Jan Trnka | Charles University, Prague (original) (raw)

Papers by Jan Trnka

Physiological Research, 2020

Granulosa cells (GCs) are somatic cells essential for establishing and maintaining bi-directional... more Granulosa cells (GCs) are somatic cells essential for establishing and maintaining bi-directional communication with the oocytes. This connection has a profound importance for the delivery of energy substrates, structural components and ions to the maturing oocyte through gap junctions. Cumulus cells, group of closely associated GCs, surround the oocyte and can diminished the effect of harmful environmental insults. Both GCs and oocytes prefer different energy substrates in their cellular metabolism: GCs are more glycolytic, whereas oocytes rely more on oxidative phosphorylation pathway. The interconnection of these cells is emphasized by the fact that GCs supply oocytes with intermediates produced in glycolysis. The number of GCs surrounding the oocyte and their age affect the energy status of oocytes. This review summarises available studies collaboration of cellular types in the ovarian follicle from the point of view of energy metabolism, signaling and protection of toxic insult...

This report presents a technical description of our agent-based epidemic model of a particular mi... more This report presents a technical description of our agent-based epidemic model of a particular middle-sized municipality. We have developed a realistic model with 56 thousand inhabitants and 2.7 million of social contacts. These form a multi-layer social network that serves as a base of our epidemic simulation. The disease is modeled by our extended SEIR model with parameters fitted to real epidemics data for Czech Republic. The model is able to simulate a whole range of non-pharmaceutical interventions on individual level, such as protective measures and physical distancing, testing, contact tracing, isolation and quarantine. The effect of government-issued measures such as contact restrictions in different environments (schools, restaurants, vendors, etc.) can also be simulated. The model is implemented in Python and is available as open source at: www.github.com/epicity-cz/model-m/releases

SummaryBackgroundEvidence is accumulating that the effectiveness of covid-19 vaccines against inf... more SummaryBackgroundEvidence is accumulating that the effectiveness of covid-19 vaccines against infection wanes, reaching relatively low values after 6 months. Published studies demonstrating this effect based their findings on a limited range of vaccines or subset of populations, and did not include booster vaccine doses or immunity obtained due to covid-19 infection. Here we evaluate effectiveness of covid-19 vaccines, booster doses or previous infection against covid-19 infection, hospital admission or death for the whole population in the Czech Republic.MethodsData used in this study cover the whole population of the Czech Republic reported as infected and/or vaccinated between the first detected case on March 1, 2020 and November 20, 2021 (for reinfections), or December 26, 2020 and November 20, 2021 (for vaccinations), including hospital admissions and deaths. Vaccinations by all vaccines approved in the EU were included in this study. Anonymous, individual-level data including ...

The Omicron variant of the SARS-CoV-2 virus carries mutations, which enable it to evade immunity ... more The Omicron variant of the SARS-CoV-2 virus carries mutations, which enable it to evade immunity conferred by vaccines and previous infections. We used a Cox proportional hazards model and a logistic regression model on individual-level data on all laboratory-confirmed SARS-CoV-2 infections in the Czech Republic to estimate the relative risk of infection, hospitalization, including severe states, for Delta and Omicron variants, adjusting for sex, age, previous infection, vaccine type and vaccination status. A recent (<2 months) two-dose vaccination reached VE 43% (95% CI: 42-44) against infection by Omicron compared to 73% (95% CI: 72-74) against Delta. A recent booster increased VE to 56% (95% CI: 55-56) against Omicron infection compared to 90% (95% CI: 90-91) for Delta. The VE against Omicron hospitalization of a recent two-dose vaccination was 45% (95% CI: 29-57), with a recent booster 87% (95% CI: 84-88). The VE against the need for oxygen therapy due to Omicron was 57% (95%...

Supplementary material. (DOCX 115 kb)

SummaryBackgroundRotations of schoolchildren on a weekly basis is one of the nonpharmaceutical in... more SummaryBackgroundRotations of schoolchildren on a weekly basis is one of the nonpharmaceutical interventions often considered in the covid-19 pandemic. This study aims to investigate the impact of different types of rotations in various testing contexts.MethodsWe built an agent-based model of interactions among pupils and teachers based on an online survey in an elementary school in Prague, Czechia. This model contains 624 schoolchildren and 55 teachers (679 nodes) and about 27 thousands social contacts (edges) in 10 layers. The layers reflect different types of contacts (in classroom, cafeteria etc.) as described in the survey. On this multi-graph structure we run a modified SEIR model of the covid-19 dynamics. The parameters of the model are calibrated on data from the outbreak in the Czech Republic in the period March to June 2020.FindingsThere are three main findings in our paper.Weekly rotations of in-class and distance learning reduce the spread of covid-19 by 75–81% and thus ...

