scholarly journals Plasticity of fibroblast transcriptional response to physical and biochemical cues revealed by dynamic network analysis

2020 ◽  
Author(s):  
Pilhwa Lee
Keyword(s):  
Regulatory Networks ◽  
Time Course ◽  
Inflammatory Responses ◽  
Dynamic Network ◽  
Transcriptional Response ◽  
Live Cells ◽  
Human Skin Fibroblast ◽  
Transcriptional Responses ◽  
External Cues ◽  
Transcription Factor Expression

Data on human skin fibroblast transcriptional responses to external cues were used to reconstruct dynamic gene regulatory networks. The goal of the reconstruction was to determine dynamic network interactions (quantitative predictive relationships of mutual regulatory influences of and on transcription factor expression) from time course data on 56 transcript expression levels obtained following different external cues. The inherently under-determined nature of this problem was addressed in part by excluding putative regulatory motifs that did not appear to be functional in multiple independent experiments from different independent external perturbations. Data were obtained from a previously published experiment in which the 56 transcripts were assayed by bioluminescence in live cells cultured on substrates of varying levels of stiffness and exposed to different levels of arginylglycylaspartic acid (RGD) peptide. The inferred dynamical networks were validated via comparison of predictions to known interactions from gene databases. We discovered that exposure to different substrate stiffnesses and to RGD stimulate responses that are mediated through GATA4, SMAD3/4, ETS-1, and STAT5 and other genes, which can initiate hypertrophic, fibrotic, and inflammatory responses.

scholarly journals The transcriptomic response of cells to a drug combination is more than the sum of the responses to the monotherapies

2019 ◽  
Author(s):  
Jennifer E. L. Diaz ◽  
Mehmet Eren Ahsen ◽  
Thomas Schaffter ◽  
Xintong Chen ◽  
Ronald B. Realubit ◽  
...  
Keyword(s):  
Time Course ◽  
Transcriptional Response ◽  
Unrelated Individual ◽  
Drug Combinations ◽  
Prediction Algorithm ◽  
Transcriptional Responses ◽  
Transcriptomic Response ◽  
Transcriptional Signature ◽  
Activation Of Transcription ◽  
Sequential Activation

AbstractOur ability to predict the effects of drug combinations is limited, in part by limited understanding of how the transcriptional response of two monotherapies results in that of their combination. We performed the first analysis of matched time course RNAseq profiling of cells treated with both single drugs and their combinations. The transcriptional signature of the synergistic combination we studied had unique gene expression not seen in either constituent monotherapy. This can be explained mechanistically by the sequential activation of transcription factors in time in the gene regulatory network. The nature of this transcriptional cascade suggests that drug synergy may ensue when the transcriptional responses elicited by two unrelated individual drugs are correlated. We used these results as the basis of a simple prediction algorithm attaining an AUROC of 0.84 in the prediction of synergistic drug combinations in an independent dataset.

scholarly journals Early whole blood transcriptional responses to radiation-attenuated Plasmodium falciparum sporozoite vaccination in malaria naïve and malaria pre-exposed adult volunteers

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Fergal J. Duffy ◽  
Ying Du ◽  
Jason Carnes ◽  
Judith E. Epstein ◽  
Stephen L. Hoffman ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Plasmodium Falciparum ◽  
Whole Blood ◽  
Inflammatory Responses ◽  
Protective Efficacy ◽  
Transcriptional Response ◽  
Interferon Response ◽  
Transcriptional Responses ◽  
Post Vaccination ◽  
Adult Participants

Abstract Background Vaccination with radiation-attenuated Plasmodium falciparum sporozoites is known to induce protective immunity. However, the mechanisms underlying this protection remain unclear. In this work, two recent radiation-attenuated sporozoite vaccination studies were used to identify potential transcriptional correlates of vaccination-induced protection. Methods Longitudinal whole blood RNAseq transcriptome responses to immunization with radiation-attenuated P. falciparum sporozoites were analysed and compared across malaria-naïve adult participants (IMRAS) and malaria-experienced adult participants (BSPZV1). Parasite dose and method of delivery differed between trials, and immunization regimens were designed to achieve incomplete protective efficacy. Observed protective efficacy was 55% in IMRAS and 20% in BSPZV1. Study vaccine dosings were chosen to elicit both protected and non-protected subjects, so that protection-associated responses could be identified. Results Analysis of comparable time points up to 1 week after the first vaccination revealed a shared cross-study transcriptional response programme, despite large differences in number and magnitude of differentially expressed genes between trials. A time-dependent regulatory programme of coherent blood transcriptional modular responses was observed, involving induction of inflammatory responses 1–3 days post-vaccination, with cell cycle responses apparent by day 7 in protected individuals from both trials. Additionally, strongly increased induction of inflammation and interferon-associated responses was seen in non-protected IMRAS participants. All individuals, except for non-protected BSPZV1 participants, showed robust upregulation of cell-cycle associated transcriptional responses post vaccination. Conclusions In summary, despite stark differences between the two studies, including route of vaccination and status of malaria exposure, responses were identified that were associated with protection after PfRAS vaccination. These comprised a moderate early interferon response peaking 2 days post vaccination, followed by a later proliferative cell cycle response steadily increasing over the first 7 days post vaccination. Non-protection is associated with deviations from this model, observed in this study with over-induction of early interferon responses in IMRAS and failure to mount a cell cycle response in BSPZV1.

