scholarly journals An atlas of human proximal epididymis reveals cell-specific functions and distinct roles for CFTR

2020 ◽  
Vol 3 (11) ◽  
pp. e202000744
Author(s):  
Shih-Hsing Leir ◽  
Shiyi Yin ◽  
Jenny L Kerschner ◽  
Wilmel Cosme ◽  
Ann Harris
Keyword(s):  
Fluid Transport ◽  
Cell Types ◽  
Efferent Ducts ◽  
Molecular Events ◽  
Specific Distribution ◽  
Multiple Cell ◽  
Cell Type Specific ◽  
Marked Cell ◽  
The Individual ◽  
Male Genital

Spermatozoa released from the testis are unable to fertilize an egg without a coordinated process of maturation in the lumen of the epididymis. Relatively little is known about the molecular events that integrate this critical progression along the male genital ducts in man. Here, we use single cell RNA-sequencing to construct an atlas of the human proximal epididymis. We find that the CFTR, which is pivotal in normal epididymis fluid transport, is most abundant in surface epithelial cells in the efferent ducts and in rare clear cells in the caput epididymis, suggesting region-specific functional properties. We reveal transcriptional signatures for multiple cell clusters, which identify the individual roles of principal, apical, narrow, basal, clear, halo, and stromal cells in the epididymis. A marked cell type–specific distribution of function is seen along the duct with local specialization of individual cell types integrating processes of sperm maturation.

scholarly journals Immunohistochemical localization of phosphoenolpyruvate carboxykinase in adult and developing mouse tissues.

1990 ◽  
Vol 38 (2) ◽  
pp. 171-178 ◽  
Author(s):  
D B Zimmer ◽  
M A Magnuson
Keyword(s):  
Nervous System ◽  
Phosphoenolpyruvate Carboxykinase ◽  
Submaxillary Gland ◽  
Cell Types ◽  
Immunohistochemical Localization ◽  
Mouse Tissues ◽  
Multiple Cell ◽  
Cell Type Specific ◽  
Immunohistochemical Techniques ◽  
Developing Nervous System

We used immunohistochemical techniques to analyze the cell distribution of phosphoenolpyruvate carboxykinase (PEPCK) in adult and developing mouse tissues. PEPCK immunoreactivity was detected in many tissues, including some that had not been previously reported to contain PEPCK enzyme activity (bladder, stomach, ovary, vagina, parotid gland, submaxillary gland, and eye). In some multicellular tissues, PEPCK immunoreactivity was observed in multiple cell types. Several tissues (spleen, thyroid, and submaxillary gland) contained no detectable PEPCK immunoreactivity. During development, PEPCK immunoreactivity was associated with the developing nervous system and somites in 15-day embryos. At prenatal day 18, PEPCK immunoreactivity was detected only in the nervous system. At prenatal day 20, PEPCK immunoreactivity was observed in many of the tissues that contain PEPCK in the adult, with the exception of liver, lung, and stomach. PEPCK immunoreactivity was detected in liver at postnatal day 1, lung at postnatal day 7, and stomach after postnatal day 21. The only tissue in which PEPCK immunoreactivity decreased during development was the pancreas, where PEPCK immunoreactivity was detected at prenatal day 20 and was present until postnatal day 21. These results suggest that PEPCK expression is cell-type specific, more widespread than previously thought, and differentially expressed during development.

scholarly journals Peroxisome Proliferator-Activated Receptor Subtype- and Cell-Type-Specific Activation of Genomic Target Genes upon Adenoviral Transgene Delivery

2006 ◽  
Vol 26 (15) ◽  
pp. 5698-5714 ◽  
Author(s):  
Ronni Nielsen ◽  
Lars Grøntved ◽  
Hendrik G. Stunnenberg ◽  
Susanne Mandrup
Keyword(s):  
Target Genes ◽  
Receptor Subtype ◽  
Peroxisome Proliferator ◽  
Cell Type ◽  
Peroxisome Proliferator Activated Receptor ◽  
Molecular Events ◽  
Adenoviral Delivery ◽  
Cell Type Specific ◽  
Peroxisome Proliferator Activated Receptors ◽  
The Individual

ABSTRACT Investigations of the molecular events involved in activation of genomic target genes by peroxisome proliferator-activated receptors (PPARs) have been hampered by the inability to establish a clean on/off state of the receptor in living cells. Here we show that the combination of adenoviral delivery and chromatin immunoprecipitation (ChIP) is ideal for dissecting these mechanisms. Adenoviral delivery of PPARs leads to a rapid and synchronous expression of the PPAR subtypes, establishment of transcriptional active complexes at genomic loci, and immediate activation of even silent target genes. We demonstrate that PPARγ2 possesses considerable ligand-dependent as well as independent transactivation potential and that agonists increase the occupancy of PPARγ2/retinoid X receptor at PPAR response elements. Intriguingly, by direct comparison of the PPARs (α, γ, and β/δ), we show that the subtypes have very different abilities to gain access to target sites and that in general the genomic occupancy correlates with the ability to activate the corresponding target gene. In addition, the specificity and potency of activation by PPAR subtypes are highly dependent on the cell type. Thus, PPAR subtype-specific activation of genomic target genes involves an intricate interplay between the properties of the subtype- and cell-type-specific settings at the individual target loci.

