Each individual perceives the world in a unique way, but little is known about the genetic basis of variation in sensory perception. In the fly eye, the random mosaic of color-detecting R7 ...photoreceptor subtypes is determined by stochastic on/off expression of the transcription factor Spineless (Ss). In a genome-wide association study, we identified a naturally occurring insertion in a regulatory DNA element in
that lowers the ratio of Ss
to Ss
cells. This change in photoreceptor fates shifts the innate color preference of flies from green to blue. The genetic variant increases the binding affinity for Klumpfuss (Klu), a zinc finger transcriptional repressor that regulates
expression. Klu is expressed at intermediate levels to determine the normal ratio of Ss
to Ss
cells. Thus, binding site affinity and transcription factor levels are finely tuned to regulate stochastic expression, setting the ratio of alternative fates and ultimately determining color preference.
Coronavirus disease (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). ACE2 (angiotensin-converting enzyme 2), and TMPRSS2 (transmembrane protease serine 2) mediate ...viral infection of host cells. We reasoned that differences in ACE2 or TMPRSS2 gene expression in sputum cells among patients with asthma may identify subgroups at risk for COVID-19 morbidity.
To determine the relationship between demographic features and sputum ACE2 and TMPRSS2 gene expression in asthma.
: We analyzed gene expression for ACE2 and TMPRSS2, and for ICAM-1 (intercellular adhesion molecule 1) (rhinovirus receptor as a comparator) in sputum cells from 330 participants in SARP-3 (Severe Asthma Research Program-3) and 79 healthy control subjects.
Gene expression of ACE2 was lower than TMPRSS2, and expression levels of both genes were similar in asthma and health. Among patients with asthma, male sex, African American race, and history of diabetes mellitus were associated with higher expression of ACE2 and TMPRSS2. Use of inhaled corticosteroids (ICS) was associated with lower expression of ACE2 and TMPRSS2, but treatment with triamcinolone acetonide did not decrease expression of either gene. These findings differed from those for ICAM-1, where gene expression was increased in asthma and less consistent differences were observed related to sex, race, and use of ICS.
Higher expression of ACE2 and TMPRSS2 in males, African Americans, and patients with diabetes mellitus provides rationale for monitoring these asthma subgroups for poor COVID-19 outcomes. The lower expression of ACE2 and TMPRSS2 with ICS use warrants prospective study of ICS use as a predictor of decreased susceptibility to SARS-CoV-2 infection and decreased COVID-19 morbidity.
Coronavirus disease 2019 (COVID-19) is caused by SARS-CoV-2, an emerging virus that utilizes host proteins ACE2 and TMPRSS2 as entry factors. Understanding the factors affecting the pattern and ...levels of expression of these genes is important for deeper understanding of SARS-CoV-2 tropism and pathogenesis. Here we explore the role of genetics and co-expression networks in regulating these genes in the airway, through the analysis of nasal airway transcriptome data from 695 children. We identify expression quantitative trait loci for both ACE2 and TMPRSS2, that vary in frequency across world populations. We find TMPRSS2 is part of a mucus secretory network, highly upregulated by type 2 (T2) inflammation through the action of interleukin-13, and that the interferon response to respiratory viruses highly upregulates ACE2 expression. IL-13 and virus infection mediated effects on ACE2 expression were also observed at the protein level in the airway epithelium. Finally, we define airway responses to common coronavirus infections in children, finding that these infections generate host responses similar to other viral species, including upregulation of IL6 and ACE2. Our results reveal possible mechanisms influencing SARS-CoV-2 infectivity and COVID-19 clinical outcomes.
Canonical Notch signaling involves Notch receptor activation via interaction with cell surface bound Notch ligand. Recent findings also indicate that Notch signaling may be modulated by cross-talk ...with other signaling mechanisms. The ECM protein MAGP2 was previously shown to regulate Notch in a cell type dependent manner, although the molecular details of this interaction have not been dissected. Here, we report that MAGP2 cell type specific control of Notch is independent of individual Notch receptor-ligand combinations but dependent on interaction with RGD binding integrins. Overexpressed MAGP2 was found to suppress transcriptional activity from the Notch responsive Hes1 promoter activity in endothelial cells, while overexpression of a RGD→RGE MAGP2 mutant increased Notch signaling in the same cell type. This effect was not unique to MAGP2 since the RGD domain of the ECM protein EGFL7 was also found to be an important modulator of Hes1 promoter activity. Independently of MAGP2 or EGFL7, inhibition of RGD-binding integrins with soluble RGD peptides also increased accumulation of active N1ICD fragments and Notch responsive promoter activity independently of changes in Notch1, Jag1, or Dll4 expression. Finally, β1 or β3 integrin blocking antibodies also enhanced Notch signaling. Collectively, these results answer the question of how MAGP2 controls cell type dependent Notch signaling, but more importantly uncover a new mechanism to understand how extracellular matrices and cellular environments impact Notch signaling.
•A novel signaling mechanism between integrins and Notch is proposed.•ECM molecules MAGP2 and EGFL7 control Notch via RGD binding integrins.•Integrin–Notch signaling allows Notch to responds to cellular microenvironment.•Integrin–Notch signaling helps explain pro- and anti-Notch activity of MAGP2.
