Biology subjects

Watanabe, H.

Publications and source records attributed to Watanabe, H..

59 records · Page 4Linked to original sources

bioRxiv2019

Cooperating lineage factors SOX2 and BRN2 govern the transcriptional program of the neural subtype of lung squamous cell carcinoma

Molecular characterization of lung squamous cell carcinoma (LUSC), a major subtype of lung cancer, has not sufficiently improved its non-stratified treatment strategies over decades. Accumulating evidence suggests that lineage-specific transcriptional regulators control differentiation states during cancer evolution, and underlie their distinct biological behaviors. In this study, by investigating the super-enhancer landscape of LUSC, we identified a previously undescribed neural subtype defined by Sox2 and a neural lineage factor Brn2, as well as the classical LUSC subtype defined by Sox2 and its classical squamous partner p63. Robust protein-protein interaction and genomic co-occupancy of Sox2 and Brn2, in place for p63 in the classical LUSC, indicated their transcriptional cooperation imparting this unique lineage state in the neural LUSC. Forced expression of p63 downregulated Brn2 in the neural LUSC cells and invoked the classical LUSC lineage with more squamous/epithelial features, which were accompanied by increased activities of ErbB/Akt and MAPK-ERK pathways suggesting differential dependency. Collectively, our data demonstrate heterogeneous cell lineage states of LUSC featured by Sox2 cooperation with Brn2 or p63, for which distinct therapeutic approaches may be warranted.

cancer biology↗

bioRxiv2019

Comparison of prokaryotic communities between the fields showing different disinfestation effects by anaerobic soil disinfestation

Anaerobic soil disinfestation (ASD) is a chemical-independent fumigation method used for reducing the abundance of pathogens at soil depths of <40 cm. However, its disinfestation efficiency is unstable under field conditions. The microbial community reflects the soil environment and is a good indicator of soil health. Therefore, soil with a good disinfestation efficiency may have a unique microbial community. The aim of the present study was to compare the prokaryotic communities among soils obtained from 17 geographically different greenhouses that experienced tomato bacterial wilt but exhibited different disinfestation efficiencies after ASD treatment with the same substrate. In the present study, soil prokaryotic communities in the field, which indicate difference in disinfestation effects after ASD treatment among several fields, were compared using next-generation sequencing. The prokaryotic communities in the fields showing different disinfestation effects were roughly separated into sampling fields. The relative abundances of Betaproteobacteria and Clostridia were significantly increased in well-disinfested fields. Overall, 25 operational taxonomic units (OTUs) were specifically increased in various well-disinfested soils and 18 OTUs belonged to phylogenetically diversified Clostridia. Other OTUs belonged to aerobic bacteria and were not previously detected in sample collected from ASD-treated fields. The results showed that the changes to the prokaryotic communities did not affect ASD efficiency, whereas changes in the abundance of specific microbes in the community were related to disinfestation.

microbiology↗

bioRxiv2019

A combined strategy of neuropeptide predictions and tandem mass spectrometry identifies evolutionarily conserved ancient neuropeptides in the sea anemone Nematostella vectensis

Neuropeptides are a class of bioactive peptides and are responsible for various physiological processes including metabolism, development and reproduction. Although accumulated genome and transcriptome data have reported a number of neuropeptide candidates, it still remains difficult to obtain a comprehensive view of neuropeptide repertoires due to their small and variable nature. Neuropeptide prediction tools usually work only for those peptides for which sequentially related homologs have previously been identified. Recent peptidomics technology has enabled systematic structural identification of neuropeptides by using the combination of liquid chromatography and tandem mass spectrometry. However, obtaining reliable identifications of endogenous peptides is still difficult using a conventional tandem mass spectrometry-based peptide identification approach using protein database because a large search space has to be scanned due to the absence of a cleavage enzyme specification. We developed a pipeline consisting of the prediction of in silico cleaved endogenous neuropeptides followed by peptide-spectrum matching enabling highly sensitive and reliable neuropeptide identification. This approach effectively reduces the search space of peptide-spectrum matching, and thus increases search sensitivity. To identify neuropeptides in Nematostella vectensis, a basal eumetazoan having one of the most primitive nervous systems, we scanned the Nematostella protein database for sequences displaying structural hallmarks of metazoan neuropeptides, including C/N-terminal structures and modifications. Peptide-spectrum matching was performed against the in silico cleaved peptides and successfully identified dozens of neuropeptides at high confidence. The identification of Nematostella neuropeptides structurally related the tachykinin, GnRH/AKH, neuromedin-U/pyrokinin peptide families indicate that these peptides already originated in the eumetazoan ancestor of all animal species, most likely concomitantly with the development of a nervous system.

