Early Transcriptional Response Research Articles

Early transcriptional response of Saccharomyces cerevisiae in mixed culture with Torulaspora delbrueckii in cherry wine

Mixed culture by Saccharomyces cerevisiae and Torulaspora delbrueckii has been proposed for the production of wine with improved aroma, but the yeast-yeast interactive mechanism still needs in-depth elucidation. This study compared the transcriptome responses of S. cerevisiae in single and mixed fermentations with T. delbrueckii, in the initial stages of cherry wine fermentation, in order to disclose the possible relationship between aroma synthesis and gene expression. Transcriptome profiling showed a total of 446 and 186 differentially expressed genes were detected in S. cerevisiae and T. delbrueckii, respectively, and several metabolic pathways such as glucose, lipid and amino acid metabolisms were observed with variations. For aroma, a total of 35 volatile compounds were identified by HS-GC-IMS, and mixed fermentation prominently enhanced the syntheses of most esters including propyl acetate, 2-methylpropyl acetate, isoamyl acetate and 2-methylbutyl acetate. By integrating the transcriptomic and volatile results, we propose that ILV5, BATs, PDCs, ADHs, ALDs, ACS1, ACC1 and ARO10 genes are possibly the decisive genes in S. cerevisiae, which showed significant variations following S. cerevisiae's adaptive responses in mixed culture and associated with the formation of certain aldehydes, alcohols and esters in cherry wine.

Moritella viscosa early infection and transcriptional responses of intraperitoneal vaccinated and unvaccinated Atlantic salmon

Skin is the first line of defence against waterborne pathogens, such as Moritella viscosa, which is the causative agent of winter ulcer disease in Atlantic salmon (Salmo salar L.). The present study revealed that vaccination protects against both M. viscosa-induced mortality and skin ulceration, but protection varied according to the strain used in the vaccine formulation. Examination of skin tissue 4 days post M. viscosa challenge indicated that M. viscosa initiated infection by colonising the scale surface. Sequencing the transcripts of the variable region of the IgM heavy chain did not detect effect of vaccination or M. viscosa challenge on antibody repertoire and B cell trafficking from the lymphatic organs to skin. Skin layer-specific responses were examined with 44 K oligonucleotide microarray. Skin responded to vaccination and M. viscosa challenge by increasing transcription of structural genes, stimulating metabolism, and regulation of developmental processes. Immune responses to dead (vaccine) and live M. viscosa were very similar and no pathogen-specific changes were found. Combined use of skin transcriptional profiles and image analysis revealed differences in the infected skin layers between the study groups. M. viscosa was likely retained in the epidermis of vaccinated salmon, whereas the dermis was colonised in unvaccinated fish. Furthermore, decreased expression of lymphocyte-specific and antiviral genes in the dermis indicated possible evasion of immune-related cells from skin in salmon challenged with M. viscosa. Our data also indicated that intraperitoneal vaccination may prime the humoral innate response, which enables a rapid response in the dermis layer of skin during M. viscosa invasion.

Early Transcriptional Responses of Human Nasal Epithelial Cells to Infection with Influenza A and SARS-CoV-2 Virus Differ and Are Influenced by Physiological Temperature.

Influenza A (IAV) and SARS-CoV-2 (SCV2) viruses represent an ongoing threat to public health. Both viruses target the respiratory tract, which consists of a gradient of cell types, receptor expression, and temperature. Environmental temperature has been an understudied contributor to infection susceptibility and understanding its impact on host responses to infection could help uncover new insight into severe disease risk factors. As the nasal passageways are the initial site of respiratory virus infection, in this study we investigated the effect of temperature on host responses in human nasal epithelial cells (hNECs) utilizing IAV and SCV2 in vitro infection models. We demonstrate that temperature affected SCV2, but not IAV, viral replicative fitness and that SCV2-infected cultures were slower to mount an infection-induced response, likely due to suppression by the virus. Additionally, we show that that temperature not only changed the basal transcriptomic landscape of epithelial cells, but that it also impacted the response to infection. The induction of interferon and other innate immune responses was not drastically affected by temperature, suggesting that while the baseline antiviral response at different temperatures remained consistent, there may be metabolic or signaling changes that affect how well the cultures were able to adapt to new pressures, such as infection. Finally, we show that hNECs responded differently to IAV and SCV2 infection in ways that give insight into how the virus is able to manipulate the cell to allow for replication and release. Taken together, these data give new insight into the innate immune response to respiratory infections and can assist in identifying new treatment strategies for respiratory infections.