Running across the globe for more than a year, the COVID-19 pandemic keeps demonstrating its stre... more Running across the globe for more than a year, the COVID-19 pandemic keeps demonstrating its strength. Despite a lot of understanding, uncertainty regarding the efficiency of interventions still persists. We developed an age-structured epidemic model parameterized with sociological data for the Czech Republic and found that (1) delaying the spring 2020 lockdown by four days produced twice as many confirmed cases by the end of the lockdown period, (2) personal protective measures such as face masks appear more effective than just a reduction of social contacts, (3) only sheltering the elderly is by no means effective, and (4) leaving schools open is a risky strategy. Despite the onset of vaccination, an evidence-based choice and timing of non-pharmaceutical interventions still remains the most important weapon against the COVID-19 pandemic.One sentence summaryWe address several issues regarding COVID-19 interventions that still elicit controversy and pursue ignorance

Metallomics, 2019

There is an ongoing need for the development of new cancer therapeutics that combine high cytotox... more There is an ongoing need for the development of new cancer therapeutics that combine high cytotoxic efficiency with low side effects, and also override resistance to the first-line chemotherapeutics. Copper(ii)–phenanthroline complexes are promising compounds that were shown previously to induce an immediate cytotoxic response over a panel of tumor cell lines in vitro. The molecular mechanism, however, remained unresolved. In this work we performed a thorough study of the copper(ii)–phenanthroline complexes containing different imidazolidine-2-thione ligands in ovarian cancer cells, and revealed that these complexes induce endoplasmic reticulum (ER) stress and subsequently cell death mediated by the unfolded protein response. Alleviation of the ER-stress by tauroursodeoxycholic acid (TUDCA) attenuated the cytotoxic effects. In summary, we have identified a novel, ER-dependent, molecular mechanism mediating cytotoxic effects of copper(ii)–phenanthroline complexes.

Biochemical and biophysical research communications, Sep 4, 2016

In-vitro investigation of the effects of hypoxia is limited by physical laws of gas diffusion and... more In-vitro investigation of the effects of hypoxia is limited by physical laws of gas diffusion and cellular O2 consumption, making prolonged exposures to stable O2 concentrations impossible. Using a gas-permeable cultureware, chronic effects of mild and severe hypoxia on triglyceride accumulation, lipid droplet size distribution, spontaneous lipolysis and gene expression of adipocyte-specific markers were assessed. 3T3-L1 cells were differentiated under 20%, 4% or 1% O2 using a gas-permeable cultureware. Triglyceride accumulation, expression of genes characteristic for advanced adipocyte differentiation and involvement of key lipogenesis enzymes were assessed after exposures. Lipogenesis increased by 375% under mild hypoxia, but dropped by 43% in severe hypoxia. Mild, but not severe, hypoxia increased formation of large lipid droplets 6.4 fold and strongly induced gene expression of adipocyte-specific markers. Spontaneous lipolysis increased by 488% in mild, but only by 135% in sever...

Physiological Research, 2016

Obesity is often associated with metabolic impairments in peripheral tissues. Evidence suggests a... more Obesity is often associated with metabolic impairments in peripheral tissues. Evidence suggests an excess of free fatty acids (FFA) as one factor linking obesity and related pathological conditions and the impact of FFA overload on skeletal muscle metabolism is described herein. Obesity is associated with dysfunctional adipose tissue unable to buffer the flux of dietary lipids. Resulting increased levels and fluxes of plasma FFA lead to ectopic lipid deposition and lipotoxicity. FFA accumulated in skeletal muscle are associated with insulin resistance and overall cellular dysfunction. Mechanisms supposed to be involved in these conditions include the Randle cycle, intracellular accumulation of lipid metabolites, inflammation and mitochondrial dysfunction or mitochondrial stress. These mechanisms are described and discussed in the view of current experimental evidence with an emphasis on conflicting theories of decreased vs. increased mitochondrial fat oxidation associated with lipid...

Lipids, 2015

observed for palmitic acid alone. Unsaturated FFA at moderate physiological concentrations as wel... more observed for palmitic acid alone. Unsaturated FFA at moderate physiological concentrations as well as GW501516, but not palmitic acid, mildly uncoupled mitochondrial respiration. Our results indicate that although unsaturated FFA are effective activators of PPARδ, their protective effect on palmitic acid-induced toxicity is not mediated by PPARδ activation and subsequent induction of lipid regulatory genes in skeletal muscle cells. Other mechanisms, such as mitochondrial uncoupling, may underlie their effect.

