New methodology approaches with a broad coverage of the biological effects are urgently needed to evaluate the safety of the universe of environmentally relevant chemicals. Here, we propose a tiered approach incorporating transcriptomics and bioassays to assess environmental mixtures. The mixture samples and the perturbed biological pathways are prioritized by concentration-dependent transcriptome (CDT) and then used to guide the selection of bioassays for toxicant identification. To evaluate omics' screening capability, we first applied a CDT technique to test mixture samples by HepG2 and MCF7 cells. The effect recoveries of large-volume solid-phase extraction on the overall bioactivity of the mixture were 48.9% in HepG2 and 58.3% in MCF7. The overall bioactivity potencies obtained by transcriptomics were positively correlated with the panel of 8 bioassays among 14 mixture samples combined with the previous data. Transcriptomics could predict their activation status (AUC = 0.783) and the relative potency ( < 0.05) of bioassays for four of the eight receptors (, , , and ). Furthermore, the CDT identified other biological pathways perturbated by mixture samples, such as the pathway related to , , , , , etc. Overall, this study demonstrates the potential of concentration-dependent omics for effect-based water quality assessment.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1021/acs.est.0c00662 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Broadband CARS Hyperspectral Classification of Single Immune Cells.
J Biophotonics
January 2025
Department of Electronic Engineering, Maynooth University, Kildare, Ireland.
Broadband CARS is a coherent Raman scattering technique that provides access to the full biological vibrational spectrum within milliseconds, facilitating the recording of widefield hyperspectral Raman images. In this work, BCARS hyperspectral images of unstained cells from two different cell lines of immune lineage (T cell [Jurkat] and pDCs [CAL-1]) were recorded and analyzed using multivariate statistical algorithms in order to determine the spectral differences between the cells. A classifier was trained which could distinguish the known cells with a 97% out-of-bag accuracy.
View Article and Find Full Text PDFCompositional data analysis enables statistical rigor in comparative glycomics.
Nat Commun
January 2025
Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
Comparative glycomics data are compositional data, where measured glycans are parts of a whole, indicated by relative abundances. Applying traditional statistical analyses to these data often results in misleading conclusions, such as spurious "decreases" of glycans when other structures increase in abundance, or high false-positive rates for differential abundance. Our work introduces a compositional data analysis framework, tailored to comparative glycomics, to account for these data dependencies.
View Article and Find Full Text PDFCharacterizing substructure via mixture modeling in large-scale genetic summary statistics.
Am J Hum Genet
January 2025
Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80204, USA; Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA. Electronic address:
Genetic summary data are broadly accessible and highly useful, including for risk prediction, causal inference, fine mapping, and incorporation of external controls. However, collapsing individual-level data into summary data, such as allele frequencies, masks intra- and inter-sample heterogeneity, leading to confounding, reduced power, and bias. Ultimately, unaccounted-for substructure limits summary data usability, especially for understudied or admixed populations.
View Article and Find Full Text PDFInvestigating polychlorinated alkanes in technical chlorinated paraffin mixtures and polymer products available in Vietnam.
Chemosphere
January 2025
Faculty of Chemistry, University of Science, Vietnam National University, Hanoi, 19 Le Thanh Tong, Hanoi, 10000, Viet Nam. Electronic address:
Chlorinated paraffins (CPs) are chemical additives mostly composed of polychlorinated alkanes (PCAs) which may impact on the environment and human health; however, little is known about their presence in Southeast Asia. To fill this knowledge gap, we assessed 74 PCA homolog groups commonly referred to as short-chain (SCCPs: PCAs-C), medium-chain (MCCPs: PCAs-C), and long-chain CPs (LCCPs: PCAs-C) in technical CP mixtures (n = 4) and polymer samples (n = 49), including recycled plastics, collected in Vietnam in 2023. The contents of measured PCA homolog groups in technical CP mixtures were 86,000-930,000 mg/kg for PCAs-C; 85,000-990,000 mg/kg for PCAs-C; and 23,000-180,000 mg/kg for PCAs-C.
View Article and Find Full Text PDFExtraction and quantitation of fentanyl in exhaled breath condensate using a magnetic dispersive solid phase based on graphene oxide and covalent organic framework composite and LC-MS/MS analysis.
J Chromatogr B Analyt Technol Biomed Life Sci
January 2025
Food and Drug Safety Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Research Center of New Material and Green Chemistry, Khazar University, 41 Mehseti Street, Baku AZ1096, Azerbaijan. Electronic address:
Free fentanyl is responsible for its pharmacological effects, but its total concentration is typically determined for therapeutic drug monitoring purposes. Determination of fentanyl concentration can help reduce the prescribed doses, leading to fewer side effects and increased effectiveness. Therefore, predicting free drug concentration in pharmaceutical research is crucial.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!