Sex and prior exposure jointly shape innate immune responses to a live herpesvirus vaccine.

Both sex and prior exposure to pathogens are known to influence responses to immune challenges, but their combined effects are not well established in humans, particularly in early innate responses critical for shaping subsequent outcomes. We employed systems immunology approaches to study responses to a replication-defective, herpes simplex virus (HSV) 2 vaccine in men and women either naive or previously exposed to HSV. Blood transcriptomic and cell population profiling showed substantial changes on day 1 after vaccination, but the responses depended on sex and whether the vaccinee was naive or previously exposed to HSV. The magnitude of early transcriptional responses was greatest in HSV naive women where type I interferon (IFN) signatures were prominent and associated negatively with vaccine-induced neutralizing antibody titers, suggesting that a strong early antiviral response reduced the uptake of this replication-defective virus vaccine. While HSV seronegative vaccine recipients had upregulation of gene sets in type I IFN (IFN-α/β) responses, HSV2 seropositive vaccine recipients tended to have responses focused more on type II IFN (IFN-γ) genes. These results together show that prior exposure and sex interact to shape early innate responses that then impact subsequent adaptive immune phenotypes. Intramural Research Program of the NIH, the National Institute of Allergy and Infectious Diseases, and other institutes supporting the Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation. The vaccine trial was supported through a clinical trial agreement between the National Institute of Allergy and Infectious Diseases and Sanofi Pasteur. Clinical trial number: NCT01915212.

ATM suppresses c-Myc overexpression in the mammary epithelium in response to estrogen

ATM gene mutation carriers are predisposed to estrogen-receptor-positive breast cancer (BC). ATM prevents BC oncogenesis by activating p53 in every cell; however, much remains unknown about tissue-specific oncogenesis after ATM loss. Here, we report that ATM controls the early transcriptional response to estrogens. This response depends on topoisomerase II (TOP2), which generates TOP2-DNA double-strand break (DSB) complexes and rejoins the breaks. When TOP2-mediated ligation fails, ATM facilitates DSB repair. After estrogen exposure, TOP2-dependent DSBs arise at the c-MYC enhancer in human BC cells, and their defective repair changes the activation profile of enhancers and induces the overexpression of many genes, including the c-MYC oncogene. CRISPR/Cas9 cleavage at the enhancer also causes c-MYC overexpression, indicating that this DSB causes c-MYC overexpression. Estrogen treatment induced c-Myc protein overexpression in mammary epithelial cells of ATM-deficient mice. In conclusion, ATM suppresses the c-Myc-driven proliferative effects of estrogens, possibly explaining such tissue-specific oncogenesis.

Physiological concentrations of glucocorticoids induce pathological DNA double-strand breaks.

Steroid hormones induce the transcription of target genes by activating nuclear receptors. Early transcriptional response to various stimuli, including hormones, involves the active catalysis of topoisomerase II (TOP2) at transcription regulatory sequences. TOP2 untangles DNAs by transiently generating double-strand breaks (DSBs), where TOP2 covalently binds to DSB ends. When TOP2 fails to rejoin, called "abortive" catalysis, the resulting DSBs are repaired by tyrosyl-DNA phosphodiesterase 2 (TDP2) and non-homologous end-joining (NHEJ). A steroid, cortisol, is the most important glucocorticoid, and dexamethasone (Dex), a synthetic glucocorticoid, is widely used for suppressing inflammation in clinics. We here revealed that clinically relevant concentrations of Dex and physiological concentrations of cortisol efficiently induce DSBs in G1 phase cells deficient in TDP2 and NHEJ. The DSB induction depends on glucocorticoid receptor (GR) and TOP2. Considering the specific role of TDP2 in removing TOP2 adducts from DSB ends, induced DSBs most likely represent stalled TOP2-DSB complexes. Inhibition of RNA polymerase II suppressed the DSBs formation only modestly in the G1 phase. We propose that cortisol and Dex frequently generate DSBs through the abortive catalysis of TOP2 at transcriptional regulatory sequences, including promoters or enhancers, where active TOP2 catalysis occurs during early transcriptional response.

