scholarly journals A cell atlas of the adult Drosophila midgut

2018 ◽  
Author(s):  
Ruei-Jiun Hung ◽  
Yanhui Hu ◽  
Rory Kirchner ◽  
Fangge Li ◽  
Chiwei Xu ◽  
...  

AbstractStudies of the adult Drosophila midgut have provided a number of insights on cell type diversity, stem cell regeneration, tissue homeostasis and cell fate decision. Advances in single-cell RNA sequencing (scRNA-seq) provide opportunities to identify new cell types and molecular features. We used inDrop to characterize the transcriptome of midgut epithelial cells and identified 12 distinct clusters representing intestinal stem cells (ISCs), enteroblasts (EBs), enteroendocrine cells (EEs), enterocytes (ECs) from different regions, and cardia. This unbiased approach recovered 90% of the known ISCs/EBs markers, highlighting the high quality of the dataset. Gene set enrichment analysis in conjunction with electron micrographs revealed that ISCs are enriched in free ribosomes and possess mitochondria with fewer cristae. We demonstrate that a subset of EEs in the middle region of the midgut expresses the progenitor marker esg and that individual EEs are capable of expressing up to 4 different gut hormone peptides. We also show that the transcription factor klumpfuss (klu) is expressed in EBs and functions to suppress EE formation. Lastly, we provide a web-based resource for visualization of gene expression in single cells. Altogether, our study provides a comprehensive resource for addressing novel functions of genes in the midgut epithelium.

Science ◽  
2019 ◽  
Vol 366 (6461) ◽  
pp. 116-120 ◽  
Author(s):  
Nathan D. Lord ◽  
Thomas M. Norman ◽  
Ruoshi Yuan ◽  
Somenath Bakshi ◽  
Richard Losick ◽  
...  

Cell fate decision circuits must be variable enough for genetically identical cells to adopt a multitude of fates, yet ensure that these states are distinct, stably maintained, and coordinated with neighboring cells. A long-standing view is that this is achieved by regulatory networks involving self-stabilizing feedback loops that convert small differences into long-lived cell types. We combined regulatory mutants and in vivo reconstitution with theory for stochastic processes to show that the marquee features of a cell fate switch in Bacillus subtilis—discrete states, multigenerational inheritance, and timing of commitments—can instead be explained by simple stochastic competition between two constitutively produced proteins that form an inactive complex. Such antagonistic interactions are commonplace in cells and could provide powerful mechanisms for cell fate determination more broadly.


Author(s):  
Trang Le ◽  
Rachel A Aronow ◽  
Arkadz Kirshtein ◽  
Leili Shahriyari

Abstract Due to the high cost of flow and mass cytometry, there has been a recent surge in the development of computational methods for estimating the relative distributions of cell types from the gene expression profile of a bulk of cells. Here, we review the five common ‘digital cytometry’ methods: deconvolution of RNA-Seq, cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT), CIBERSORTx, single sample gene set enrichment analysis and single-sample scoring of molecular phenotypes deconvolution method. The results show that CIBERSORTx B-mode, which uses batch correction to adjust the gene expression profile of the bulk of cells (‘mixture data’) to eliminate possible cross-platform variations between the mixture data and the gene expression data of single cells (‘signature matrix’), outperforms other methods, especially when signature matrix and mixture data come from different platforms. However, in our tests, CIBERSORTx S-mode, which uses batch correction for adjusting the signature matrix instead of mixture data, did not perform better than the original CIBERSORT method, which does not use any batch correction method. This result suggests the need for further investigations into how to utilize batch correction in deconvolution methods.


2020 ◽  
Vol 4 (Supplement_1) ◽  
pp. 742-742
Author(s):  
Judith Campisi

Abstract Cellular senescence is a cell fate decision that is made by many mammalian cell types in response to damage, stress or certain physiological signals. Senescent cells arrest proliferation, essentially permanently, and develop a complex multi-component senescence-associated secretory phenotype (SASP). Recent studies using human and rodent cells, tissue samples and transgenic mouse models have defined a causal role for senescent cells, acting largely through the SASP, in a surprisingly large and diverse number of age-related diseases. Subsequently, several synthetic and natural compounds have been identified that have the ability to selectively kill senescent, but not non-senescent, cells. These compounds, termed senolytics, are now of intense interest to both basic research groups and biotechnology companies because they hold promise for postponing, ameliorating or, in some cases, reversing certain age-related pathologies. A related group of compounds, termed senomorphics, hold similar promise and act by selectively suppressing certain modules of the SASP. This symposium will feature presentations on some of the latest developments in the fields of cellular senescence and the SASP and how these cellular responses affect organismal health span. The symposium will particularly emphasize recent findings on the identification and activities of senolytic and senomorphic agents that have the potential to significantly extend the health span of mammalian organisms.


