High-Throughput Transcriptomics Platform for Screening Environmental Chemicals

2021 ◽  
Author(s):  
Joshua A Harrill ◽  
Logan J Everett ◽  
Derik E Haggard ◽  
Thomas Sheffield ◽  
Joseph L Bundy ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Throughput ◽  
Gene Expression Signature ◽  
Environmental Chemicals ◽  
Hazard Evaluation ◽  
Response Analysis ◽  
Chemical Treatments ◽  
Response Modeling ◽  
Reference Samples

Abstract New approach methodologies (NAMs) that efficiently provide information about chemical hazard without using whole animals are needed to accelerate the pace of chemical risk assessments. Technological advancements in gene expression assays have made in vitro high-throughput transcriptomics (HTTr) a feasible option for NAMs-based hazard characterization of environmental chemicals. In this study, we evaluated the Templated Oligo with Sequencing Readout (TempO-Seq) assay for HTTr concentration-response screening of a small set of chemicals in the human-derived MCF7 cell model. Our experimental design included a variety of reference samples and reference chemical treatments in order to objectively evaluate TempO-Seq assay performance. To facilitate analysis of these data, we developed a robust and scalable bioinformatics pipeline using open-source tools. We also developed a novel gene expression signature-based concentration-response modeling approach and compared the results to a previously implemented workflow for concentration-response analysis of transcriptomics data using BMDExpress. Analysis of reference samples and reference chemical treatments demonstrated highly reproducible differential gene expression signatures. In addition, we found that aggregating signals from individual genes into gene signatures prior to concentration-response modeling yielded in vitro transcriptional biological pathway altering concentrations (BPACs) that were closely aligned with previous ToxCast high-throughput screening assays. Often these identified signatures were associated with the known molecular target of the chemicals in our test set as the most sensitive components of the overall transcriptional response. This work has resulted in a novel and scalable in vitro HTTr workflow that is suitable for high-throughput hazard evaluation of environmental chemicals.

scholarly journals Protein arginine methyltransferase 6-dependent gene expression and splicing: association with breast cancer outcomes

2012 ◽  
Vol 19 (4) ◽  
pp. 509-526 ◽  
Author(s):  
Dennis H Dowhan ◽  
Matthew J Harrison ◽  
Natalie A Eriksson ◽  
Peter Bailey ◽  
Michael A Pearen ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Alternative Splicing ◽  
Cancer Cells ◽  
Breast Cancer Cells ◽  
Gene Expression Signature ◽  
Human Breast ◽  
Arginine Methyltransferase ◽  
Breast Tumours

Protein arginine methyltransferase-6 (PRMT6) regulates steroid-dependent transcription and alternative splicing and is implicated in endocrine system development and function, cell death, cell cycle, gene expression and cancer. Despite its role in these processes, little is known about its function and cellular targets in breast cancer. To identify novel gene targets regulated by PRMT6 in breast cancer cells, we used a combination of small interfering RNA and exon-specific microarray profilingin vitrocoupled toin vivovalidation in normal breast and primary human breast tumours. This approach, which allows the examination of genome-wide changes in individual exon usage and total transcript levels, demonstrated thatPRMT6knockdown significantly affected i) the transcription of 159 genes and ii) alternate splicing of 449 genes. ThePRMT6-dependent transcriptional and alternative splicing targets identifiedin vitrowere validated in human breast tumours. Using the list of genes differentially expressed between normal andPRMT6knockdown cells, we generated aPRMT6-dependent gene expression signature that provides an indication of PRMT6 dysfunction in breast cancer cells. Interrogation of several well-studied breast cancer microarray expression datasets with thePRMT6gene expression signature demonstrated that PRMT6 dysfunction is associated with better overall relapse-free and distant metastasis-free survival in the oestrogen receptor (ER (ESR1)) breast cancer subgroup. These results suggest that dysregulation ofPRMT6-dependent transcription and alternative splicing may be involved in breast cancer pathophysiology and the molecular consequences identifying a unique and informative biomarker profile.

