Post-transcriptional regulation of the transition from neural stem cells to early neuroblasts

In mammals, the process of neurogenesis consists in the generation of various types of neuronal and glial cells from neural stem cells (NSCs). It begins intensively at the embryonic stage and continues through the whole adulthood. In adult rodents, neurogenesis is mainly located in two regions: the ventricular-subventricular zone (V-SVZ) of the lateral ventricles and the dentate gyrus of the hippo-campus. In the last two decades huge progress has been made to characterize the process in detail and to get further insights of its regulation. However, still some fundamental questions remain unanswered. Among those, whether post-transcriptional regulation plays a critical role in NSC activation and differentiation. In this project, I investigated protein synthesis and its modulation upon activation of NSCs using the mouse adult brain as an experimental model. The analysis of the nascent synthesized peptides in NSCs and early neuroblasts (ENBs) of the same lineage revealed that the level of global protein synthesis decreases upon the transition from NSCs to ENBs. The transcriptome and translatome analysis of NSCs and ENBs clearly showed an active involvement of post-transcriptional regulation in gene expression at the onset of NSC differentiation. In particular, translation of neuronal specification transcripts such as Sp8 and Dusp4 was enhanced. On the contrary, the translation of some mRNAs carrying the Terminal Oligo Pyrimidine (TOP) and the Pyrimidine Rich Motif (PRM) such as Sox2 and Rpl18 were selectively repressed. At this transition, we also observed a drop of mTOR activity upon cell cycle exit that was causally linked to repression of TOP- and PRM-transcripts. Altogether, our study underscored the role of protein synthesis and its regulation in NSC differentiation. It also demonstrated a causal link between cell cycle exit, TOR activity and exit of the stem cell state

The Thioesterase ACOT1 as a Regulator of Lipid Metabolism in Type 2 Diabetes Detected in a Multi-Omics Study of Human Liver

Type 2 diabetes (T2D) is characterized by pathophysiological alterations in lipid metabolism. One strategy to understand the molecular mechanisms behind these abnormalities is to identify cis-regulatory elements (CREs) located in chromatin-accessible regions of the genome that regulate key genes. In this study we integrated assay for transposase-accessible chromatin followed by sequencing (ATAC-seq) data, widely used to decode chromatin accessibility, with multi-omics data and publicly available CRE databases to identify candidate CREs associated with T2D for further experimental validations. We performed high-sensitive ATAC-seq in nine human liver samples from normal and T2D donors, and identified a set of differentially accessible regions (DARs). We identified seven DARs including a candidate enhancer for the ACOT1 gene that regulates the balance of acyl-CoA and free fatty acids (FFAs) in the cytoplasm. The relevance of ACOT1 regulation in T2D was supported by the analysis of transcriptomics and proteomics data in liver tissue. Long-chain acyl-CoA thioesterases (ACOTs) are a group of enzymes that hydrolyze acyl-CoA esters to FFAs and coenzyme A. ACOTs have been associated with regulation of triglyceride levels, fatty acid oxidation, mitochondrial function, and insulin signaling, linking their regulation to the pathogenesis of T2D. Our strategy integrating chromatin accessibility with DNA binding and other types of omics provides novel insights on the role of genetic regulation in T2D and is extendable to other complex multifactorial diseases

Phenotypic Diversity Analysis in <i>Elaeagnus angustifolia</i> Populations in Gansu Province, China

As a highly resistant urban ornamental plant, Elaeagnus angustifolia L. is often used in dry land, saline-alkali land shelter forest, and landscape horticulture. It is the main windbreak and sand-fixing tree species in Gansu Province, China. The special geographical and climatic environment makes the distribution and growth of E. angustifolia in Gansu Province show different degrees of difference. In order to evaluate the phenotypic diversity of E. angustifolia in different populations and its variation patterns under different geographical and climatic conditions, 35 phenotypic traits (trunk, branch, leaf, and flower related traits) of 90 plants from 10 populations in Gansu Province were measured and analyzed. The results showed the following: (1) E. angustifolia has rich phenotypic variation. The variation is greater among populations. The traits with the largest and smallest coefficients of variation were “under-branch height” and “flower diameter”, respectively. The variation in the Qilihe population was the largest, and the variation in the Ganzhou population was the smallest. The diversity of flowers and leaves is relatively higher. (2) Correlation analysis showed that most of traits were closely related. Leaf traits showed a gradient variation law dominated by altitude and precipitation. Flower traits were affected by the synergistic effects of various geographical and climatic factors. (3) The results of the principal component analysis (PCA) showed that the primary traits affecting the phenotypic diversity of E. angustifolia were leaf size and branch length among the related traits of trunk, branch, leaf, and flower. (4) Cluster analysis showed that 90 E. angustifolia plants were clustered into four clusters that were not completely clustered according to geographical distance and may be randomly affected by genotypic or environmental factors. These results will lay a foundation for further analysis of the genetic mechanism of phenotypic traits of E. angustifolia and also provide a reference for the collection, preservation, and variety improvement of E. angustifolia germplasm resources

Data from: Wnt/PCP controls spreading of Wnt/β-catenin signals by cytonemes in vertebrates

