scholarly journals Building and Regenerating the Lung Cell by Cell

2019 ◽  
Vol 99 (1) ◽  
pp. 513-554 ◽  
Author(s):  
Jeffrey A. Whitsett ◽  
Tanya V. Kalin ◽  
Yan Xu ◽  
Vladimir V. Kalinichenko

The unique architecture of the mammalian lung is required for adaptation to air breathing at birth and thereafter. Understanding the cellular and molecular mechanisms controlling its morphogenesis provides the framework for understanding the pathogenesis of acute and chronic lung diseases. Recent single-cell RNA sequencing data and high-resolution imaging identify the remarkable heterogeneity of pulmonary cell types and provides cell selective gene expression underlying lung development. We will address fundamental issues related to the diversity of pulmonary cells, to the formation and function of the mammalian lung, and will review recent advances regarding the cellular and molecular pathways involved in lung organogenesis. What cells form the lung in the early embryo? How are cell proliferation, migration, and differentiation regulated during lung morphogenesis? How do cells interact during lung formation and repair? How do signaling and transcriptional programs determine cell-cell interactions necessary for lung morphogenesis and function?


2007 ◽  
Vol 87 (1) ◽  
pp. 219-244 ◽  
Author(s):  
Yutaka Maeda ◽  
Vrushank Davé ◽  
Jeffrey A. Whitsett

The vertebrate lung consists of multiple cell types that are derived primarily from endodermal and mesodermal compartments of the early embryo. The process of pulmonary organogenesis requires the generation of precise signaling centers that are linked to transcriptional programs that, in turn, regulate cell numbers, differentiation, and behavior, as branching morphogenesis and alveolarization proceed. This review summarizes knowledge regarding the expression and proposed roles of transcription factors influencing lung formation and function with particular focus on knowledge derived from the study of the mouse. A group of transcription factors active in the endodermally derived cells of the developing lung tubules, including thyroid transcription factor-1 (TTF-1), β-catenin, Forkhead orthologs (FOX), GATA, SOX, and ETS family members are required for normal lung morphogenesis and function. In contrast, a group of distinct proteins, including FOXF1, POD1, GLI, and HOX family members, play important roles in the developing lung mesenchyme, from which pulmonary vessels and bronchial smooth muscle develop. Lung formation is dependent on reciprocal signaling among cells of both endodermal and mesenchymal compartments that instruct transcriptional processes mediating lung formation and adaptation to breathing after birth.



2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kolja Becker ◽  
Holger Klein ◽  
Eric Simon ◽  
Coralie Viollet ◽  
Christian Haslinger ◽  
...  

AbstractDiabetic Retinopathy (DR) is among the major global causes for vision loss. With the rise in diabetes prevalence, an increase in DR incidence is expected. Current understanding of both the molecular etiology and pathways involved in the initiation and progression of DR is limited. Via RNA-Sequencing, we analyzed mRNA and miRNA expression profiles of 80 human post-mortem retinal samples from 43 patients diagnosed with various stages of DR. We found differentially expressed transcripts to be predominantly associated with late stage DR and pathways such as hippo and gap junction signaling. A multivariate regression model identified transcripts with progressive changes throughout disease stages, which in turn displayed significant overlap with sphingolipid and cGMP–PKG signaling. Combined analysis of miRNA and mRNA expression further uncovered disease-relevant miRNA/mRNA associations as potential mechanisms of post-transcriptional regulation. Finally, integrating human retinal single cell RNA-Sequencing data revealed a continuous loss of retinal ganglion cells, and Müller cell mediated changes in histidine and β-alanine signaling. While previously considered primarily a vascular disease, attention in DR has shifted to additional mechanisms and cell-types. Our findings offer an unprecedented and unbiased insight into molecular pathways and cell-specific changes in the development of DR, and provide potential avenues for future therapeutic intervention.



2020 ◽  
Vol 21 (24) ◽  
pp. 9514
Author(s):  
Genevieve Saw ◽  
Feng Ru Tang

The hippocampus is crucial in learning, memory and emotion processing, and is involved in the development of different neurological and neuropsychological disorders. Several epigenetic factors, including DNA methylation, histone modifications and non-coding RNAs, have been shown to regulate the development and function of the hippocampus, and the alteration of epigenetic regulation may play important roles in the development of neurocognitive and neurodegenerative diseases. This review summarizes the epigenetic modifications of various cell types and processes within the hippocampus and their resulting effects on cognition, memory and overall hippocampal function. In addition, the effects of exposure to radiation that may induce a myriad of epigenetic changes in the hippocampus are reviewed. By assessing and evaluating the current literature, we hope to prompt a more thorough understanding of the molecular mechanisms that underlie radiation-induced epigenetic changes, an area which can be further explored.