255 THE ESTROGENIC EVALUATION OF PARABENS USING RAT UTERINE CALBINDIN-D9k

2010 ◽  
Vol 22 (1) ◽  
pp. 285
Author(s):  
T. T. B. Vo ◽  
E. B. Jeung
Keyword(s):  
Gene Expression ◽  
Adverse Effects ◽  
Treated Group ◽  
Environmental Chemicals ◽  
Female Rats ◽  
Protein Levels ◽  
Calbindin D9k ◽  
The Difference

In the current study, calbindin-D9k (CaBP-9k), a potent biomarker for screening estrogen-like environmental chemicals in vivo and in vitro, was adopted to examine the potential estrogen-like property of the following parabens: propyl-, isopropyl-, butyl-, and isobutyl-paraben. Immature female rats were administered for 3 days from postnatal day 14 to 16 with 17?-ethinylestradiol (EE, 1 mg/kg of body weight (BW) per day) or parabens (62.5, 250, and 1000 mg/kg of BW per day). In uterotrophic assays, significantly increased uterus weights were detected in the EE-treated group and in the groups treated with the greatest dose of isopropyl-, butyl- and isobutyl-paraben. In addition, these parabens induced uterine CaBP-9k mRNA and protein levels, whereas co-treatment of parabens and fulvestrant (Faslodex, formerly known as ICI 182, 780), a pure estrogen receptor (ER) antagonist, completely reversed the paraben-induced gene expression and increased uterine weights. To investigate the ER-mediated mechanism(s) by which parabens exert their effects, the expression level of ERα and progesterone receptor (PR) was analyzed. Exposure to EE or parabens caused a dramatic decrease in expression of both ER? mRNA and protein levels, whereas co-treatment with fulvestrant reversed these effects. These data showed the difference of CaBP-9k and ER? expression, suggesting that CaBP-9k might not express via ER? pathway. In the effect of parabens on CaBP-9k expression through PR mediation, a significantly increased expression of uterine PR gene, a well-known ER regulating gene, at both transcriptional and translational levels was indicated in the greatest dose of isopropyl- and butyl-paraben. These parabens induced PR gene expression that was completely blocked by fulvestrant. This result indicates that CaBP-9k expression might involve PR mediates in the estrogenic effect of paraben in immature rat uteri. Taken together, parabens exhibited an estrogen-like property in vivo, which might be mediated by a PR and/or ER? signaling pathway. In addition, our results expanded the current understanding of the potential adverse effects of parabens associated with their estrogen-like activities. Further investigation is needed to elucidate in greater detail the adverse effects of parabens in humans and wildlife.

scholarly journals Reversible Gene Expression Control inYersinia pestisby Using an Optimized CRISPR Interference System

2019 ◽  
Vol 85 (12) ◽  
Author(s):  
Tong Wang ◽  
Min Wang ◽  
Qingwen Zhang ◽  
Shiyang Cao ◽  
Xiang Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Throughput ◽  
Biofilm Formation ◽  
Prevention And Control ◽  
Target Gene ◽  
Gene Knockdown ◽  
Content Type ◽  
Short Palindromic Repeat ◽  
And Control

ABSTRACTMany genes in the bacterial pathogenYersinia pestis, the causative agent of three plague pandemics, remain uncharacterized, greatly hampering the development of measures for plague prevention and control. Clustered regularly interspaced short palindromic repeat interference (CRISPRi) has been shown to be an effective tool for gene knockdown in model bacteria. In this system, a catalytically dead Cas9 (dCas9) and a small guide RNA (sgRNA) form a complex, binding to the specific DNA target through base pairing, thereby impeding RNA polymerase binding and causing target gene repression. Here, we introduce an optimized CRISPRi system usingStreptococcus pyogenesCas9-derived dCas9 for gene knockdown inY. pestis. Multiple genes harbored on either the chromosome or plasmids ofY. pestiswere efficiently knocked down (up to 380-fold) in a strictly anhydrotetracycline-inducible manner using this CRISPRi approach. Knockdown ofhmsH(responsible for biofilm formation) orcspB(encoding a cold shock protein) resulted in greatly decreased biofilm formation or impaired cold tolerance inin vitrophenotypic assays. Furthermore, silencing of the virulence-associated genesyscBorailusing this CRISPRi system resulted in attenuation of virulence in HeLa cells and mice similar to that previously reported foryscBandailnull mutants. Taken together, our results confirm that this optimized CRISPRi system can reversibly and efficiently repress the expression of target genes inY. pestis, providing an alternative to conventional gene knockdown techniques, as well as a strategy for high-throughput phenotypic screening ofY. pestisgenes with unknown functions.IMPORTANCEYersiniapestisis a lethal pathogen responsible for millions of human deaths in history. It has also attracted much attention for potential uses as a bioweapon or bioterrorism agent, against which new vaccines are desperately needed. However, manyY. pestisgenes remain uncharacterized, greatly hampering the development of measures for plague prevention and control. Clustered regularly interspaced short palindromic repeat interference (CRISPRi) has been successfully used in a variety of bacteria in functional genomic studies, but no such genetic tool has been reported inY. pestis. Here, we systematically optimized the CRISPRi approach for use inY. pestis, which ultimately repressed target gene expression with high efficiency in a reversible manner. Knockdown of functional genes using this method produced phenotypes that were readily detected byin vitroassays, cell infection assays, and mouse infection experiments. This is a report of a CRISPRi approach inY. pestisand highlights the potential use of this approach in high-throughput functional genomics studies of this pathogen.

