Proteome Coverage after Simultaneous Proteo-Metabolome Liquid-Liquid Extraction.

Proteomics and metabolomics are essential in systems biology, and simultaneous proteo-metabolome liquid-liquid extraction (SPM-LLE) allows isolation of the metabolome and proteome from the same sample. Since the proteome is present as a pellet in SPM-LLE, it must be solubilized for quantitative proteomics. Solubilization and proteome extraction are critical factors in the information obtained at the proteome level. In this study, we investigated the performance of two surfactants (sodium deoxycholate (SDC), sodium dodecyl sulfate (SDS)) and urea in terms of proteome coverage and extraction efficiency of an interphase proteome pellet generated by methanol-chloroform based SPM-LLE. We also investigated how the performance differs when the proteome is extracted from the interphase pellet or by direct cell lysis. We quantified 12 lipids covering triglycerides and various phospholipid classes, and 25 polar metabolites covering central energy metabolism in chloroform and methanol extracts. Our study reveals that the proteome coverages between the two surfactants and urea for the SPM-LLE interphase pellet were similar, but the extraction efficiencies differed significantly. While SDS led to enrichment of basic proteins, which were mainly ribosomal and ribonuclear proteins, urea was the most efficient extraction agent for simultaneous proteo-metabolome analysis. The results of our study also show that the performance of surfactants for quantitative proteomics is better when the proteome is extracted through direct cell lysis rather than an interphase pellet. In contrast, the performance of urea for quantitative proteomics was significantly better when the proteome was extracted from an interphase pellet than by direct cell lysis. We demonstrated that urea is superior to surfactants for proteome extraction from SPM-LLE interphase pellets, with a particularly good performance for the extraction of proteins associated with metabolic pathways. Data are available via ProteomeXchange with identifier PXD027338.

PI(18:1/18:1) is a SCD1-derived lipokine that limits stress signaling.

Cytotoxic stress activates stress-activated kinases, initiates adaptive mechanisms, including the unfolded protein response (UPR) and autophagy, and induces programmed cell death. Fatty acid unsaturation, controlled by stearoyl-CoA desaturase (SCD)1, prevents cytotoxic stress but the mechanisms are diffuse. Here, we show that 1,2-dioleoyl-sn-glycero-3-phospho-(1'-myo-inositol) [PI(18:1/18:1)] is a SCD1-derived signaling lipid, which inhibits p38 mitogen-activated protein kinase activation, counteracts UPR, endoplasmic reticulum-associated protein degradation, and apoptosis, regulates autophagy, and maintains cell morphology and proliferation. SCD1 expression and the cellular PI(18:1/18:1) proportion decrease during the onset of cell death, thereby repressing protein phosphatase 2 A and enhancing stress signaling. This counter-regulation applies to mechanistically diverse death-inducing conditions and is found in multiple human and mouse cell lines and tissues of Scd1-defective mice. PI(18:1/18:1) ratios reflect stress tolerance in tumorigenesis, chemoresistance, infection, high-fat diet, and immune aging. Together, PI(18:1/18:1) is a lipokine that links fatty acid unsaturation with stress responses, and its depletion evokes stress signaling.

Monitoring drug consumption in Innsbruck during coronavirus disease 2019 (COVID-19) lockdown by wastewater analysis.

The coronavirus disease 2019 (COVID-19) has developed into a serious pandemic with millions of cases diagnosed worldwide. To fight COVID-19 pandemic, over 100 countries instituted either a full or partial lockdown, affecting billions of people. In Tyrol, first lockdown measures were taken on 10 March 2020. On 16 March 2020, a curfew went into force which ended on 1 May 2020. On 19 March 2020, Tyrol as a whole was placed in quarantine which ended on 7 April 2020. The governmental actions helped reducing the spread of COVID-19 at the cost of significant effects on social life and behaviour. Accordingly, to provide a comprehensive picture of the population health status not only input from medical and biological sciences is required, but also from other sciences able to provide lifestyle information such as drug use. Herein, wastewater-based epidemiology was used for studying temporal trends of licit and illicit drug consumption during lockdown and quarantine in the area of the Tyrolean capital Innsbruck (174,000 inhabitants). On 35 days between 12 March 2020 and 15 April 2020, loads of 23 markers were monitored in wastewater. Loads determined on 292 days between March 2016 and January 2020 served as reference. During lockdown, changes in the consumption patterns of recreational drugs (i.e. cocaine, amphetamine, 3,4-methylenedioxymethamphetamine, methamphetamine, and alcohol) and pharmaceuticals for short-term application (i.e. acetaminophen, codeine, and trimethoprim) were detected. For illicit drugs and alcohol, it is very likely that observed changes were linked to the shutdown of the hospitality industry and event cancelation which led to a reduced demand of these compounds particularly on weekends. For the pharmaceuticals, further work will be necessary to clarify if the observed declines are indicators of improved population health or of some kind of restraining effect that reduced the number of consultations of medical doctors and pharmacies.