Author(s):  
Kousik Kundu ◽  
Alice L. Mann ◽  
Manuel Tardaguila ◽  
Stephen Watt ◽  
Hannes Ponstingl ◽  
...  

AbstractThe identification of causal genetic variants for common diseases improves understanding of disease biology. Here we use data from the BLUEPRINT project to identify regulatory quantitative trait loci (QTL) for three primary human immune cell types and use these to fine-map putative causal variants for twelve immune-mediated diseases. We identify 340 unique, non major histocompatibility complex (MHC) disease loci that colocalise with high (>98%) posterior probability with regulatory QTLs, and apply Bayesian frameworks to fine-map associations at each locus. We show that fine-mapping applied to regulatory QTLs yields smaller credible set sizes and higher posterior probabilities for candidate causal variants compared to disease summary statistics. We also describe a systematic under-representation of insertion/deletion (INDEL) polymorphisms in credible sets derived from publicly available disease meta-analysis when compared to QTLs based on genome-sequencing data. Overall, our findings suggest that fine-mapping applied to disease-colocalising regulatory QTLs can enhance the discovery of putative causal disease variants and provide insights into the underlying causal genes and molecular mechanisms.



2020 ◽  
Vol 21 (5) ◽  
pp. 1754 ◽  
Author(s):  
Enrico Gaffo ◽  
Michele Bortolomeazzi ◽  
Andrea Bisognin ◽  
Piero Di Battista ◽  
Federica Lovisa ◽  
...  

MicroRNA-offset RNAs (moRNAs) are microRNA-like small RNAs generated by microRNA precursors. To date, little is known about moRNAs and bioinformatics tools to inspect their expression are still missing. We developed miR&moRe2, the first bioinformatics method to consistently characterize microRNAs, moRNAs, and their isoforms from small RNA sequencing data. To illustrate miR&moRe2 discovery power, we applied it to several published datasets. MoRNAs identified by miR&moRe2 were in agreement with previous research findings. Moreover, we observed that moRNAs and new microRNAs predicted by miR&moRe2 were downregulated upon the silencing of the microRNA-biogenesis pathway. Further, in a sizeable dataset of human blood cell populations, tens of novel miRNAs and moRNAs were discovered, some of them with significantly varied expression levels among the cell types. Results demonstrate that miR&moRe2 is a valid tool for a comprehensive study of small RNAs generated from microRNA precursors and could help to investigate their biogenesis and function.



2020 ◽  
Author(s):  
Wendy Fung ◽  
Leigh Wexler ◽  
Maxwell G. Heiman

ABSTRACTGlia shape the development and function of the C. elegans nervous system, especially its sense organs and central neuropil (nerve ring). Cell-type-specific promoters allow investigators to label or manipulate individual glial cell types, and therefore provide a key tool for deciphering glial function. In this technical resource, we compare the specificity, brightness, and consistency of cell-type-specific promoters for C. elegans glia. We identify a set of promoters for the study of seven glial cell types (F16F9.3, amphid and phasmid sheath glia; F11C7.2, amphid sheath glia only; grl-2, amphid and phasmid socket glia; hlh-17, cephalic (CEP) sheath glia; and grl-18, inner labial (IL) socket glia) as well as a pan-glial promoter (mir-228). We compare these promoters to promoters that are expressed more variably in combinations of glial cell types (delm-1 and itx-1). We note that the expression of some promoters depends on external conditions or the internal state of the organism, such as developmental stage, suggesting glial plasticity. Finally, we demonstrate an approach for prospectively identifying cell-type-specific glial promoters using existing single-cell sequencing data, and we use this approach to identify two novel promoters specific to IL socket glia (col-53 and col-177).



Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 224-224
Author(s):  
Akihiro Tamura ◽  
Hideyo Hirai ◽  
Asumi Yokota ◽  
Atsushi Sato ◽  
Hisayuki Yao ◽  
...  