scholarly journals The transcriptomic response of cells to a drug combination is more than the sum of the responses to the monotherapies

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Jennifer EL Diaz ◽  
Mehmet Eren Ahsen ◽  
Thomas Schaffter ◽  
Xintong Chen ◽  
Ronald B Realubit ◽  
...  
Keyword(s):  
Time Course ◽  
Transcriptional Response ◽  
Unrelated Individual ◽  
Drug Combinations ◽  
Prediction Algorithm ◽  
Transcriptional Responses ◽  
Transcriptomic Response ◽  
Transcriptional Signature ◽  
Activation Of Transcription ◽  
Sequential Activation

Our ability to discover effective drug combinations is limited, in part by insufficient understanding of how the transcriptional response of two monotherapies results in that of their combination. We analyzed matched time course RNAseq profiling of cells treated with single drugs and their combinations and found that the transcriptional signature of the synergistic combination was unique relative to that of either constituent monotherapy. The sequential activation of transcription factors in time in the gene regulatory network was implicated. The nature of this transcriptional cascade suggests that drug synergy may ensue when the transcriptional responses elicited by two unrelated individual drugs are correlated. We used these results as the basis of a simple prediction algorithm attaining an AUROC of 0.77 in the prediction of synergistic drug combinations in an independent dataset.

scholarly journals Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol

2017 ◽  
Author(s):  
Noah Dukler ◽  
Gregory T. Booth ◽  
Yi-Fei Huang ◽  
Nathaniel Tippens ◽  
Charles G. Danko ◽  
...  
Keyword(s):  
Time Course ◽  
Transcriptional Response ◽  
Distinct Group ◽  
K562 Cells ◽  
Careful Analysis ◽  
Transcriptional Responses ◽  
Time Course Data ◽  
Nascent Rna ◽  
Polymerase Pausing ◽  
Key Aspects

AbstractMost studies of responses to transcriptional stimuli measure changes in cellular mRNA concentrations. By sequencing nascent RNA instead, it is possible to detect changes in transcription in minutes rather than hours, and thereby distinguish primary from secondary responses to regulatory signals. Here, we describe the use of PRO-seq to characterize the immediate transcriptional response in human cells to celastrol, a compound derived from traditional Chinese medicine that has potent anti-inflammatory, tumor-inhibitory and obesity-controlling effects. Our analysis of PRO-seq data for K562 cells reveals dramatic transcriptional effects soon after celastrol treatment at a broad collection of both coding and noncoding transcription units. This transcriptional response occurred in two major waves, one within 10 minutes, and a second 40-60 minutes after treatment. Transcriptional activity was generally repressed by celastrol, but one distinct group of genes, enriched for roles in the heat shock response, displayed strong activation. Using a regression approach, we identified key transcription factors that appear to drive these transcriptional responses, including members of the E2F and RFX families. We also found sequence-based evidence that particular TFs drive the activation of enhancers. We observed increased polymerase pausing at both genes and enhancers, suggesting that pause release may be widely inhibited during the celastrol response. Our study demonstrates that a careful analysis of PRO-seq time course data can disentangle key aspects of a complex transcriptional response, and it provides new insights into the activity of a powerful pharmacological agent.

scholarly journals Quantitative relationships between SMAD dynamics and target gene activation kinetics in single live cells

2018 ◽  
Author(s):  
Onur Tidin ◽  
Elias T. Friman ◽  
Felix Naef ◽  
David M. Suter
Keyword(s):  
Transcriptional Activation ◽  
Target Gene ◽  
Target Genes ◽  
Nuclear Translocation ◽  
Gene Activation ◽  
Transcriptional Response ◽  
Tissue Growth ◽  
Live Cells ◽  
High Temporal Resolution ◽  
Transcriptional Responses