scholarly journals Alternative super-enhancers result in similar gene expression in different tissues

2018 ◽  
Author(s):  
Dora Bojcsuk ◽  
Gergely Nagy ◽  
Balint Laszlo Balint
Keyword(s):  
Cell Types ◽  
Cell Functions ◽  
Highly Active ◽  
Oestrogen Receptor Alpha ◽  
Ishikawa Cells ◽  
Cell Type Specific ◽  
The Individual ◽  
Fine Tune ◽  
Similar Gene ◽  
Mcf 7

Super-enhancers (SEs) are clusters of highly active enhancers, regulating cell type-specific and disease-related genes, including oncogenes. The individual regulatory regions within SEs might be simultaneously bound by different transcription factors (TFs) and co-regulators such as P300, BRD4 and Mediator, which together establish a chromatin environment conducting to effective gene induction. While cells with distinct TF profiles can have different functions, an unanswered question is how different cells control overlapping genetic programmes. Here, we show that the construction of oestrogen receptor alpha (ERα)-driven SEs is tissue specific, and both the collaborating TFs and the active SE components are largely differing between human breast cancer-derived MCF-7 and endometrial cancer-derived Ishikawa cells; nonetheless, SEs common to both cell types have similar transcriptional outputs. In the MCF-7 cell line, ERα-dominated SEs are also driven by the well-known FoxA1 and AP2γ TFs, as described previously, whereas in Ishikawa cells, FoxM1, TCF12 and TEAD4 are as important as ERα for SE formation. Our results show that SEs can be constructed in several ways, but the overall activity of common SEs is the same between cells with a common master regulator. These findings may reshape our current understanding of how these regulatory units can fine-tune cell functions. From a broader perspective, we show that systems assembled from different components can perform similar tasks if a common functional trigger drives their assembly.

scholarly journals Comparative DNA methylation analysis to decipher common and cell type-specific patterns among multiple cell types

2016 ◽  
pp. elw013 ◽  
Author(s):  
Xiaofei Yang ◽  
Xiaojian Shao ◽  
Lin Gao ◽  
Shihua Zhang
Keyword(s):  
Dna Methylation ◽  
Cell Types ◽  
Cell Type ◽  
Methylation Analysis ◽  
Multiple Cell ◽  
Cell Type Specific ◽  
Dna Methylation Analysis

scholarly journals Biological Functions of HMGN Chromosomal Proteins

2020 ◽  
Vol 21 (2) ◽  
pp. 449
Author(s):  
Ravikanth Nanduri ◽  
Takashi Furusawa ◽  
Michael Bustin
Keyword(s):  
Biological Function ◽  
High Mobility ◽  
Cell Types ◽  
Vertebrate Development ◽  
Cellular Functions ◽  
Cell Identity ◽  
Multiple Cell ◽  
Cell Type Specific ◽  
Nucleosome Binding ◽  
Regulatory Sites

Chromatin plays a key role in regulating gene expression programs necessary for the orderly progress of development and for preventing changes in cell identity that can lead to disease. The high mobility group N (HMGN) is a family of nucleosome binding proteins that preferentially binds to chromatin regulatory sites including enhancers and promoters. HMGN proteins are ubiquitously expressed in all vertebrate cells potentially affecting chromatin function and epigenetic regulation in multiple cell types. Here, we review studies aimed at elucidating the biological function of HMGN proteins, focusing on their possible role in vertebrate development and the etiology of disease. The data indicate that changes in HMGN levels lead to cell type-specific phenotypes, suggesting that HMGN optimize epigenetic processes necessary for maintaining cell identity and for proper execution of specific cellular functions. This manuscript contains tables that can be used as a comprehensive resource for all the English written manuscripts describing research aimed at elucidating the biological function of the HMGN protein family.

scholarly journals Effects of metabolic acidosis on intracellular pH responses in multiple cell types

2014 ◽  
Vol 307 (12) ◽  
pp. R1413-R1427 ◽  
Author(s):  
Ahlam Ibrahim Salameh ◽  
Vernon A. Ruffin ◽  
Walter F. Boron
Keyword(s):  
Metabolic Acidosis ◽  
Intracellular Ph ◽  
Skeletal Muscles ◽  
Individual Cell ◽  
Cell Types ◽  
Cell Type ◽  
Ratiometric Fluorescence ◽  
Multiple Cell ◽  
Definition Of ◽  
The Individual