Transcriptome analysis reveals distinct innate immunity and ribosomal response at early stage of AcMNPV infection in haemocyte of silkworm resistant and susceptible strains

We propose a schematic diagram for the early transcriptional responses between the susceptible and resistant silkworm strains after AcMNPV infection. In brief, when AcMNPV infect susceptible strains of silkworm, the inhibition of innate immunity and host translational machinery, as well as up-regulation of cytoskeleton, that these responses promote baculoviral BV transport and ingress into the nucleus, thus facilitating the replication of baculovirus. However, when AcMNPV infect resistant strains of silkworm, down-regulation of endocytosis and RNA transport weakened the ability of the baculoviral BV entry into the nucleus, while up-regulation of ribosomal proteins and energy metabolic to inhibit the replication of the virus. • Early transcriptional responses were analyzed in different resistant strains of silkworm to AcMNPV infection. • Distinct innate immunity and ribosomal response were found between the resistant and susceptible silkworm strains. • Provide basic data for the initial host transcriptional responses to viral infection in silkworm. Baculoviruses are enveloped rod-shaped viruses that with circular double-stranded and large DNA genome. Baculoviruses successfully invade by using the host factors, especially at the process of establishing early infection. In this study, we investigated the different resistant strains of silkworm in response to AcMNPV early infection by RNA-sequencing. Our data revealed that the genes involved in innate immunity and ribosomal proteins were suppressed and cytoskeleton were induced in susceptible strain p50, thus facilitating the viral replication. However, in resistant strain C108, the genes participated in endocytosis and RNA transport were down-regulated, while up-regulation of ribosomal proteins and energy metabolic to inhibit the infection of the virus. These data provide a new sight of the initial host transcriptional responses to viral infection in silkworm.

Abstract P3108: Induced-Pluripotent Stem Cell-Derived Cardiomyocytes As A Model To Investigate Cardiotoxicity Of A Panel Of Breast Cancer Drugs

Anthracyclines (AC) are a class of antineoplastic drugs which are used to treat breast cancer (BC) subtypes including triple-negative BC. The 2019 Surveillance, Epidemiology, and End Results study indicates high BC survival rates and low reoccurrence with chemotherapy regimens that include AC. AC treatment, however, is associated with developing cardiovascular disease (CVD) in a subset of people, despite these patients having no history of CVD. Because CVD is typically irreversible, understanding patient susceptibility to AC toxicity is critical to cancer treatment management and long-term patient survival. As a first step towards understanding the genetic and mechanistic basis for AC-induced cardiotoxicity, we have developed an in vitro cardiomyocyte (CM) model using a panel of four genotyped induced-Pluripotent Stem Cell (iPSC) lines to test the effects of three AC (Doxorubicin, Epirubicin and Daunorubicin) and two non-AC (Mitoxantrone and Trastuzumab) BC drugs. We can reliably differentiate beating CMs at a median purity 90.5% based on the expression of cardiac-specific troponin T. Drug exposure for 48 hours reveals cardiotoxicity at micromolar concentrations across all drugs except for Trastuzumab, with Daunorubicin and Mitoxantrone exhibiting the greatest effect. We observe mRNA expression changes of stress response genes such as p53 within six hours of drug treatment, suggesting that an early transcriptional response mediates these effects. Using this model, we plan to measure the global transcriptional response to drug exposure across individuals and correlate these changes with each individual’s genetic variants to gain insight into cardiotoxicity susceptibility.

Transcriptomic Response of the Diazotrophic Bacteria Gluconacetobacter diazotrophicus Strain PAL5 to Iron Limitation and Characterization of the fur Regulatory Network.

