Regulation of Actin Dynamics in the C. elegans Somatic Gonad

The reproductive system of the hermaphroditic nematode C. elegans consists of a series of contractile cell types—including the gonadal sheath cells, the spermathecal cells and the spermatheca–uterine valve—that contract in a coordinated manner to regulate oocyte entry and exit of the fertilized embryo into the uterus. Contraction is driven by acto-myosin contraction and relies on the development and maintenance of specialized acto-myosin networks in each cell type. Study of this system has revealed insights into the regulation of acto-myosin network assembly and contractility in vivo.

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A multi-layered and dynamic apical extracellular matrix shapes the vulva lumen in Caenorhabditis elegans

10.1101/2020.04.14.041483 ◽

2020 ◽

Cited By ~ 1

Author(s):

Jennifer D. Cohen ◽

Alessandro P. Sparacio ◽

Alexandra C. Belfi ◽

Rachel Forman-Rubinsky ◽

David H. Hall ◽

...

Keyword(s):

Electron Microscopy ◽

Cell Types ◽

Extracellular Matrices ◽

Cell Type ◽

C Elegans ◽

Transmission Electron ◽

Genetic Perturbations ◽

Lipid Transporters ◽

Matrix Factors

AbstractBiological tubes must develop and maintain their proper diameter in order to transport materials efficiently. These tubes are molded and protected in part by apical extracellular matrices (aECMs) that line their lumens. Despite their importance, aECMs are difficult to image in vivo and therefore poorly understood. The C. elegans vulva has been a paradigm for understanding many aspects of organogenesis. Here we describe the vulva luminal matrix, which contains chondroitin proteoglycans, Zona Pellucida (ZP) domain proteins, and other glycoproteins and lipid transporters related to those in mammals. Confocal and transmission electron microscopy revealed, with unprecedented detail, a complex and dynamic aECM. Different matrix factors assemble on the apical surfaces of each vulva cell type, with clear distinctions seen between Ras-dependent (1°) and Notch-dependent (2°) cell types. Genetic perturbations suggest that chondroitin and other aECM factors together generate a structured scaffold that both expands and constricts lumen shape.

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Cell-type specific analysis of physiological action of estrogen in mouse oviducts

10.1101/2020.12.18.423483 ◽

2020 ◽

Author(s):

Emily A. McGlade ◽

Gerardo G. Herrera ◽

Kalli K. Stephens ◽

Sierra L. W. Olsen ◽

Sarayut Winuthayanon ◽

...

Keyword(s):

Hormone Replacement ◽

Cell Types ◽

Normal Embryo ◽

Developmental Defect ◽

Cell Type ◽

Specific Analysis ◽

Cell Type Specific ◽

17Β Estradiol ◽

Oviductal Cell

AbstractOne of the endogenous estrogens, 17β-estradiol (E2) is a female steroid hormone secreted from the ovary. It is well established that E2 causes biochemical and histological changes in the uterus. The oviduct response to E2 is virtually unknown in an in vivo environment. In this study, we assessed the effect of E2 on each oviductal cell type, using an ovariectomized-hormone-replacement mouse model, single cell RNA-sequencing (scRNA-seq), in situ hybridization, and cell-type-specific deletion in mice. We found that each cell type in the oviduct responded to E2 distinctively, especially ciliated and secretory epithelial cells. The treatment of exogenous E2 did not drastically alter the transcriptomic profile from that of endogenous E2 produced during estrus. Moreover, we have identified and validated genes of interest in our datasets that may be used as cell- and region-specific markers in the oviduct. Insulin-like growth factor 1 (Igf1) was characterized as an E2-target gene in the mouse oviduct and was also expressed in human Fallopian tubes. Deletion of Igf1 in progesterone receptor (Pgr)-expressing cells resulted in female subfertility, partially due to an embryo developmental defect and embryo retention within the oviduct. In summary, we have shown that oviductal cell types are differentially regulated by E2 and support gene expression changes that are required for normal embryo development and transport in mouse models.

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Profound functional and molecular diversity of mitochondria revealed by cell type-specific profiling in vivo

10.1101/403774 ◽

2018 ◽

Cited By ~ 1

Author(s):

Caroline Fecher ◽

Laura Trovò ◽

Stephan A. Müller ◽

Nicolas Snaidero ◽

Jennifer Wettmarshausen ◽

...