Abstract Accumulating evidences have shown that mouse monocytes can be divided into two subsets, based on the expression of a surface marker Ly6C. Although distinct functions of Ly6C+ monocytes (also called classical or inflammatory monocytes) and Ly6C– monocytes (also known as patrolling monocytes) have been gradually uncovered, molecular mechanisms which govern development of these monocytes remain largely unknown. We have previously reported the requirement of CCAAT Enhancer Binding Protein β (C/EBPβ), a leucine zipper transcription factor, for ‘emergency’ granulopoiesis (Nat Immunol, 2006, J Immunol, 2012, Leukemia 2013). C/EBPβ is also known to play roles in the differentiation and function of macrophages. However, involvement of C/EBPβ in monocyte development has not been fully investigated. The aim of this study is to elucidate the roles of C/EBPβ in monopoiesis. First, we measured C/EBPβ mRNA expression in purified hematopoietic stem cells, myeloid progenitors and monocyte subsets, and found that monocytes, especially Ly6C– monocytes, expressed C/EBPβ mRNA at extremely higher level than any of other cell types examined. When we analyzed peripheral blood, the frequencies of total monocytes (CD11b+ CD115+ cells) in C/EBPβ–/– mice was significantly lower than those in wild type (WT) mice (4.24±2.71% in WT mice vs. 0.72±0.50% in C/EBPβ–/– mice, p<0.001). Of note, Ly6C– monocytes were almost absent in peripheral blood of C/EBPβ–/– mice (0.67±0.57% in WT mice vs. 0.017±0.021% in C/EBPβ–/– mice). In order to clarify whether the defects in C/EBPβ–/– monopoiesis were cell-intrinsic or cell-extrinsic, we generated mixed bone marrow (BM) chimeras by reconstituting lethally irradiated mice (CD45.1+) with BM cells from WT (CD45.1+) mice together with the equal number of BM cells from either WT or C/EBPβ–/– (CD45.2+) mice. Six weeks after reconstitution, we confirmed that C/EBPβ–/– BM-derived Ly6C– monocytes were absent in peripheral blood of the recipient mice, suggesting that monopoiesis in C/EBPβ–/– mice is impaired in a cell-intrinsic manner. A recent report revealed that MX1-Cre transgenic system can be used for monocyte specific deletion of genes of interest, as MX1 is highly expressed by monocytes (Hashimoto D et al. Immunity 2013). In MX1-Cre+ C/EBPβfloxed/floxed mice, the number of monocytes were decreased to the level similar to C/EBPβ–/– mice, suggesting that C/EBPβ is specifically required in monocytes rather than other progenitors during monopoiesis. As cell cycle status of myeloid progenitors and monocytes did not differ between WT mice and C/EBPβ–/– mice, we evaluated apoptosis by flow cytometry. The frequencies of late apoptotic/dead cells within Ly6C– monocytes in peripheral blood of C/EBPβ–/– mice were significantly higher than those in peripheral blood of WT mice (5.84±2.90% in WT mice vs. 50.4±22.4% in C/EBPβ–/– mice, p<0.001). These enhanced apoptosis of C/EBPβ–/– Ly6C– monocyte was partially reversed by retroviral transduction of Bcl2 gene. Previous reports have shown that Nr4a1, CX3CR1 and S1PR5 are required for survival or BM egress of Ly6C– monocytes. We found that mRNA expressions of these factors are severely reduced in C/EBPβ–/– Ly6C– monocytes. These results suggested that C/EBPβ maintains survival of Ly6C– monocytes through direct or indirect association of these molecules. Collectively, our data strongly indicate that C/EBPβ is essential for survival of Ly6C– monocytes. We are currently investigating the molecular mechanisms involved in the enhanced apoptosis of of Ly6C– monocytes in C/EBPβ–/– mice. Disclosures No relevant conflicts of interest to declare.



2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Bo Xiong ◽  
Xia Qiu ◽  
Shengjia Huang ◽  
Xiaojia Wang ◽  
Xu Zhang ◽  
...  