Signaling filopodia, termed cytonemes, are dynamic actin-based membrane structures that regulate the exchange of signaling molecules and their receptors within tissues. However, how cytoneme formation is regulated remains unclear. Here, we show that Wnt/PCP autocrine signaling controls the emergence of cytonemes, and that cytonemes subsequently control paracrine Wnt/β-catenin signal activation. Upon binding of the Wnt family member Wnt8a, the receptor tyrosine kinase Ror2 gets activated. Ror2/PCP signaling leads to induction of cytonemes, which mediate transport of Wnt8a to neighboring cells. In the Wnt receiving cells, Wnt8a on cytonemes triggers Wnt/β-catenin-dependent gene transcription and proliferation. We show that cytoneme-based Wnt transport operates in diverse processes, including zebrafish development, the murine intestinal crypt, and human cancer organoids, demonstrating that Wnt transport by cytonemes and its control via the Ror2 pathway is highly conserved in vertebrates

Cell-lineage controlled epigenetic regulation in glioblastoma stem cells determines functionally distinct subgroups and predicts patient survival

The epigenetic regulation of glioblastoma stem cell (GSC) function remains poorly understood. Here, the authors compare the chromatin accessibility landscape of GSC cultures from mice and patients and suggest that the epigenome of GSCs is cell lineage-regulated and could predict patient survival. There is ample support for developmental regulation of glioblastoma stem cells. To examine how cell lineage controls glioblastoma stem cell function, we present a cross-species epigenome analysis of mouse and human glioblastoma stem cells. We analyze and compare the chromatin-accessibility landscape of nine mouse glioblastoma stem cell cultures of three defined origins and 60 patient-derived glioblastoma stem cell cultures by assay for transposase-accessible chromatin using sequencing. This separates the mouse cultures according to cell of origin and identifies three human glioblastoma stem cell clusters that show overlapping characteristics with each of the mouse groups, and a distribution along an axis of proneural to mesenchymal phenotypes. The epigenetic-based human glioblastoma stem cell clusters display distinct functional properties and can separate patient survival. Cross-species analyses reveals conserved epigenetic regulation of mouse and human glioblastoma stem cells. We conclude that epigenetic control of glioblastoma stem cells primarily is dictated by developmental origin which impacts clinically relevant glioblastoma stem cell properties and patient survival.De två första författarna delar förstaförfattarskapet.De två sista författarna delar sistaförfattarskapet.</p

FACT-seq : profiling histone modifications in formalin-fixed paraffin-embedded samples with low cell numbers

The majority of biopsies in both basic research and translational cancer studies are preserved in the format of archived formalin-fixed paraffin-embedded (FFPE) samples. Profiling histone modifications in archived FFPE tissues is critically important to understand gene regulation in human disease. The required input for current genome-wide histone modification profiling studies from FFPE samples is either 10-20 tissue sections or whole tissue blocks, which prevents better resolved analyses. But it is desirable to consume a minimal amount of FFPE tissue sections in the analysis as clinical tissues of interest are limited. Here, we present FFPE tissue with antibody-guided chromatin tagmentation with sequencing (FACT-seq), the first highly sensitive method to efficiently profile histone modifications in FFPE tissues by combining a novel fusion protein of hyperactive Tn5 transposase and protein A (T7-pA-Tn5) transposition and T7 in vitro transcription. FACT-seq generates high-quality chromatin profiles from different histone modifications with low number of FFPE nuclei. We proved a very small piece of FFPE tissue section containing similar to 4000 nuclei is sufficient to decode H3K27ac modifications with FACT-seq. H3K27ac FACT-seq revealed disease-specific super enhancers in the archived FFPE human colorectal and human glioblastoma cancer tissue. In summary, FACT-seq allows decoding the histone modifications in archival FFPE tissues with high sensitivity and help researchers to better understand epigenetic regulation in cancer and human disease

Data from Mattes 2018

Kinase Screen and automated image-analysis identifies the receptor tyrosine kinase Ror2 as a potential cytoneme regulator upstream of Cdc42. Wnt8a-GFP and a membrane bound mCherry was co-transfected with kinase library genes in Pac2 cells in a 96-well plate. Images were acquired automatically and analyzed for filopodia length and numbers by a filopodia detection software. Automated Image analysis software detects and counts filopodia of single cells using the memCherry signal and quantifies their length by automatically tracing the tips back to the cell body. Table shows transfected kinase genes and their relative filopodia number/cell and length

Focal amplifications are associated with chromothripsis events and diverse prognoses in gastric cardia adenocarcinoma

The role of focal amplifications and extrachromosomal DNA (ecDNA) is unknown in gastric cardia adenocarcinoma (GCA). Here, we identify frequent focal amplifications and ecDNAs in Chinese GCA patient samples, and find focal amplifications in the GCA cohort are associated with the chromothripsis process and may be induced by accumulated DNA damage due to local dietary habits. We observe diverse correlations between the presence of oncogene focal amplifications and prognosis, where ERBB2 focal amplifications positively correlate with prognosis and EGFR focal amplifications negatively correlate with prognosis. Large-scale ERBB2 immunohistochemistry results from 1668 GCA patients show survival probability of ERBB2 positive patients is lower than that of ERBB2 negative patients when their surviving time is under 2 years, however, the tendency is opposite when their surviving time is longer than 2 years. Our observations indicate that the ERBB2 focal amplifications may represent a good prognostic marker in GCA patients