Genomics and Systems Biology.

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. sci-51-sci-51
Author(s):  
Todd R. Golub
Keyword(s):  
Gene Expression ◽  
High Throughput ◽  
Biological Networks ◽  
High Throughput Screening ◽  
Expression Profiles ◽  
Low Cost ◽  
Gene Expression Profiles ◽  
Gene Expression Signature ◽  
Small Molecule Libraries ◽  
Approved Drugs

Genomics holds particular potential for the elucidation of biological networks that underlie disease. For example, gene expression profiles have been used to classify human cancers, and have more recently been used to predict graft rejection following organ transplantation. Such signatures thus hold promise both as diagnostic approaches and as tools with which to dissect biological mechanism. Such systems-based approaches are also beginning to impact the drug discovery process. For example, it is now feasible to measure gene expression signatures at low cost and high throughput, thereby allowing for the screening libraries of small molecule libraries in order to identify compounds capable of perturbing a signature of interest (even if the critical drivers of that signature are not yet known). This approach, known as Gene Expression-Based High Throughput Screening (GE-HTS), has been shown to identify candidate therapeutic approaches in AML, Ewing sarcoma, and neuroblastoma, and has identified tool compounds capable of inhibiting PDGF receptor signaling. A related approach, known as the Connectivity Map (www.broad.mit.edu/cmap) attempts to use gene expression profiles as a universal language with which to connect cellular states, gene product function, and drug action. In this manner, a gene expression signature of interest is used to computationally query a database of gene expression profiles of cells systematically treated with a large number of compounds (e.g., all off-patent FDA-approved drugs), thereby identifying potential new applications for existing drugs. Such systems level approaches thus seek chemical modulators of cellular states, even when the molecular basis of such altered states is unknown.

scholarly journals ISMARA: Completely automated inference of gene regulatory networks from high-throughput data

2017 ◽  
Author(s):  
Mikhail Pachkov ◽  
Piotr J Balwierz ◽  
Phil Arnold ◽  
Andreas J Gruber ◽  
Mihaela Zavolan ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Throughput ◽  
Regulatory Networks ◽  
Target Genes ◽  
Chromatin State ◽  
Response Analysis ◽  
Rna Seq ◽  
High Throughput Data ◽  
Micro Rnas ◽  
Gene Regulatory

As the costs of high-throughput measurement technologies continue to fall, experimental approaches in biomedicine are increasingly data intensive and the advent of big data is justifiably seen as holding the promise to transform medicine. However, as data volumes mount, researchers increasingly realize that extracting concrete, reliable, and actionable biological predictions from high-throughput data can be very challenging. Our laboratory has pioneered a number of methods for inferring key gene regulatory interactions from high-throughput data. For example, we developed motif activity response analysis (MARA)[, which models genome-wide gene expression (RNA-Seq, or microarray) and chromatin state (ChIP-Seq) data in terms of comprehensive predictions of regulatory sites for hundreds of mammalian regulators (TFs and micro-RNAs). Using these models, MARA identifies the key regulators driving gene expression and chromatin state changes, the activities of these regulators across the input samples, their target genes, and the sites on the genome through which these regulators act. We recently completely automated MARA in an integrated web-server (ismara.unibas.ch) that allows researchers to analyze their own data by simply uploading RNA-Seq or ChIP-Seq datasets, and provides results in an integrated web interface as well as in downloadable flat form.

Genomics: An In Vitro Toxicology Point of View

2002 ◽  
Vol 30 (2_suppl) ◽  
pp. 129-131 ◽  
Author(s):  
Raffaella Corvi
Keyword(s):  
Gene Expression ◽  
Cell Culture ◽  
Dna Microarray ◽  
High Throughput ◽  
Point Of View ◽  
In Vitro Toxicology ◽  
Predictive Toxicology ◽  
Cell Culture Systems ◽  
The Impact