Abstract Citrus species are among the most economically important fruit crops. Physiological characteristics and molecular mechanisms associated with de-etiolation have been partially revealed. However, little is known about the mechanisms controlling the expression and function of genes associated with photosynthesis and chlorophyll biosynthesis in variegated citrus seedlings. The lower biomass, chlorophyll contents, and photosynthetic parameter values recorded for the variegated seedlings suggested that chlorophyll biosynthesis was partially inhibited. Additionally, roots of the variegated seedlings were longer than the roots of green seedlings. We obtained 567.07 million clean reads and 85.05 Gb of RNA-sequencing data, with more than 94.19% of the reads having a quality score of Q30 (sequencing error rate = 0.1%). Furthermore, we detected 4,786 and 7,007 differentially expressed genes (DEGs) between variegated and green Shiranuhi and Huangguogan seedlings. Thirty common pathways were differentially regulated, including pathways related to photosynthesis (GO: 0015979) and the chloroplast (GO: 0009507). Photosynthesis (44 and 63 DEGs), photosynthesis-antenna proteins (14 and 29 DEGs), and flavonoid biosynthesis (16 and 29 DEGs) pathways were the most common KEGG pathways detected in two analyzed libraries. Differences in the expression patterns of PsbQ, PetF, PetB, PsaA, PsaN, PsbP, PsaF, Cluster-2274.8338 (ZIP1), Cluster-2274.38688 (PTC52), and Cluster-2274.78784 might be responsible for the variegation in citrus seedlings. We completed a physiological- and transcriptome-level comparison of the Shiranuhi and Huangguogan cultivars that differ in terms of seedling variegation. We performed mRNA-seq analyses of variegated and green Shiranuhi and Huangguogan seedlings to explore the genes and regulatory pathways involved in the inhibition of chlorophyll biosynthesis and decreases in Chl a and Chl b contents. The candidate genes described herein should be investigated in greater detail to further characterize variegated citrus seedlings.



2012 ◽  
Vol 3 (3) ◽  
pp. 241-253 ◽  
Author(s):  
Sabine Hübner ◽  
Jan Tuckermann

AbstractGlucocorticoids (GCs) are potent anti-inflammatory agents that are used to treat chronic inflammatory diseases, allergic conditions, and some cancers. However, their therapeutic effects are hampered by severe side effects, such as muscle weakness, insulin resistance, fat redistribution, and osteoporosis. GCs act on many cell types that express the GC receptor (GR) via several modes of action. One of them includes GR homodimers recognizing binding sequences in the DNA of gene promoters. Another mode involves the modulation of other DNA-bound transcription factors via dimer-independent mechanisms. To what extent these mechanisms contribute to GC-mediated effects is currently being elucidated from analyses of mice with conditional and function-selective mutations of the GR and is summarized in this review. Whether GR homodimerization or its monomer activity is decisive in the therapeutic effectiveness and associated side effects of GCs for the treatment of inflammatory conditions depends on the type of the pathological condition. Thus, the classic criterion for selective GR modulators, discrimination between GR dimer- and GR monomer-dependent protein-protein interaction, will not help in any condition to avoid side effects and maintain anti-inflammatory activity. Rather, novel criteria for selective GR modulators have to be defined that take into consideration the tissue-specific mechanisms of the GR to achieve optimized anti-inflammatory therapies with reduced side effects. In the case of avoiding osteoporosis as a side effect, a first example of such optimized compounds can be provided.



2020 ◽  
Author(s):  
Juliet Mwirigi ◽  
Moeno Kume ◽  
Shayne N Hassler ◽  
Ayesha Ahmad ◽  
Pradipta R. Ray ◽  
...  

ABSTRACTThe protease activated receptor (PAR) family is a group of G-protein coupled receptors (GPCRs) activated by proteolytic cleavage of the extracellular domain. PARs are expressed in a variety of cell types with crucial roles in hemostasis, immune responses, inflammation, and pain. PAR3 is the least researched of the four PARs, with little known about its expression and function. We sought to better understand its potential function in the peripheral sensory nervous system. Mouse single-cell RNA sequencing data demonstrates that PAR3 is widely expressed in dorsal root ganglion (DRG) neurons. Co-expression of PAR3 mRNA with other PARs was identified in various DRG neuron subpopulations, consistent with its proposed role as a coreceptor of other PARs. We developed a lipid tethered PAR3 agonist, C660, that selectively activates PAR3 by eliciting a Ca2+ response in DRG and trigeminal (TG) neurons. In vivo, C660 induces mechanical hypersensitivity and facial grimacing in WT but not PAR3-/- mice. We characterized other nociceptive phenotypes in PAR3-/- mice and found a loss of hyperalgesic priming in response to IL-6, carrageenan, and a PAR2 agonist, suggesting that PAR3 contributes to long-lasting nociceptor plasticity in some contexts. To examine a potential role of PAR3 in regulating activity of other PARs in sensory neurons, we administered PAR1, PAR2, and PAR4 agonists and assessed mechanical and affective pain behaviors in WT and PAR3-/- mice. We observed that the nociceptive effects of PAR1 agonists were potentiated in the absence of PAR3. Our findings suggest a complex role of PAR3 in the physiology and plasticity of nociceptors.



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