Gluconacetobacter diazotrophicus has been the focus of several studies aiming to understand the mechanisms behind this endophytic diazotrophic bacterium. The present study is the first global analysis of the early transcriptional response of exponentially growing G. diazotrophicus to iron, an essential cofactor for many enzymes involved in various metabolic pathways. RNA-seq, targeted gene mutagenesis and computational motif discovery tools were used to define the G. diazotrophicus fur regulon. The data analysis showed that genes encoding functions related to iron homeostasis were significantly upregulated in response to iron limitations. Certain genes involved in secondary metabolism were overexpressed under iron-limited conditions. In contrast, it was observed that the expression of genes involved in Fe-S cluster biosynthesis, flagellar biosynthesis and type IV secretion systems were downregulated in an iron-depleted culture medium. Our results support a model that controls transcription in G. diazotrophicus by fur function. The G. diazotrophicus fur protein was able to complement an E. coli fur mutant. These results provide new insights into the effects of iron on the metabolism of G. diazotrophicus, as well as demonstrate the essentiality of this micronutrient for the main characteristics of plant growth promotion by G. diazotrophicus.

Post-Transcriptional Dynamics is Involved in Rapid Adaptation to Hypergravity in Jurkat T Cells.

The transcriptome of human immune cells rapidly reacts to altered gravity in a highly dynamic way. We could show in previous experiments that transcriptional patterns show profound adaption after seconds to minutes of altered gravity. To gain further insight into these transcriptional alteration and adaption dynamics, we conducted a highly standardized RNA-Seq experiment with human Jurkat T cells exposed to 9xg hypergravity for 3 and 15 min, respectively. We investigated the frequency with which individual exons were used during transcription and discovered that differential exon usage broadly appeared after 3 min and became less pronounced after 15 min. Additionally, we observed a shift in the transcript pool from coding towards non-coding transcripts. Thus, adaption of gravity-sensitive differentially expressed genes followed a dynamic transcriptional rebound effect. The general dynamics were compatible with previous studies on the transcriptional effects of short hypergravity on human immune cells and suggest that initial up-regulatory changes mostly result from increased elongation rates. The shift correlated with a general downregulation of the affected genes. All chromosome bands carried homogenous numbers of gravity-sensitive genes but showed a specific tendency towards up- or downregulation. Altered gravity affected transcriptional regulation throughout the entire genome, whereby the direction of differential expression was strongly dependent on the structural location in the genome. A correlation analysis with potential mediators of the early transcriptional response identified a link between initially upregulated genes with certain transcription factors. Based on these findings, we have been able to further develop our model of the transcriptional response to altered gravity.

Early Transcriptional Response to Monensin in Sensitive and Resistant Strains of Eimeria tenella.

Eimeria parasites are the causative agents of coccidiosis, a common parasitic disease in poultry and livestock that causes significant economic losses to the animal husbandry industry. Ionophore coccidiostats, such as monensin and salinomycin, are widely used for prophylaxis of coccidiosis in poultry. Unfortunately, widespread drug resistance has compromised their efficacy. As a result, there is an increasing need to understand the targets and resistance mechanisms to anticoccidials. However, how Eimeria parasite genes respond to ionophores remains unclear. In this study, resistance to monensin was induced in E. tenella through serial generations of selection. Both sensitive and resistant E. tenella sporozoites were treated with 5 μg/ml monensin for 0, 2, and 4 h, respectively. Gene transcription profiles were then compared by high-throughput sequencing. The results showed that protein translation-related genes were significantly downregulated after drug induction. A total of 1,848 DEGs were detected in the sensitive strain after 2 h of exposure, whereas only 31 were detected in the resistant strain. Among these DEGs in the sensitive strain, genes associated with protein degradation were significantly upregulated, supporting the autophagy-like parasite killing theory. Then, 4 h of exposure resulted in additional 626 and 621 DEGs for sensitive and resistant strains, respectively. This result implies that the gene transcription in sensitive strain is more susceptible to monensin treatment. Our results provide gene expression landscapes of E. tenella following monensin treatment. These data will contribute to a better understanding of the mechanism of drug resistance to polyether ionophores in coccidia.