The extracellular Matrix (ECM) has recently been implicated with the regulation of angiogenesis via manipulation of the Notch signaling system however the molecular basis for this has not been ...explored. We previously showed that the ECM protein microfibril‐associated glycoprotein 2 (MAGP2), suppresses Notch signaling in endothelial cells but promotes Notch signaling in non‐endothelial cells. The goal of this work was to dissect the molecular mechanism by which MAGP2 manipulates Notch signaling. We found that control of Notch by MAGP2 was not dependent on specific Notch receptor‐ligand expression patterns. Interestingly however, we found that mutation of the MAGP2 RGD to a non‐integrin binding RGE caused MAGP2 to promote rather than suppress Notch signaling in endothelial cells. Similarly, soluble integrin blocking RGD peptides and αVβ3 blocking antibodies also increased Notch signaling even in the absence of MAGP2. Further mechanistic dissection revealed that inhibitors of SRC and FAK kinases but not other kinases also increased Notch signaling. Interestingly, in addition to intensifying Notch signaling, RGD peptides and SRC inhibitors also triggered an increase in higher mobility NICD western blot bands and extended NICD half‐life. Our results suggest that these high mobility NICD bands are non‐ubiquitinated forms of NICD fragments. Collectively, we believe these results have revealed a previously undiscovered interaction between integrins and the Notch signaling system that acts to limit Notch signaling via ubiquitination and degradation of active NICD fragments. This novel mechanism may be responsible for ECM control of Notch signaling and angiogenesis.
Grant Funding Source: Supported by NIH (NIGMS)
The Hippo pathway is crucial for not only normal growth and apoptosis but also cell fate specification during development. What controls Hippo pathway activity during cell fate specification is ...incompletely understood. In this article, we identify the insulator protein BEAF-32 as a regulator of Hippo pathway activity in Drosophila photoreceptor differentiation. Though morphologically uniform, the fly eye is composed of two subtypes of R8 photoreceptor neurons defined by expression of light-detecting Rhodopsin proteins. In one R8 subtype, active Hippo signaling induces Rhodopsin 6 (Rh6) and represses Rhodopsin 5 (Rh5), whereas in the other subtype, inactive Hippo signaling induces Rh5 and represses Rh6. The activity state of the Hippo pathway in R8 cells is determined by the expression of warts, a core pathway kinase, which interacts with the growth regulator melted in a double-negative feedback loop. We show that BEAF-32 is required for expression of warts and repression of melted Furthermore, BEAF-32 plays a second role downstream of Warts to induce Rh6 and prevent Rh5 fate. BEAF-32 is dispensable for Warts feedback, indicating that BEAF-32 differentially regulates warts and Rhodopsins. Loss of BEAF-32 does not noticeably impair the functions of the Hippo pathway in eye growth regulation. Our study identifies a context-specific regulator of Hippo pathway activity in post-mitotic neuronal fate, and reveals a developmentally specific role for a broadly expressed insulator protein.
The Hippo pathway is critical for not only normal growth and apoptosis but also cell fate specification during development. What controls Hippo pathway activity during cell fate specification is ...incompletely understood. In this research report, we identify the BEAF-32 insulator protein as a regulator of Hippo pathway activity in Drosophila photoreceptor differentiation. Though morphologically uniform, the fly eye is composed of two subtypes of R8 photoreceptor neurons defined by expression of light-detecting Rhodopsin proteins. In one R8 subtype, active Hippo signaling induces Rhodopsin6 (Rh6) and represses Rhodopsin5 (Rh5) whereas in the alternate subtype, inactive Hippo signaling induces Rh5 and represses Rh6. The activity state of the Hippo pathway in R8 is determined by the expression of warts, a core pathway kinase, which interacts with the growth regulator melted in a double negative feedback loop. We show that the BEAF-32 insulator is required for expression of warts and repression of melted. Furthermore, BEAF-32 plays a second role downstream of Warts to induce Rh6 and prevent Rh5 fate. BEAF-32 is dispensable for Warts feedback, indicating that BEAF-32 differentially regulates warts and Rhodopsins. Loss of BEAF-32 does not noticeably impair the functions of the Hippo pathway in eye growth regulation. Our study identifies a context-specific regulator of Hippo pathway activity in post-mitotic neuronal fate, and reveals a developmentally specific role for a broadly expressed insulator protein.
The rapid rise of high-throughput, data intensive experimental techniques has thrust many biologists into the role of data analyst - a role many biologists feel ill equipped to fill. Novices often ...struggle to find the resources and expertise they need to analyze their experimental results in a wet-lab environment. To fill this need, we developed an educational resource as part of a National Center for Biotechnology Information (NCBI) hackathon. Using RNA-seq as a model, our tutorial guides new users through the steps of data analysis, while placing an emphasis on understanding the motivation behind choices made in the process. To advance the goal of providing a deeper understanding of the analysis process, we developed a new tool, bamDiff. bamDiff allows users to compare the performance of multiple RNA-seq aligners, allowing users to select the most appropriate aligner for the data in question and experimental end-goal. Our tutorial is accessible via a GitHub wiki, with associated data and software provided on an Amazon Machine Image (AMI), which can be completed at no cost to the user through the Amazon Educate Program. Following the hackathon, our tutorial was integrated into the October 2015 offering of NCBI NOW (Next Generation Sequencing (NGS) Online Workshop) a free online experience targeting individuals new to NGS analysis.
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