AbstractThe transduction of extracellular signals through signaling pathways that culminate in a transcriptional response is central to many biological processes. However, quantitative relationships between activities of signaling pathway components and transcriptional output of target genes remain poorly explored. Here we developed a dual bioluminescence imaging strategy allowing simultaneous monitoring of nuclear translocation of the SMAD4 and SMAD2 transcriptional activators upon TGF-β stimulation, and the transcriptional response of the endogenous connective tissue growth factor (ctgf) gene. Using cell lines allowing to vary exogenous SMAD4/2 expression levels, we performed quantitative measurements of the temporal profiles of SMAD4/2 translocation and ctgf transcription kinetics in hundreds of individual cells at high temporal resolution. We found that while nuclear translocation efficiency had little impact on initial ctgf transcriptional activation, high total cellular SMAD4 but not SMAD2 levels increased the probability of cells to exhibit a sustained ctgf transcriptional response. The approach we present here allows time-resolved single cell quantification of transcription factor dynamics and transcriptional responses and thereby sheds light on the quantitative relationship between SMADs and target gene responses.

scholarly journals Disentangling transcriptional responses in plant defense against arthropod herbivores

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Alejandro Garcia ◽  
M. Estrella Santamaria ◽  
Isabel Diaz ◽  
Manuel Martinez
Keyword(s):  
Regulatory Networks ◽  
Pieris Rapae ◽  
Meta Analysis ◽  
Plant Response ◽  
Plant Responses ◽  
Transcriptional Responses ◽  
Crop Species ◽  
Physiological Processes ◽  
Meta Analyses ◽  
Plant Herbivore

AbstractThe success in the response of a plant to a pest depends on the regulatory networks that connect plant perception and plant response. Meta-analyses of transcriptomic responses are valuable tools to discover novel mechanisms in the plant/herbivore interplay. Considering the quantity and quality of available transcriptomic analyses, Arabidopsis thaliana was selected to test the ability of comprehensive meta-analyses to disentangle plant responses. The analysis of the transcriptomic data showed a general induction of biological processes commonly associated with the response to herbivory, like jasmonate signaling or glucosinolate biosynthesis. However, an uneven induction of many genes belonging to these biological categories was found, which was likely associated with the particularities of each specific Arabidopsis-herbivore interaction. A thorough analysis of the responses to the lepidopteran Pieris rapae and the spider mite Tetranychus urticae highlighted specificities in the perception and signaling pathways associated with the expression of receptors and transcription factors. This information was translated to a variable alteration of secondary metabolic pathways. In conclusion, transcriptomic meta-analysis has been revealed as a potent way to sort out relevant physiological processes in the plant response to herbivores. Translation of these transcriptomic-based analyses to crop species will permit a more appropriate design of biotechnological programs.

scholarly journals Copper Availability Influences the Transcriptomic Response of Candida albicans to Fluconazole Stress

2021 ◽  
Vol 11 (4) ◽  
Author(s):  
Elizabeth W Hunsaker ◽  
Chen-Hsin Albert Yu ◽  
Katherine J Franz
Keyword(s):  
Candida Albicans ◽  
Time Course ◽  
Transcriptional Response ◽  
Metal Homeostasis ◽  
Metal Availability ◽  
Drug Induced ◽  
Transcriptomic Response ◽  
Opportunistic Fungal Pathogen ◽  
Whole Transcriptome Analysis ◽  
Whole Transcriptome

Abstract The ability of pathogens to maintain homeostatic levels of essential biometals is known to be important for survival and virulence in a host, which itself regulates metal availability as part of its response to infection. Given this importance of metal homeostasis, we sought to address how the availability of copper in particular impacts the response of the opportunistic fungal pathogen Candida albicans to treatment with the antifungal drug fluconazole. The present study reports whole transcriptome analysis via time-course RNA-seq of C. albicans cells exposed to fluconazole with and without 10 µM supplemental CuSO4 added to the growth medium. The results show widespread impacts of small changes in Cu availability on the transcriptional response of C. albicans to fluconazole. Of the 2359 genes that were differentially expressed under conditions of cotreatment, 50% were found to be driven uniquely by exposure to both Cu and fluconazole. The breadth of metabolic processes that were affected by cotreatment illuminates a fundamental intersectionality between Cu metabolism and fungal response to drug stress. More generally, these results show that seemingly minor fluctuations in Cu availability are sufficient to shift cells’ transcriptional response to drug stress. Ultimately, the findings may inform the development of new strategies that capitalize on drug-induced vulnerabilities in metal homeostasis pathways.