Keyword(s):

Molecular Diversity ◽

Molecular Level ◽

Cell Types ◽

Long Chain Fatty Acids ◽

Cell Type ◽

Mitochondrial Proteome ◽

Novel Approach ◽

Cell Type Specific ◽

And Function

AbstractMitochondria vary in morphology and function in different tissues, however little is known about their molecular diversity among cell types. To investigate mitochondrial diversity in vivo, we developed an efficient protocol to isolate cell type-specific mitochondria based on a new MitoTag mouse. We profiled the mitochondrial proteome of three major neural cell types in cerebellum and identified a substantial number of differential mitochondrial markers for these cell types in mice and humans. Based on predictions from these proteomes, we demonstrate that astrocytic mitochondria metabolize long-chain fatty acids more efficiently than neurons. Moreover, we identified Rmdn3 as a major determinant of ER-mitochondria proximity in Purkinje cells. Our novel approach enables exploring mitochondrial diversity on the functional and molecular level in many in vivo contexts.

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Renal cell markers: lighthouses for managing renal diseases

AJP Renal Physiology ◽

10.1152/ajprenal.00182.2021 ◽

2021 ◽

Author(s):

Shivangi Agarwal ◽

Yashwanth R Sudhini ◽

Onur K Polat ◽

Jochen Reiser ◽

Mehmet Mete Altintas

Keyword(s):

High Efficiency ◽

Imaging Techniques ◽

Unmet Need ◽

Cell Types ◽

Whole Body ◽

Renal Diseases ◽

Cell Type ◽

Cell Markers ◽

Urine Production

Kidneys, one of the vital organs in our body, are responsible for maintaining whole-body homeostasis. The complexity of renal function (e.g., filtration, reabsorption, fluid and electrolyte regulation, urine production) demands diversity not only at the level of cell types but also in their overall distribution and structural framework within the kidney. To gain an in-depth molecular-level understanding of the renal system, it is imperative to discern the components of kidney and the types of cells residing in each of the sub-regions. Recent developments in labeling, tracing, and imaging techniques enabled us to mark, monitor and identify these cells in vivo with high efficiency in a minimally invasive manner. In this review, we have summarized different cell types, specific markers that are uniquely associated with those cell types, and their distribution in kidney, which altogether make kidneys so special and different. Cellular sorting based on the presence of certain proteins on the cell surface allowed for assignment of multiple markers for each cell type. However, different studies using different techniques have found contradictions in the cell-type specific markers. Thus, the term "cell marker" might be imprecise and sub-optimal, leading to uncertainty when interpreting the data. Therefore, we strongly believe that there is an unmet need to define the best cell markers for a cell type. Although, the compendium of renal-selective marker proteins presented in this review is a resource that may be useful to the researchers, we acknowledge that the list may not be necessarily exhaustive.

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Revisiting the role of IRF3 in inflammation and immunity by conditional and specifically targeted gene ablation in mice

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1803936115 ◽

2018 ◽

Vol 115 (20) ◽

pp. 5253-5258 ◽

Cited By ~ 19

Author(s):

Hideyuki Yanai ◽

Shiho Chiba ◽

Sho Hangai ◽

Kohei Kometani ◽

Asuka Inoue ◽

...

Keyword(s):

Immune Cell ◽

Cell Types ◽

Type I ◽

Type I Ifn ◽

Cell Type ◽

Gene Ablation ◽

Cell Type Specific

IFN regulatory factor 3 (IRF3) is a transcription regulator of cellular responses in many cell types that is known to be essential for innate immunity. To confirm IRF3’s broad role in immunity and to more fully discern its role in various cellular subsets, we engineered Irf3-floxed mice to allow for the cell type-specific ablation of Irf3. Analysis of these mice confirmed the general requirement of IRF3 for the evocation of type I IFN responses in vitro and in vivo. Furthermore, immune cell ontogeny and frequencies of immune cell types were unaffected when Irf3 was selectively inactivated in either T cells or B cells in the mice. Interestingly, in a model of lipopolysaccharide-induced septic shock, selective Irf3 deficiency in myeloid cells led to reduced levels of type I IFN in the sera and increased survival of these mice, indicating the myeloid-specific, pathogenic role of the Toll-like receptor 4–IRF3 type I IFN axis in this model of sepsis. Thus, Irf3-floxed mice can serve as useful tool for further exploring the cell type-specific functions of this transcription factor.