Early and late genome-wide gastric epithelial transcriptome response during infection with the human carcinogen Helicobacterpylori.

Infection of the stomach by Helicobacter pylori is a major risk factor for the development of gastric cancer. Colonization of the gastric epithelium leads to the activation of multiple disease-related signaling pathways. Serine protease HtrA represents an important secreted virulence factor that mediates cleavage of cellular junctions. However, its potential role in nuclear responses is unknown. Here, we performed a genome-wide RNA-seq analysis of polarized gastric epithelial cells infected by wild-type (wt) and ΔhtrA mutant bacteria. Fluorescence microscopy showed that H.pylori wt, but not ΔhtrA bacteria, preferably localized at cellular junctions. Our results pinpointed early (2h) and late (6h) transcriptional responses, with most differentially expressed genes at 6h post infection. The transcriptomes revealed HtrA-dependent targeting of genes associated with inflammation and apoptosis (e.g. IL8, ZFP36, TNF). Accordingly, infection with the ΔhtrA mutant induced increased apoptosis rates in host cells, which was associated with reduced H.pylori CagA expression. In contrast, transcription of various carcinogenesis-associated genes (e.g. DKK1, DOCK8) was affected by H.pylori independent of HtrA. These findings suggest that H.pylori disturbs previously unknown molecular pathways in an HtrA-dependent and HtrA-independent manner, and provide valuable new insights of this significant pathogen in humans and thus potential targets for better controlling the risk of malignant transformation.

MiRNA-200b-A Potential Biomarker Identified in a Porcine Model of Cardiogenic Shock and Mechanical Unloading.

BackgroundCardiogenic shock (CS) alters whole body metabolism and circulating biomarkers serve as prognostic markers in CS patients. Percutaneous ventricular assist devices (pVADs) unload the left ventricle by actively ejecting blood into the aorta. The goal of the present study was to identify alterations in circulating metabolites and transcripts in a large animal model that might serve as potential prognostic biomarkers in acute CS and additional left ventricular unloading by Impella ® pVAD support.MethodsCS was induced in a preclinical large animal model by injecting microspheres into the left coronary artery system in six pigs. After the induction of CS, mechanical pVAD support was implemented for 30 min total. Serum samples were collected under basal conditions, after the onset of CS, and following additional pVAD unloading. Circulating metabolites were determined by metabolomic analysis, circulating RNA entities by RNA sequencing.ResultsCS and additional pVAD support alter the abundance of circulating metabolites involved in Aminoacyl-tRNA biosynthesis and amino acid metabolism. RNA sequencing revealed decreased abundance of the hypoxia sensitive miRNA-200b following the induction of CS, which was reversed following pVAD support.ConclusionThe hypoxamir miRNA-200b is a potential circulating marker that is repressed in CS and is restored following pVAD support. The early transcriptional response with increased miRNA-200b expression following only 30 min of pVAD support suggests that mechanical unloading alters whole body metabolism. Future studies are required to delineate the impact of serum miRNA-200b levels as a prognostic marker in patients with acute CS and pVAD unloading.

Dehydroascorbate induces plant resistance in rice against root-knot nematode Meloidogyne graminicola.

Ascorbic acid (AsA) is an important antioxidant in plants and regulates various physiological processes. In this study, we show that exogenous treatments with the oxidized form of AsA, that is, dehydroascorbate (DHA), activates induced systemic resistance in rice against the root‐knot nematode Meloidogyne graminicola, and investigate the molecular and biochemical mechanisms underlying this phenotype. Detailed transcriptome analysis on roots of rice plants showed an early and robust transcriptional response on foliar DHA treatment, with induction of several genes related to plant stress responses, immunity, antioxidant activity, and secondary metabolism already at 1 day after treatment. Quantitative and qualitative evaluation of H2O2 levels confirmed the appearance of a reactive oxygen species (ROS) burst on DHA treatment, both at the site of treatment and systemically. Experiments using chemical ROS inhibitors or scavengers confirmed that H2O2 accumulation contributes to DHA‐based induced resistance. Furthermore, hormone measurements in DHA‐treated plants showed a significant systemic accumulation of the defence hormone salicylic acid (SA). The role of the SA pathway in DHA‐based induced resistance was confirmed by nematode infection experiments using an SA‐signalling deficient WRKY45‐RNAi line and reverse transcription‐quantitative PCR on SA marker genes. Our results collectively reveal that DHA activates induced systemic resistance in rice against the root‐knot nematode M. graminicola, mediated through the production of ROS and activation of the SA pathway.