EMBO reports, Jan 20, 2017

Altered cell metabolism is a hallmark of cancer, and targeting specific metabolic nodes is consid... more Altered cell metabolism is a hallmark of cancer, and targeting specific metabolic nodes is considered an attractive strategy for cancer therapy. In this study, we evaluate the effects of metabolic stressors on the deregulated ERK pathway in melanoma cells bearing activating mutations of the NRAS or BRAF oncogenes. We report that metabolic stressors promote the dimerization of KSR proteins with CRAF in NRAS-mutant cells, and with oncogenic BRAF in BRAFV600E-mutant cells, thereby enhancing ERK pathway activation. Despite this similarity, the two genomic subtypes react differently when a higher level of metabolic stress is induced. In NRAS-mutant cells, the ERK pathway is even more stimulated, while it is strongly downregulated in BRAFV600E-mutant cells. We demonstrate that this is caused by the dissociation of mutant BRAF from KSR and is mediated by activated AMPK. Both types of ERK regulation nevertheless lead to cell cycle arrest. Besides studying the effects of the metabolic stress...

Frontiers in endocrinology, 2018

Metabolic impairments associated with obstructive sleep apnea syndrome (OSA) are linked to tissue... more Metabolic impairments associated with obstructive sleep apnea syndrome (OSA) are linked to tissue hypoxia, however, the explanatory molecular and endocrine mechanisms remain unknown. Using gas-permeable cultureware, we studied the chronic effects of mild and severe hypoxia on free fatty acid (FFA) uptake, storage, and oxidation in L6 myotubes under 20, 4, or 1% O. Additionally, the impact of metformin and the peroxisome proliferator-activated receptor (PPAR) β/δ agonist, called GW501516, were investigated. Exposure to mild and severe hypoxia reduced FFA uptake by 37 and 32%, respectively, while metformin treatment increased FFA uptake by 39% under mild hypoxia. GW501516 reduced FFA uptake under all conditions. Protein expressions of CD36 (cluster of differentiation 36) and SCL27A4 (solute carrier family 27 fatty acid transporter, member 4) were reduced by 17 and 23% under severe hypoxia. Gene expression of UCP2 (uncoupling protein 2) was reduced by severe hypoxia by 81%. Metformin i...

Critical care medicine, Jan 13, 2017

Propofol may adversely affect the function of mitochondria and the clinical features of propofol ... more Propofol may adversely affect the function of mitochondria and the clinical features of propofol infusion syndrome suggest that this may be linked to propofol-related bioenergetic failure. We aimed to assess the effect of therapeutic propofol concentrations on energy metabolism in human skeletal muscle cells. In vitro study on human skeletal muscle cells. University research laboratories. Patients undergoing hip surgery and healthy volunteers. Vastus lateralis biopsies were processed to obtain cultured myotubes, which were exposed to a range of 1-10 μg/mL propofol for 96 hours. Extracellular flux analysis was used to measure global mitochondrial functional indices, glycolysis, fatty acid oxidation, and the functional capacities of individual complexes of electron transfer chain. In addition, we used [1-C]palmitate to measure fatty acid oxidation and spectrophotometry to assess activities of individual electron transfer chain complexes II-IV. Although cell survival and basal oxygen c...

PLOS ONE, 2016

Methyltriphenylphosphonium (TPMP) salts have been widely used to measure the mitochondrial membra... more Methyltriphenylphosphonium (TPMP) salts have been widely used to measure the mitochondrial membrane potential and the triphenylphosphonium (TPP +) moiety has been attached to many bioactive compounds including antioxidants to target them into mitochondria thanks to their high affinity to accumulate in the mitochondrial matrix. The adverse effects of these compounds on cellular metabolism have been insufficiently studied and are still poorly understood. Micromolar concentrations of TPMP cause a progressive inhibition of cellular respiration in adherent cells without a marked effect on mitochondrial coupling. In permeabilized cells the inhibition was limited to NADH-linked respiration. We found a mixed inhibition of the Krebs cycle enzyme 2-oxoglutarate dehydrogenase complex (OGDHC) with an estimated IC 50 3.93 [3.70-4.17] mM, which is pharmacologically plausible since it corresponds to micromolar extracellular concentrations. Increasing the lipophilic character of the used TPP + compound further potentiates the inhibition of OGDHC activity. This effect of TPMP on the Krebs cycle ought to be taken into account when interpreting observations on cells and mitochondria in the presence of TPP + derivatives. Compounds based on or similar to TPP + derivatives may also be used to alter OGDHC activity for experimental or therapeutic purposes.