Genomics, and in particular its derived discipline, toxicogenomics, are rapidly developing technologies, which permit studies on the impact of chemicals and drugs on gene expression in particular biological systems. Enormous amounts of data will be provided in the context of mechanistic and predictive toxicology from the use of the DNA microarray approach for the simultaneous analysis of the expression pattern of multiple genes. The high-throughput requirement of these approaches necessitates in vitro cell culture systems. This article will give a short overview of the areas of ECVAM's research in which this technology will initially be applied.

scholarly journals A Bayesian Method for Population-wide Cardiotoxicity Hazard and Risk Characterization Using an In Vitro Human Model

2020 ◽  
Vol 178 (2) ◽  
pp. 391-403
Author(s):  
Alexander D Blanchette ◽  
Sarah D Burnett ◽  
Fabian A Grimm ◽  
Ivan Rusyn ◽  
Weihsueh A Chiu
Keyword(s):  
Induced Pluripotent Stem Cell ◽  
Population Based ◽  
Environmental Chemicals ◽  
Population Variability ◽  
Human Model ◽  
Population Exposure ◽  
Induced Pluripotent ◽  
Response Modeling

Abstract Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes are an established model for testing potential chemical hazards. Interindividual variability in toxicodynamic sensitivity has also been demonstrated in vitro; however, quantitative characterization of the population-wide variability has not been fully explored. We sought to develop a method to address this gap by combining a population-based iPSC-derived cardiomyocyte model with Bayesian concentration-response modeling. A total of 136 compounds, including 54 pharmaceuticals and 82 environmental chemicals, were tested in iPSC-derived cardiomyocytes from 43 nondiseased humans. Hierarchical Bayesian population concentration-response modeling was conducted for 5 phenotypes reflecting cardiomyocyte function or viability. Toxicodynamic variability was quantified through the derivation of chemical- and phenotype-specific variability factors. Toxicokinetic modeling was used for probabilistic in vitro-to-in vivo extrapolation to derive population-wide margins of safety for pharmaceuticals and margins of exposure for environmental chemicals. Pharmaceuticals were found to be active across all phenotypes. Over half of tested environmental chemicals showed activity in at least one phenotype, most commonly positive chronotropy. Toxicodynamic variability factor estimates for the functional phenotypes were greater than those for cell viability, usually exceeding the generally assumed default of approximately 3. Population variability-based margins of safety for pharmaceuticals were correctly predicted to be relatively narrow, including some below 10; however, margins of exposure for environmental chemicals, based on population exposure estimates, generally exceeded 1000, suggesting they pose little risk at current general population exposures even to sensitive subpopulations. Overall, this study demonstrates how a high-throughput, human population-based, in vitro-in silico model can be used to characterize toxicodynamic population variability in cardiotoxic risk.

scholarly journals Graded regulation of cellular quiescence depth between proliferation and senescence by a lysosomal dimmer switch

2019 ◽  
Vol 116 (45) ◽  
pp. 22624-22634 ◽  
Author(s):  
Kotaro Fujimaki ◽  
Ruoyan Li ◽  
Hengyu Chen ◽  
Kimiko Della Croce ◽  
Hao Helen Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Signature ◽  
Cell Types ◽  
The Body ◽  
Cellular Mechanisms ◽  
Lysosomal Function ◽  
Quiescent Cells ◽  
Common Transition

The reactivation of quiescent cells to proliferate is fundamental to tissue repair and homeostasis in the body. Often referred to as the G0 state, quiescence is, however, not a uniform state but with graded depth. Shallow quiescent cells exhibit a higher tendency to revert to proliferation than deep quiescent cells, while deep quiescent cells are still fully reversible under physiological conditions, distinct from senescent cells. Cellular mechanisms underlying the control of quiescence depth and the connection between quiescence and senescence are poorly characterized, representing a missing link in our understanding of tissue homeostasis and regeneration. Here we measured transcriptome changes as rat embryonic fibroblasts moved from shallow to deep quiescence over time in the absence of growth signals. We found that lysosomal gene expression was significantly up-regulated in deep quiescence, and partially compensated for gradually reduced autophagy flux. Reducing lysosomal function drove cells progressively deeper into quiescence and eventually into a senescence-like irreversibly arrested state; increasing lysosomal function, by lowering oxidative stress, progressively pushed cells into shallower quiescence. That is, lysosomal function modulates graded quiescence depth between proliferation and senescence as a dimmer switch. Finally, we found that a gene-expression signature developed by comparing deep and shallow quiescence in fibroblasts can correctly classify a wide array of senescent and aging cell types in vitro and in vivo, suggesting that while quiescence is generally considered to protect cells from irreversible arrest of senescence, quiescence deepening likely represents a common transition path from cell proliferation to senescence, related to aging.

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