scholarly journals Molecular Basis of AmpC β-Lactamase Induction by Avibactam in Pseudomonas aeruginosa: PBP Occupancy, Live Cell Binding Dynamics and Impact on Resistant Clinical Isolates Harboring PDC-X Variants

2021 ◽  
Vol 22 (6) ◽  
pp. 3051
Author(s):  
Silvia López-Argüello ◽  
María Montaner ◽  
Antonio Oliver ◽  
Bartolome Moya
Keyword(s):  
Time Course ◽  
Clinical Isolates ◽  
Live Cells ◽  
Cell Binding ◽  
Penicillin Binding Proteins ◽  
New Class ◽  
Inhibitory Spectrum ◽  
Mechanistic Basis ◽  
Outer Membrane Permeability ◽  
Strain Dependent

Avibactam belongs to the new class of diazabicyclooctane β-lactamase inhibitors. Its inhibitory spectrum includes class A, C and D enzymes, including P. aeruginosa AmpC. Nonetheless, recent reports have revealed strain-dependent avibactam AmpC induction. In the present work, we wanted to assess the mechanistic basis underlying AmpC induction and determine if derepressed PDC-X mutated enzymes from ceftazidime/avibactam-resistant clinical isolates were further inducible. We determined avibactam concentrations that half-maximally inhibited (IC50) bocillin FL binding. Inducer β-lactams were also studied as comparators. Live cells’ time-course penicillin-binding proteins (PBPs) occupancy of avibactam was studied. To assess the ampC induction capacity of avibactam and comparators, qRT-PCR was performed in wild-type PAO1, PBP4, triple PBP4, 5/6 and 7 knockout derivatives and two ceftazidime/avibactam-susceptible/resistant XDR clinical isolates belonging to the epidemic high-risk clone ST175. PBP4 inhibition was observed for avibactam and β-lactam comparators. Induction capacity was consistently correlated with PBP4 binding affinity. Outer membrane permeability-limited PBP4 binding was observed in the live cells’ assay. As expected, imipenem and cefoxitin showed strong induction in PAO1, especially for carbapenem; avibactam induction was conversely weaker. Overall, the inducer effect was less remarkable in ampC-derepressed mutants and nonetheless absent upon avibactam exposure in the clinical isolates harboring mutated AmpC variants and their parental strains.

scholarly journals Tumor hypoxia induces nuclear paraspeckle formation through HIF-2α dependent transcriptional activation of NEAT1 leading to cancer cell survival

Oncogene ◽  
2014 ◽  
Vol 34 (34) ◽  
pp. 4482-4490 ◽  
Author(s):  
H Choudhry ◽  
A Albukhari ◽  
M Morotti ◽  
S Haider ◽  
D Moralli ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cancer Cell ◽  
Transcriptional Activation ◽  
Cellular Proliferation ◽  
Hypoxia Inducible Factor ◽  
Tumor Hypoxia ◽  
Transcriptional Response ◽  
Clonogenic Survival ◽  
Breast Cancer Cell Lines ◽  
Transcriptional Responses

Abstract Activation of cellular transcriptional responses, mediated by hypoxia-inducible factor (HIF), is common in many types of cancer, and generally confers a poor prognosis. Known to induce many hundreds of protein-coding genes, HIF has also recently been shown to be a key regulator of the non-coding transcriptional response. Here, we show that NEAT1 long non-coding RNA (lncRNA) is a direct transcriptional target of HIF in many breast cancer cell lines and in solid tumors. Unlike previously described lncRNAs, NEAT1 is regulated principally by HIF-2 rather than by HIF-1. NEAT1 is a nuclear lncRNA that is an essential structural component of paraspeckles and the hypoxic induction of NEAT1 induces paraspeckle formation in a manner that is dependent upon both NEAT1 and on HIF-2. Paraspeckles are multifunction nuclear structures that sequester transcriptionally active proteins as well as RNA transcripts that have been subjected to adenosine-to-inosine (A-to-I) editing. We show that the nuclear retention of one such transcript, F11R (also known as junctional adhesion molecule 1, JAM1), in hypoxia is dependent upon the hypoxic increase in NEAT1, thereby conferring a novel mechanism of HIF-dependent gene regulation. Induction of NEAT1 in hypoxia also leads to accelerated cellular proliferation, improved clonogenic survival and reduced apoptosis, all of which are hallmarks of increased tumorigenesis. Furthermore, in patients with breast cancer, high tumor NEAT1 expression correlates with poor survival. Taken together, these results indicate a new role for HIF transcriptional pathways in the regulation of nuclear structure and that this contributes to the pro-tumorigenic hypoxia-phenotype in breast cancer.

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