RHY‐1 Promotes Hydrogen Sulfide Tolerance

Once known best for its toxic effects, recent work has shown that hydrogen sulfide (H2 S) has many roles as a cellular messenger. For example, both endogenously produced and exogenously supplied H2 S protect against cellular damage and death associated with ischemia/reperfusion injury in mammals. The mechanistic relationship between beneficial and toxic effects of H2 S is not understood. We have developed C. elegans as a model to understand the mechanistic basis of H2 S effects in animals. In addition to facile genetic and genomic tools, using C. elegans provides the ability to precisely control both genotype and cellular H2 S exposure. C. elegans grown in 50 ppm H2 S are long-lived and resistant to hypoxia-induced disruption of protein homeostasis. The early transcriptional response to H2 S requires the C. elegans orthologue of the hypoxia-inducible transcription factor, hif-1. HIF-1 promotes survival in H2 S, at least in part, by upregulating expression of sqrd-1, which encodes the sulfide-quinone oxidoreductase. SQRD-1 catalyzes the first step in the mitochondrial oxidation of H2 S. In an unbiased forward genetic screen, we found that expression of rhy-1 suppresses lethality of hif-1 mutant animals in 50 ppm H2 S. RHY-1 is an integral-membrane ER protein with predicted acyltransferase (ACYL3) activity. The ACYL3 family is large and conserved across species from bacteria to primates, but the function of these enzymes is largely unstudied. RHY-1 was first characterized as a negative regulator of HIF-1, and our data indicate that it also promotes survival in H2 S independently of HIF-1. To understand RHY-1 function we have used biotinylation by antibody recognition (BAR) to identify proteins that interact with RHY-1. We show that RHY-1 directly associates with CYSL proteins, which are orthologues of cystathionine β-synthase. Mutations in cysl-1 abrogate RHY-1 function to regulate HIF-1 and to promote survival independently of HIF-1. We have also identified a novel methyltransferase, RIPS-1, that is required for RHY-1 to promote survival in H2 S but which is dispensable for the proper regulation of HIF-1. Together, our data show that RHY-1 promotes survival in H2 S through a novel mechanism which can bypass the only known catabolic pathway for H2 S in vivo. Understanding the mechanism of RHY-1 activity in H2 S will begin to elucidate the relationship between H2 S signaling and toxicity, and could lead to new therapeutic strategies to modulate endogenous H2 S levels.

O-12 - Epigenetic modifiers in somatostatin type 2 receptor radionuclide theranostics and early transcriptional response of mouse pheochromocytoma models

O-12 - Epigenetic modifiers in somatostatin type 2 receptor radionuclide theranostics and early transcriptional response of mouse pheochromocytoma models

The oncogene-dependent resistance to reprogramming unveils cancer therapeutic targets

The resistance to transcription factor-mediated reprogramming into pluripotent stem cells is one of the distinctive features of cancer cells. Here we dissect the profiles of reprogramming factor binding and the subsequent transcriptional response in cancer cells to reveal its underlying mechanisms. Using clear cell sarcomas (CCSs), we show that the driver oncogene EWS/ATF1 misdirects the reprogramming factors to cancer-specific enhancers and thereby impairs the transcriptional response toward pluripotency that is otherwise provoked. Sensitization to the reprogramming cue is observed in other cancer types when the corresponding oncogenic signals are pharmacologically inhibited. Exploiting this oncogene dependence of the transcriptional "stiffness," we identify mTOR signaling pathways downstream of EWS/ATF1 and discover that inhibiting mTOR activity substantially attenuates the propagation of CCS cells invitro and invivo. Our results demonstrate that the early transcriptional response to cell fate perturbations can be a faithful readout to identify effective therapeutics targets in cancer cells.

