Assessment of the effects of As(III) treatment on cyanobacteria lipidomic profiles by LC-MS and MCR-ALS

Stoichiometric gene-to-reaction associations enhance model-driven analysis performance: Metabolic response to chronic exposure to Aldrin in prostate cancer

BACKGROUND

Genome-scale metabolic models (GSMM) integrating transcriptomics have been widely used to study cancer metabolism. This integration is achieved through logical rules that describe the association between genes, proteins, and reactions (GPRs). However, current gene-to-reaction formulation lacks the stoichiometry describing the transcript copies necessary to generate an active catalytic unit, which limits our understanding of how genes modulate metabolism. The present work introduces a new state-of-the-art GPR formulation that considers the stoichiometry of the transcripts (S-GPR). As case of concept, this novel gene-to-reaction formulation was applied to investigate the metabolic effects of the chronic exposure to Aldrin, an endocrine disruptor, on DU145 prostate cancer cells. To this aim we integrated the transcriptomic data from Aldrin-exposed and non-exposed DU145 cells through S-GPR or GPR into a human GSMM by applying different constraint-based-methods.

RESULTS

Our study revealed a significant improvement of metabolite consumption/production predictions when S-GPRs are implemented. Furthermore, our computational analysis unveiled important alterations in carnitine shuttle and prostaglandine biosynthesis in Aldrin-exposed DU145 cells that is supported by bibliographic evidences of enhanced malignant phenotype.

CONCLUSIONS

The method developed in this work enables a more accurate integration of gene expression data into model-driven methods. Thus, the presented approach is conceptually new and paves the way for more in-depth studies of aberrant cancer metabolism and other diseases with strong metabolic component with important environmental and clinical implications.

Phenotypic and lipidomic characterization of primary human epidermal keratinocytes exposed to simulated solar UV radiation

BACKGROUND

Ultraviolet (UV) radiation is known to be one of the most important environmental hazards acting on the skin. The most part of UV radiation is absorbed in the epidermis, where keratinocytes are the most abundant and exposed cell type. Lipids have an important role in skin biology, not only for their important contribution to the maintenance of the permeability barrier but also for the production and storage of energy, membrane organization and cell signalling functions. However, the effects on the lipid composition of keratinocytes under UV radiation are little explored.

OBJECTIVE

The present work aims to explore the effects on the phenotype and lipid content of primary human keratinocytes exposed to simulated solar UV radiation.

METHODS

Keratinocytes were exposed to a single (acute exposure) and repeated simulated solar UV irradiations for 4 weeks (chronic exposure). Cell viability and morphology were explored, as well as the production of reactive oxygen species. Then, lipid extracts were analysed through liquid chromatography coupled to mass spectrometry (LC-MS) and the data generated was processed using the ROIMCR chemometric methodology together with partial least squares discriminant analysis (PLS-DA), to finally reveal the most relevant lipid changes that occurred in keratinocytes upon UV irradiation. Also, the potential induction of keratinocyte differentiation was explored by measuring the increase of involucrin.

RESULTS

Under acute irradiation, cell viability and morphology were not altered. However, a general increase of phosphatidylcholines (PC) phosphatidylethanolamines (PE) and phosphatidylglycerol (PG) together with a slight sphingomyelin (SM) decrease were found in UV irradiated cells, among other changes. In addition, keratinocyte cultures did not present any differentiation hallmark. Contrary to acute-irradiated cells, in chronic exposures, cell viability was reduced and keratinocytes presented an altered morphology. Also, hallmarks of differentiation, such as the increase of involucrin protein and the autophagy induction were detected. Among the main lipid changes that accompanied this phenotype, the increase of long-chain ceramides, lysoPC and glycerolipid species were found.

CONCLUSION

Important lipid changes were detected under acute and chronic UV irradiation. The lipid profile under chronic exposure may represent a lipid fingerprint of the keratinocyte differentiation phenotype.

Deciphering the Underlying Metabolomic and Lipidomic Patterns Linked to Thermal Acclimation in Saccharomyces cerevisiae

Temperature is one of the most critical parameters for yeast growth, and it has deep consequences in many industrial processes where yeast is involved. Nevertheless, the metabolic changes required to accommodate yeast cells at high or low temperatures are still poorly understood. In this work, the ultimate responses of these induced transcriptomic effects have been examined using metabolomics-derived strategies. The yeast metabolome and lipidome have been characterized by 1D proton nuclear magnetic resonance spectroscopy and ultra-high-performance liquid chromatography-mass spectrometry at four temperatures, corresponding to low, optimal, high, and extreme thermal conditions. The underlying pathways that drive the acclimation response of yeast to these nonoptimal temperatures were evaluated using multivariate curve resolution-alternating least-squares. The analysis revealed three different thermal profiles (cold, optimal, and high temperature), which include changes in the lipid composition, secondary metabolic pathways, and energy metabolism, and we propose that they reflect the acclimation strategy of yeast cells to low and high temperatures. The data suggest that yeast adjusts membrane fluidity by changing the relative proportions of the different lipid families (acylglycerides, phospholipids, and ceramides, among others) rather than modifying the average length and unsaturation levels of the corresponding fatty acids.

Untargeted lipidomic analysis of primary human epidermal melanocytes acutely and chronically exposed to UV radiation

Ultraviolet (UV) radiation present in sunlight has been related to harmful effects on skin such as premature aging and skin cancer.