Metabolic acidosis (MAc), a decrease in extracellular pH (pHo) caused by a decrease in [HCO3−]o at a fixed [CO2]o, is a common clinical condition and causes intracellular pH (pHi) to fall. Although previous work has suggested that MAc-induced decreases in pHi (ΔpHi) differ among cell types, what is not clear is the extent to which these differences are the result of the wide variety of methodologies employed by various investigators. In the present study, we evaluated the effects of two sequential MAc challenges (MAc1 and MAc2) on pHi in 10 cell types/lines: primary-cultured hippocampal (HCN) neurons and astrocytes (HCA), primary-cultured medullary raphé (MRN) neurons, and astrocytes (MRA), CT26 colon cancer, the C2C12 skeletal muscles, primary-cultured bone marrow-derived macrophages (BMDM) and dendritic cells (BMDC), Ink4a/ARF-null melanocytes, and XB-2 keratinocytes. We monitor pHi using ratiometric fluorescence imaging of 2′,7′-bis-(2-carboxyethyl)-5-(and-6)-carboxyfluorescein while imposing MAc: lowering (pHo) from 7.4 to 7.2 by decreasing [HCO3−]o from 22 to 14 mM at 5% CO2 for 7 min. After MAc1, we return cells to the control solution for 10 min and impose MAc2. Using our definition of MAc resistance [(ΔpHi/ΔpHo) ≤ 40%], during MAc1, ∼70% of CT26 and ∼50% of C2C12 are MAc-resistant, whereas the other cell types are predominantly MAc-sensitive. During MAc2, some cells adapt [(ΔpHi/ΔpHo)2 < (ΔpHi/ΔpHo)1], particularly HCA, C2C12, and BMDC. Most maintain consistent responses [(ΔpHi/ΔpHo)2 ≅ (ΔpHi/ΔpHo)1], and a few decompensate [(ΔpHi/ΔpHo)2>(ΔpHi/ΔpHo)1], particularly HCN, C2C12, and XB-2. Thus, responses to twin MAc challenges depend both on the individual cell and cell type.

scholarly journals A high-throughput microfluidic bilayer co-culture platform to study endothelial-pericyte interactions

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Miles T. Rogers ◽  
Ashley L. Gard ◽  
Robert Gaibler ◽  
Thomas J. Mulhern ◽  
Rivka Strelnikov ◽  
...  
Keyword(s):  
High Throughput ◽  
Fluid Shear Stress ◽  
Cell Types ◽  
Fluid Shear ◽  
Multiple Cell ◽  
Cell Type Specific ◽  
On Chip ◽  
Tissue Models ◽  
Macromolecular Permeability

AbstractMicrophysiological organ-on-chip models offer the potential to improve the prediction of drug safety and efficacy through recapitulation of human physiological responses. The importance of including multiple cell types within tissue models has been well documented. However, the study of cell interactions in vitro can be limited by complexity of the tissue model and throughput of current culture systems. Here, we describe the development of a co-culture microvascular model and relevant assays in a high-throughput thermoplastic organ-on-chip platform, PREDICT96. The system consists of 96 arrayed bilayer microfluidic devices containing retinal microvascular endothelial cells and pericytes cultured on opposing sides of a microporous membrane. Compatibility of the PREDICT96 platform with a variety of quantifiable and scalable assays, including macromolecular permeability, image-based screening, Luminex, and qPCR, is demonstrated. In addition, the bilayer design of the devices allows for channel- or cell type-specific readouts, such as cytokine profiles and gene expression. The microvascular model was responsive to perturbations including barrier disruption, inflammatory stimulation, and fluid shear stress, and our results corroborated the improved robustness of co-culture over endothelial mono-cultures. We anticipate the PREDICT96 platform and adapted assays will be suitable for other complex tissues, including applications to disease models and drug discovery.

scholarly journals Cell-type-specific alternative polyadenylation (APA) genes reveal the function of dynamic APA in complex tissues

2020 ◽  
Author(s):  
Yulong Bai ◽  
Yidi Qin ◽  
Zhenjiang Fan ◽  
Robert M. Morrison ◽  
KyongNyon Nam ◽  
...  
Keyword(s):  
Mouse Brain ◽  
Peripheral Blood ◽  
Human Peripheral Blood ◽  
Alternative Polyadenylation ◽  
Cell Types ◽  
Cell Type ◽  
Simulation Data ◽  
Multiple Cell ◽  
Cell Type Specific ◽  
Brain Data