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The expression, lamin-dependent localization and RNAi depletion phenotype for emerin inC. elegans

Journal of Cell Science ◽

10.1242/jcs.115.5.923 ◽

2002 ◽

Vol 115 (5) ◽

pp. 923-929 ◽

Cited By ~ 4

Author(s):

Yosef Gruenbaum ◽

Kenneth K. Lee ◽

Jun Liu ◽

Merav Cohen ◽

Katherine L. Wilson

Keyword(s):

Nuclear Envelope ◽

Molecular Mechanisms ◽

Cell Types ◽

Growth Conditions ◽

Rnai Phenotype ◽

Lamin B ◽

C Elegans ◽

Nuclear Lamins ◽

First Time

Emerin belongs to the LEM-domain family of nuclear membrane proteins, which are conserved in metazoans from C. elegans to humans. Loss of emerin in humans causes the X-linked form of Emery-Dreifuss muscular dystrophy(EDMD), but the disease mechanism is not understood. We have begun to address the function of emerin in C. elegans, a genetically tractable nematode. The emerin gene (emr-1) is conserved in C. elegans. We detect Ce-emerin protein in the nuclear envelopes of all cell types except sperm, and find that Ce-emerin co-immunoprecipitates with Ce-lamin from embryo lysates. We show for the first time in any organism that nuclear lamins are essential for the nuclear envelope localization of emerin during early development. We further show that four other types of nuclear envelope proteins, including fellow LEM-domain protein Ce-MAN1, as well as Ce-lamin, UNC-84 and nucleoporins do not depend on Ce-emerin for their localization. This result suggests that emerin is not essential to organize or localize the only lamin (B-type) expressed in C. elegans. We also analyzed the RNAi phenotype resulting from the loss of emerin function in C. elegans under laboratory growth conditions, and found no detectable phenotype throughout development. We propose that C. elegans is an appropriate system in which to study the molecular mechanisms of emerin function in vivo.

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Chagas Disease Chemotherapy: What Do We Know So Far?

Current Pharmaceutical Design ◽

10.2174/1381612827666210216152654 ◽

2021 ◽

Vol 27 ◽

Author(s):

Aline Araujo Zuma ◽

Wanderley de Souza

Keyword(s):

Host Cell ◽

Chagas Disease ◽

Chronic Phase ◽

Cell Types ◽

Neglected Tropical Disease ◽

Cell Type ◽

Cure Rate ◽

New Compounds

: Chagas disease is a Neglected Tropical Disease (NTD), and although endemic in Latin America, affects around 6-7 million people infected worldwide. The treatment of Chagas disease is based on benznidazole and nifurtimox, which are the only available drugs. However, they are not effective during the chronic phase and cause several side effects. Furthermore, BZ promotes cure in 80% of the patients in the acute phase, but the cure rate drops to 20% in adults in the chronic phase of the disease. In this review, we present several studies published in the last six years, which describes the antiparasitic potential of distinct drugs, from the synthesis of new compounds aiming to target the parasite, as well as the repositioning and the combination of drugs. We highlight several compounds for having shown results that are equivalent or superior to BZ, which means that they should be further studied, either in vitro or in vivo. Furthermore, we stand out the differences in the effects of BZ on the same strain of T. cruzi, which might be related to methodological differences such as parasite and cell ratios, host cell type and the time of adding the drug. In addition, we discuss the wide variety of strains and also the cell types used as a host cell, which makes it difficult to compare the trypanocidal effect of the compounds.