JPEN. Journal of parenteral and enteral nutrition, Jan 29, 2016

Functional mitochondria in skeletal muscle of patients with protracted critical illness and inten... more Functional mitochondria in skeletal muscle of patients with protracted critical illness and intensive care unit-acquired weakness are depleted, but remaining mitochondria have increased functional capacities of respiratory complexes II and III. This can be an adaptation to relative abundancy of fatty acid over glucose caused by insulin resistance. We hypothesized that the capacity of muscle mitochondria to oxidize fatty acid is increased in protracted critical illness. We assessed fatty acid oxidation (FAO) and mitochondrial functional indices in vitro by using extracellular flux analysis in cultured myotubes obtained by isolating and culturing satellite cells from vastus lateralis muscle biopsy samples from patients with ICU-acquired weakness (n = 6) and age-matched healthy controls (n = 7). Bioenergetic measurements were performed at baseline and after 6 days of exposure to free fatty acids (FFAs). Mitochondrial density in myotubes from ICU patients was 69% of healthy controls (P ...

Critical Care, 2015

Background Mitochondrial damage occurs in the acute phase of critical illness, followed by activa... more Background Mitochondrial damage occurs in the acute phase of critical illness, followed by activation of mitochondrial biogenesis in survivors. It has been hypothesized that bioenergetics failure of skeletal muscle may contribute to the development of ICU-acquired weakness. The aim of the present study was to determine whether mitochondrial dysfunction persists until protracted phase of critical illness. Methods In this single-centre controlled-cohort ex vivo proof-of-concept pilot study, we obtained vastus lateralis biopsies from ventilated patients with ICU-acquired weakness (n = 8) and from age and sex-matched metabolically healthy controls (n = 8). Mitochondrial functional indices were measured in cytosolic context by high-resolution respirometry in tissue homogenates, activities of respiratory complexes by spectrophotometry and individual functional capacities were correlated with concentrations of electron transport chain key subunits from respiratory complexes II, III, IV and...

PLOS ONE, 2015

Background The lipophilic positively charged moiety of triphenylphosphonium (TPP +) has been used... more Background The lipophilic positively charged moiety of triphenylphosphonium (TPP +) has been used to target a range of biologically active compounds including antioxidants, spin-traps and other probes into mitochondria. The moiety itself, while often considered biologically inert, appears to influence mitochondrial metabolism. Methodology/Principal Findings We used the Seahorse XF flux analyzer to measure the effect of a range of alkylTPP + on cellular respiration and further analyzed their effect on mitochondrial membrane potential and the activity of respiratory complexes. We found that the ability of alkylTPP + to inhibit the respiratory chain and decrease the mitochondrial membrane potential increases with the length of the alkyl chain suggesting that hydrophobicity is an important determinant of toxicity. Conclusions/Significance More hydrophobic TPP + derivatives can be expected to have a negative impact on mitochondrial membrane potential and respiratory chain activity in addition to the effect of the biologically active moiety attached to them. Using shorter linker chains or adding hydrophilic functional groups may provide a means to decrease this negative effect.

This is an Open Access article licensed under the terms of the Creative Commons Attribution-NonCo... more This is an Open Access article licensed under the terms of the Creative Commons Attribution-NonCommercial 3.0 Unported license (CC BY-NC) (www.karger.com/OA-license), applicable to the online version of the article only. Distribution permitted for non-commercial purposes only.

PLoS ONE, 2013

Background: Substituting galactose for glucose in cell culture media has been suggested to enhanc... more Background: Substituting galactose for glucose in cell culture media has been suggested to enhance mitochondrial metabolism in a variety of cell lines. We studied the effects of carbohydrate availability on growth, differentiation and metabolism of C2C12 myoblasts and myotubes. Methodology/Principal Findings: We measured growth rates, ability to differentiate, citrate synthase and respiratory chain activities and several parameters of mitochondrial respiration in C2C12 cells grown in media with varying carbohydrate availability (5 g/l glucose, 1 g/l glucose, 1 g/l galactose, and no added carbohydrates). C2C12 myoblasts grow more slowly without glucose irrespective of the presence of galactose, which is not consumed by the cells, and they fail to differentiate without glucose in the medium. Cells grown in a no-glucose medium (with or without galactose) have lower maximal respiration and spare respiratory capacity than cells grown in the presence of glucose. However, increasing glucose concentration above physiological levels decreases the achievable maximal respiration. C2C12 myotubes differentiated at a high glucose concentration showed higher dependency on oxidative respiration under basal conditions but had lower maximal and spare respiratory capacity when compared to cells differentiated under low glucose condition. Citrate synthase activity or mitochondrial yield were not significantly affected by changes in the available substrate concentration but a trend towards a higher respiratory chain activity was observed at reduced glucose levels. Conclusions/Significance: Our results show that using galactose to increase oxidative metabolism may not be applicable to every cell line, and the changes in mitochondrial respiratory parameters associated with treating cells with galactose are mainly due to glucose deprivation. Moderate concentrations of glucose (1 g/l) in a growth medium are optimal for mitochondrial respiration in C2C12 cell line while supraphysiological concentrations of glucose cause mitochondrial dysfunction in C2C12 myoblasts and myotubes.