biochemistry↗

bioRxiv2018

Generation of white-eyed Daphnia magna mutants lacking scarlet function

The crustacean Daphnia magna is an important model in multi-disciplinary scientific fields such as genetics, evolutionary developmental biology, toxicology, and ecology. Recently, draft genome sequence and transcriptome data became publicly available for this species. Genetic transformation by introduction of plasmid DNA into a genome has been achieved. To further advance D. magna functional genomics, identification of a screenable marker gene and generation of its mutant are indispensable. Because Daphnia is more closely related to insects among crustaceans, we hypothesized that eye color-related genes can function as a marker gene as used in Drosophila genetics. We searched orthologs of Drosophila eye pigment transporters White, Scarlet, and Brown in the genome of D. magna. Amino acid sequence alignment and phylogenetic analysis suggested that D. magna has six white and one scarlet orthologs, but lacks the brown ortholog. Due to a multiplicity of white orthologs, we analyzed function of the scarlet ortholog, DapmaSt, using RNA interference. DapmaSt RNAi embryos showed disappearance of black pigments both in the compound eye and in the ocellus, suggesting that DapmaSt is necessary for black pigmentation in Daphnia eyes. To disrupt DapmaSt by using the Crispr/Cas9 system, we co-injected DapmaSt-targeting gRNAs with Cas9 mRNAs into eggs and established white-eyed DapmaSt mutant lines that lack eye pigments throughout their lifespan. Our results suggest that DapmaSt can be used as a transformation marker in D. magng+a and the DapmaSt mutants would be an important resource for genetic transformation of this species in the future.

genetics↗

bioRxiv2017

Repeated co-option of a conserved gene regulatory module underpins the evolution of the crustacean carapace, insect wings and other flat outgrowths

Summary statementThe genes vestigial, scalloped and wingless comprise a conserved regulatory module that was co-opted repeatedly for the evolution of flat structures, such as insect wings, and crustacean carapace, tergites and coxal plates.\n\nSummaryHow novelties arise is a key question in evolutionary developmental biology. The crustacean carapace is a novelty that evolved in the early Cambrian. In an extant crustacean, Daphnia magna, the carapace grows from the body wall as a double-layered sheet with a specialized margin. We show that the growing margin of this carapace expresses vestigial, scalloped and wingless, genes that are known to play key roles in regulating growth at the insect wing margin. RNAi-mediated knockdown of scalloped and wingless impair carapace development, indicating that carapace and wing might share a common mechanism for margin outgrowth. However, carapace and wings arise in different parts of the body and their margins have different orientations, arguing that these structures have independent evolutionary origins. We show that scalloped is also expressed at the margin of unrelated flat outgrowths (tergites and coxal plates) in the distantly related crustacean Parhyale hawaiensis. Based on these observations, we propose that the vestigial-scalloped-wingless gene module has a common role in the margin of diverse flat structures, originating before the divergence of major crustacean lineages and the emergence of insects. Repeated co-option of this module occurred independently in the carapace, wing and other flat outgrowths, underpinning the evolution of distinct novelties in different arthropod lineages.

developmental biology↗