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Immune responses to hapten conjugates in vitro

Quarterly Reviews of Biophysics ◽

10.1017/s0033583500001979 ◽

1975 ◽

Vol 8 (4) ◽

pp. 507-522

Author(s):

Sirkka Kontiainen ◽

O. Mäkelä ◽

M. Hurme

Keyword(s):

Tissue Culture ◽

Immune Responses ◽

Cell Types ◽

Antibody Responses ◽

Tissue Cultures ◽

Cell Type ◽

Animal Body ◽

Do So

Several functions of the animal body can take place in cell or tissue cultures with almost unreduced efficiency and precision. Functions, where only one cell type is involved, often do so, but also some differentiation steps where interactions between two or more cell types are clearly needed can take place in tissue culture (Saxén et al. 1968).Most immune responses require collaboration between two or more cell types (Claman, Chaperon & Triplett, 1966; Miller & Mitchell, 1968; Feldmann & Nossal 1972c). Some of them can be easily induced in vitro but others cannot. Even when antibody responses can be induced in vitro their intensity varies a great deal. With some antigens and under some circumstances a response in vitro can be nearly as strong as one in vivo. A crude comparison can be derived from responses in vitro and in vivo to the same antigen, conjugate of hapten NIP and pneumococcal polysaccharide type III (NIP-SIll, Nakamura, Ray & Mäkelä, 1973).

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Transit-amplifying cells coordinate changes in intestinal epithelial cell-type composition

10.1101/840371 ◽

2019 ◽

Author(s):

Laura E. Sanman ◽

Ina W. Chen ◽

Jake M. Bieber ◽

Veronica Steri ◽

Byron Hann ◽

...

Keyword(s):

Quantitative Imaging ◽

Cell Types ◽

Culture Conditions ◽

Tissue Cell ◽

Specific Cell ◽

Cell Type ◽

Cell Type Composition ◽

Type Composition ◽

Coordinate Changes

AbstractRenewing tissues have the remarkable ability to continually produce both proliferative progenitor and specialized differentiated cell-types. How are complex milieus of microenvironmental signals interpreted to coordinate tissue cell-type composition? Here, we develop a high-throughput approach that combines organoid technology and quantitative imaging to address this question in the context of the intestinal epithelium. Using this approach, we comprehensively survey enteroid responses to individual and paired perturbations to eight epithelial signaling pathways. We uncover culture conditions that enrich for specific cell-types, including Lgr5+ stem and enteroendocrine cells. We analyze interactions between perturbations and dissect mechanisms underlying an unexpected mutual antagonism between EGFR and IL-4 signals. Finally, we show that, across diverse perturbations, modulating proliferation of transit-amplifying cells also consistently changes the composition of differentiated secretory and absorptive cell-types. This property is conserved in vivo and can arise from differential amplification of secretory and absorptive progenitor cells. Taken together, the observations highlight an underappreciated role for transit-amplifying cells in which proliferation of these short-lived progenitors provides a lineage-based mechanism for tuning differentiated cell-type composition.

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Modular Combinatorial Binding among HumanTrans-acting Factors Reveals Direct and Indirect Factor Binding

10.1101/027953 ◽

2015 ◽

Author(s):

Yuchun Guo ◽

David K. Gifford

Keyword(s):

Topic Model ◽

Regulatory Region ◽

Cell Types ◽

Joint Analysis ◽

Modular Organization ◽

Cell Type ◽

Regulatory Regions ◽

Regulatory Program ◽

Cell Type Specific

The combinatorial binding of trans-acting factors (TFs) to regulatory genomic regions is an important basis for the spatial and temporal specificity of gene regulation. We present a new computational approach that reveals how TFs are organized into combinatorial regulatory programs. We define a regulatory program to be a set of TFs that bind together at a regulatory region. Unlike other approaches to characterizing TF binding, we permit a regulatory region to be bound by one or more regulatory programs. We have developed a method called regulatory program discovery (RPD) that produces compact and coherent regulatory programs from in vivo binding data using a topic model. Using RPD we find that the binding of 115 TFs in K562 cells can be organized into 49 interpretable regulatory programs that bind ~140,000 distinct regulatory regions in a modular manner. The discovered regulatory programs recapitulate many published protein-protein physical interactions and have consistent functional annotations of chromatin states. We found that, for certain TFs, direct (motif present) and indirect (motif absent) binding is characterized by distinct sets of binding partners and that the binding of other TFs can predict whether the TF binds directly or indirectly with high accuracy. Joint analysis across two cell types reveals both cell-type-specific and shared regulatory programs and that thousands of regulatory regions use different programs in different cell types. Overall, our results provide comprehensive cell-type-specific combinatorial binding maps and suggest a modular organization of binding programs in regulatory regions.

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