Development ◽  
1996 ◽  
Vol 122 (11) ◽  
pp. 3617-3626 ◽  
Author(s):  
A.P. Newman ◽  
J.G. White ◽  
P.W. Sternberg

We have undertaken electron micrographic reconstruction of the Caenorhabditis elegans hermaphrodite uterus and determined the correspondence between cells defined by their lineage history and differentiated cell types. In this organ, many cells do not move during morphogenesis and the cell lineage may function to put cells where they are needed. Differentiated uterine cell types include the toroidal ut cells that make structural epithelium, and specialized utse and uv cells that make the connection between the uterus and the vulva. A cell fate decision in which the anchor cell (AC) induces adjacent ventral uterine intermediate precursor cells to adopt the pi fate, rather than the ground state rho, has profound consequences for terminal differentiation: all pi progeny are directly involved in making the uterine-vulval connection whereas all rho progeny contribute to ut toroids or the uterine-spermathecal valve. In addition to specifying certain uterine cell fates, the AC also induces the vulva. Its multiple inductions thereby function to coordinate the connection of an internal to an external epithelium. The AC induces the pi cells and ultimately fuses with a subset of their progeny. This is an example of reciprocal cell-cell interaction that can be studied at single cell resolution. The AC is thus a transitory cell type that plays a pivotal role in organizing the morphogenesis of the uterine-vulval connection.


2021 ◽  
Vol 27 (1) ◽  
Author(s):  
Zhendong Liu ◽  
Wang Zhang ◽  
Xingbo Cheng ◽  
Hongbo Wang ◽  
Lu Bian ◽  
...  

Abstract Background XRCC2, a homologous recombination-related gene, has been reported to be associated with a variety of cancers. However, its role in glioma has not been reported. This study aimed to find out the role of XRCC2 in glioma and reveal in which glioma-specific biological processes is XRCC2 involved based on thousands of glioma samples, thereby, providing a new perspective in the treatment and prognostic evaluation of glioma. Methods The expression characteristics of XRCC2 in thousands of glioma samples from CGGA and TCGA databases were comprehensively analyzed. Wilcox or Kruskal test was used to analyze the expression pattern of XRCC2 in gliomas with different clinical and molecular features. The effect of XRCC2 on the prognosis of glioma patients was explored by Kaplan–Meier and Cox regression. Gene set enrichment analysis (GSEA) revealed the possible cellular mechanisms involved in XRCC2 in glioma. Connectivity map (CMap) was used to screen small molecule drugs targeting XRCC2 and the expression levels of XRCC2 were verified in glioma cells and tissues by RT-qPCR and immunohistochemical staining. Results We found the overexpression of XRCC2 in glioma. Moreover, the overexpressed XRCC2 was associated with a variety of clinical features related to prognosis. Cox and meta-analyses showed that XRCC2 is an independent risk factor for the poor prognosis of glioma. Furthermore, the results of GSEA indicated that overexpressed XRCC2 could promote malignant progression through involved signaling pathways, such as in the cell cycle. Finally, doxazosin, quinostatin, canavanine, and chrysin were identified to exert anti-glioma effects by targeting XRCC2. Conclusions This study analyzed the expression pattern of XRCC2 in gliomas and its relationship with prognosis using multiple datasets. This is the first study to show that XRCC2, a novel oncogene, is significantly overexpressed in glioma and can lead to poor prognosis in glioma patients. XRCC2 could serve as a new biomarker for glioma diagnosis, treatment, and prognosis evaluation, thus bringing new insight into the management of glioma.