Visualization, benchmarking and characterization of nested single-cell heterogeneity as dynamic forest mixtures.

A major topic of debate in developmental biology centers on whether development is continuous, discontinuous, or a mixture of both. Pseudo-time trajectory models, optimal for visualizing cellular progression, model cell transitions as continuous state manifolds and do not explicitly model real-time, complex, heterogeneous systems and are challenging for benchmarking with temporal models. We present a data-driven framework that addresses these limitations with temporal single-cell data collected at discrete time points as inputs and a mixture of dependent minimum spanning trees (MSTs) as outputs, denoted as dynamic spanning forest mixtures (DSFMix). DSFMix uses decision-tree models to select genes that account for variations in multimodality, skewness and time. The genes are subsequently used to build the forest using tree agglomerative hierarchical clustering and dynamic branch cutting. We first motivate the use of forest-based algorithms compared to single-tree approaches for visualizing and characterizing developmental processes. We next benchmark DSFMix to pseudo-time and temporal approaches in terms of feature selection, time correlation, and network similarity. Finally, we demonstrate how DSFMix can be used to visualize, compare and characterize complex relationships during biological processes such as epithelial-mesenchymal transition, spermatogenesis, stem cell pluripotency, early transcriptional response from hormones and immune response to coronavirus disease. Our results indicate that the expression of genes during normal development exhibits a high proportion of non-uniformly distributed profiles that are mostly right-skewed and multimodal; the latter being a characteristic of major steady states during development. Our study also identifies and validates gene signatures driving complex dynamic processes during somatic or germline differentiation.

Severe Intrauterine Infection Induces an Epithelial-to-Mesenchymal Transition Within the Chorionic Villous Tree

Group B Streptococci (GBS) and Escherichia coli are bacteria linked to preterm birth, stillbirth and neonatal sepsis. The impact of a severe bacterial infection on the transcriptional and immune response of placental chorionic villi is unknown, but may predispose to abruption and adverse neonatal outcomes. The study objective was to investigate early transcriptional responses, pathways and gene networks within placental chorionic villi after an experimental severe GBS or E. coli infection.

Early transcriptional responses of bronchial epithelial cells to whole cigarette smoke mirror those of in-vivo exposed human bronchial mucosa

BackgroundDespite the well-known detrimental effects of cigarette smoke (CS), little is known about the complex gene expression dynamics in the early stages after exposure. This study aims to investigate early transcriptomic responses following CS exposure of airway epithelial cells in culture and compare these to those found in human CS exposure studies.MethodsPrimary bronchial epithelial cells (PBEC) were differentiated at the air–liquid interface (ALI) and exposed to whole CS. Bulk RNA-sequencing was performed at 1 h, 4 h, and 24 h hereafter, followed by differential gene expression analysis. Results were additionally compared to data retrieved from human CS studies.ResultsALI-PBEC gene expression in response to CS was most significantly changed at 4 h after exposure. Early transcriptomic changes (1 h, 4 h post CS exposure) were related to oxidative stress, xenobiotic metabolism, higher expression of immediate early genes and pro-inflammatory pathways (i.e., Nrf2, AP-1, AhR). At 24 h, ferroptosis-associated genes were significantly increased, whereas PRKN, involved in removing dysfunctional mitochondria, was downregulated. Importantly, the transcriptome dynamics of the current study mirrored in-vivo human studies of acute CS exposure, chronic smokers, and inversely mirrored smoking cessation.ConclusionThese findings show that early after CS exposure xenobiotic metabolism and pro-inflammatory pathways were activated, followed by activation of the ferroptosis-related cell death pathway. Moreover, significant overlap between these transcriptomic responses in the in-vitro model and human in-vivo studies was found, with an early response of ciliated cells. These results provide validation for the use of ALI-PBEC cultures to study the human lung epithelial response to inhaled toxicants.