ABSTRACTAlternative polyadenylation (APA) causes shortening or lengthening of the 3’-untranslated region (3’-UTR) of genes across multiple cell types. Bioinformatic tools have been developed to identify genes that are affected by APA (APA genes) in single-cell RNA-Seq (scRNA-Seq) data. However, they suffer from low power, and they cannot identify APA genes specific to each cell type (cell-type-specific APA) when multiple cell types are analyzed. To address these limitations, we developed scMAPA that systematically integrates two novel steps. First, scMAPA quantifies 3’-UTR long and short isoforms without requiring assumptions on the read density shape of input data. Second, scMAPA estimates the significance of the APA genes for each cell type while controlling confounders. In the analyses on our novel simulation data and human peripheral blood mono cellular data, scMAPA showed enhanced power in identifying APA genes. Further, in mouse brain data, scMAPA identifies cell-type-specific APA genes, improving interpretability for the cell-type-specific function of APA. We further showed that this improved interpretability helps to understand a novel role of APA on the interaction between neurons and blood vessels, which is critical to maintaining the operational condition of brains. With high sensitivity and interpretability, scMAPA shed novel insights into the function of dynamic APA in complex tissues.Key PointsWe developed a bioinformatic tool, scMAPA, that identifies dynamic APA across multiple cell types and a novel simulation pipeline to assess performance of such tools in APA calling.In simulation data of various scenarios from our novel simulation pipeline, scMAPA achieves sensitivity with a minimal loss of specificity.In human peripheral blood monocellular data, scMAPA identifies APA genes accurately and robustly, finding unique associations of APA with hematological processes.scMAPA identifies APA genes specific to each cell type in mouse brain data while controlling confounders that sheds novel insights into the complex molecular processes.

scholarly journals A Single Cell Transcriptomic Atlas Characterizes Aging Tissues in the Mouse

2019 ◽  
Author(s):  
◽  
Angela Oliveira Pisco ◽  
Aaron McGeever ◽  
Nicholas Schaum ◽  
Jim Karkanias ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Types ◽  
Cell Type ◽  
Cellular Processes ◽  
Progressive Loss ◽  
Age Related ◽  
Multiple Cell ◽  
Cell Type Specific ◽  
Molecular Information ◽  
Insight Into

AbstractAging is characterized by a progressive loss of physiological integrity, leading to impaired function and increased vulnerability to death1. Despite rapid advances over recent years, many of the molecular and cellular processes which underlie progressive loss of healthy physiology are poorly understood2. To gain a better insight into these processes we have created a single cell transcriptomic atlas across the life span of Mus musculus which includes data from 23 tissues and organs. We discovered cell-specific changes occurring across multiple cell types and organs, as well as age related changes in the cellular composition of different organs. Using single-cell transcriptomic data we were able to assess cell type specific manifestations of different hallmarks of aging, such as senescence3, genomic instability4 and changes in the organism’s immune system2. This Tabula Muris Senis provides a wealth of new molecular information about how the most significant hallmarks of aging are reflected in a broad range of tissues and cell types.

scholarly journals Antioxidant Regulation of Cell Reprogramming

Antioxidants ◽  
2019 ◽  
Vol 8 (8) ◽  
pp. 323 ◽  
Author(s):  
Yuichiro J. Suzuki ◽  
Nataliia V. Shults
Keyword(s):  
Transcription Factors ◽  
New Technologies ◽  
Cell Types ◽  
Cell Reprogramming ◽  
Target Cells ◽  
Direct Reprogramming ◽  
Heart Muscle Cells ◽  
Multiple Cell ◽  
Cell Type Specific ◽  
Induced Pluripotent

Discovery of induced pluripotent stem cells (iPSCs) has revolutionized regeneration biology, providing further mechanistic insights and possible therapeutic applications. The original discovery by Yamanaka and co-workers showed that the expression of four transcription factors in fibroblasts resulted in the generation of iPSCs that can be differentiated into various cell types. This technology should be particularly useful for restoring cells with limited proliferative capacities such as adult heart muscle cells and neurons, in order to treat diseases affecting these cell types. More recently, iPSCs-mediated cell reprogramming has advanced to new technologies including direct reprogramming and pharmacological reprogramming. Direct reprogramming allows for the conversion of fibroblasts into cardiomyocytes, neurons or other cells by expressing multiple cell type-specific transcription factors without going through the production of iPSCs. Both iPSC-mediated reprogramming as well as direct reprogramming can also be promoted by a combination of small molecules, opening up a possibility for pharmacological therapies to induce cell reprogramming. However, all of these processes have been shown to be affected by reactive oxygen species that reduce the efficacies of reprogramming fibroblasts into iPSCs, differentiating iPSCs into target cells, as well as direct reprogramming. Accordingly, antioxidants have been shown to support these reprogramming processes and this review article summarizes these findings. It should be noted however, that the actions of antioxidants to support cell reprogramming may be through their ROS inhibiting abilities, but could also be due to mechanisms that are independent of classical antioxidant actions.

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