Development ◽  
2001 ◽  
Vol 128 (5) ◽  
pp. 711-722 ◽  
Author(s):  
T.E. Rusten ◽  
R. Cantera ◽  
J. Urban ◽  
G. Technau ◽  
F.C. Kafatos ◽  
...  

Genes of the spalt family encode nuclear zinc finger proteins. In Drosophila melanogaster, they are necessary for the establishment of head/trunk identity, correct tracheal migration and patterning of the wing imaginal disc. Spalt proteins display a predominant pattern of expression in the nervous system, not only in Drosophila but also in species of fish, mouse, frog and human, suggesting an evolutionarily conserved role for these proteins in nervous system development. Here we show that Spalt works as a cell fate switch between two EGFR-induced cell types, the oenocytes and the precursors of the pentascolopodial organ in the embryonic peripheral nervous system. We show that removal of spalt increases the number of scolopodia, as a result of extra secondary recruitment of precursor cells at the expense of the oenocytes. In addition, the absence of spalt causes defects in the normal migration of the pentascolopodial organ. The dual function of spalt in the development of this organ, recruitment of precursors and migration, is reminiscent of its role in tracheal formation and of the role of a spalt homologue, sem-4, in the Caenorhabditis elegans nervous system.


PLoS Genetics ◽  
2012 ◽  
Vol 8 (6) ◽  
pp. e1002732 ◽  
Author(s):  
Sudeep D. Agarwala ◽  
Hannah G. Blitzblau ◽  
Andreas Hochwagen ◽  
Gerald R. Fink

1966 ◽  
Vol 166 (1004) ◽  
pp. 358-368 ◽  

The work which I have been asked to review began a little over a year ago with an experiment which I made in collaboration with Dr J. F. Watkins (Harris & Watkins 1965). We showed that an animal virus, killed by irradiation with ultraviolet light, could be used to fuse together cells derived from mouse and man to produce artificial man-mouse hybrid cells. The idea of using viruses in this way has its origins in observations which go back for more than a century. (For a review of the relevant literature see Harris, Watkins, Ford & Schoefl 1966). Many diseases have long been known to be associated with lesions in which multi-nucleate cells are found. In the medical literature of the nineteenth century there is a protracted and vigorous controversy about the mode of formation of these cells. Multinucleate cells are commonly found in the lesions produced by certain pathogenic viruses and, during the last decade, it has become clear that in at least some cases the virus produces the multinucleate cell by fusing single cells together. It was thus a very small step to attempt to see whether a virus could be used to fuse together cells of different kinds, and whether the resulting hybrid cells, if they were formed, would survive. And since the survival of the hybrid cells might be jeopardized by infection with a living virus, the virus was killed before the cells were treated with it. In the event, it turned out that viruses, inactivated by ultraviolet light, could be used to provide a general method for fusing together both differentiated and undifferentiated cells from different species and even different orders of vertebrate. The resulting interspecific hybrid cells survived for long periods and proved in some cases to be capable of multiplication. They thus offered interesting possibilities for the study of nucleo-cytoplasmic relationships and lent themselves to experiments of a kind which had not hitherto been feasible. It is these experiments which I propose to discuss. The virus used in this work was the ‘Sendai’ virus, a member of the para-influenza group of myxoviruses; other members of this group of viruses have since been used by other workers. Sendai virus was chosen because it had been shown by Okada (1958, 1962) that animal tumour cells in suspension could be rapidly fused together by high concentrations of this virus. The virus was irradiated with doses of ultraviolet light which reduced its infectivity by at least 10 6 ; but the dead virus retained its ability to fuse cells together. The two cell types studied in the first instance were the HeLa cell (a cell of human origin which has been grown for many years in artificial culture) and the Ehrlich ascites cell (a tumour which grows as a cell suspension in the peritoneal cavity of the mouse). These two cell types were chosen for a number of technical reasons, but mainly because their nuclei were easily distinguishable on morphological grounds. When a suspension containing a mixture of the two cell types is treated with the dead virus under appropriate conditions the cells clump together, and, during the ensuing 20 to 30 min, at 37 °C, the cell surfaces at the points of contact between the cells undergo dissolution. This process results in the progressive coalescence of the cytoplasms of neighbouring cells, so that multinucleate cells containing varying numbers of nuclei are formed.


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