURE calculates the importance scores of the regulatory modules on each context to rank the regulatory modules. We evaluated CONFIGURE on the Cancer Genome Atlas (TCGA) breast cancer RNA-seq dataset to determine whether it can produce biologically meaningful regulatory modules for breast cancer subtypes. We first evaluated whether RMESs are useful for differentiating breast cancer subtypes using a multi-class classifier and one-vs-rest binary SVM classifiers. The multi-class and one-vs-rest binary classifiers were trained using the RMESs as features and outperformed baseline classifiers. Furthermore, we conducted literature surveys on the basal-like type specific regulatory modules obtained by CONFIGURE and showed that highly ranked modules were associated with the phenotypes of basal-like type breast cancers. Conclusions We showed that enrichment scores of regulatory modules are useful for differentiating breast cancer subtypes and validated the basal-like type specific regulatory modules by literature surveys. In doing so, we found regulatory module candidates that have not been reported in previous literature. This demonstrates that CONFIGURE can be used to predict novel regulatory markers which can be validated by downstream wet lab experiments. We validated CONFIGURE on the breast cancer RNA-seq dataset in this work but CONFIGURE can be applied to any gene expression dataset containing context information.

Abstract Background Genetic engineering technology such as clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system provides a powerful tool for developing disease models and determining gene functions. Recent interests in canine cancer models have highlighted the necessity of developing genetic engineering tools for dogs. In this study, we attempted to generate optimized CRISPR/Cas9 system to target canine tumor protein 53 (TP53), one of the most crucial tumor suppressor genes, to establish TP53 knockout canine cells for canine cancer research. Results We constructed CRISPR/Cas9 vectors using each of three TP53 gene-targeting guide RNAs (gRNAs) with minimal off-target potential. After transfection, we obtained several clones of TP53 knockout cells containing “indel” mutations in the targeted locus which had infinite cellular life span, resistance to genotoxicity, and unstable genomic status in contrast to normal cells. Of the established TP53 knockout cells, TP53KO#30 cells targeted by TP53 gRNA #30 showed non-cancerous phenotypes without oncogenic activation both in vitro and in vivo. More importantly, no off-target alteration was detected in TP53KO#30 cells. We also tested the developmental capacity of TP53 knockout cells after application of the somatic cell nuclear transfer technique. Conclusions Our results indicated that TP53 in canine cells was effectively and specifically targeted by our CRISPR/Cas9 system. Thus, we suggest our CRISPR/Cas9-derived canine TP53 knockout cells as a useful platform to reveal novel oncogenic functions and effects of developing anti-cancer therapeutics.

Abstract Background The porcine brain is gyrencephalic with similar gray and white matter composition and size more comparable to the human rather than the rodent brain; however, there is lack of information about neural progenitor cells derived from this model. Results Here, we isolated GFAP-positive porcine neural stem cells (NSCs) from the brain explant of a transgenic piglet, with expression of CreERT2 under the control of the GFAP promoter (pGFAP-CreERT2). The isolated pGFAP-CreERT2 NSCs showed self-renewal and expression of representative NSC markers such as Nestin and Sox2. Pharmacological inhibition studies revealed that Notch1 signaling is necessary to maintain NSC identity, whereas serum treatment induced cell differentiation into reactive astrocytes and neurons. Conclusions Collectively, these results indicate that GFAP promoter-driven porcine CreERT2 NSCs would be a useful tool to study neurogenesis of the porcine adult central nervous system and furthers our understanding of its potential clinical application in the future. Graphical abstract ᅟ