Showing papers by "Alexei Vazquez published in 2020"

Formate metabolism in health and disease.

Abstract: Background Formate is a one-carbon molecule at the crossroad between cellular and whole body metabolism, between host and microbiome metabolism, and between nutrition and toxicology. This centrality confers formate with a key role in human physiology and disease that is currently unappreciated. Scope of review Here we review the scientific literature on formate metabolism, highlighting cellular pathways, whole body metabolism, and interactions with the diet and the gut microbiome. We will discuss the relevance of formate metabolism in the context of embryonic development, cancer, obesity, immunometabolism, and neurodegeneration. Major conclusions We will conclude with an outlook of some open questions bringing formate metabolism into the spotlight.

Targeting the Metabolic Response to Statin-Mediated Oxidative Stress Produces a Synergistic Antitumor Response.

Abstract: Statins are widely prescribed inhibitors of the mevalonate pathway, acting to lower systemic cholesterol levels. The mevalonate pathway is critical for tumorigenesis and is frequently upregulated in cancer. Nonetheless, reported effects of statins on tumor progression are ambiguous, making it unclear if statins, alone or in combination, can be used for chemotherapy. Here, using advanced mass spectrometry and isotope tracing, we showed that statins only modestly affected cancer cholesterol homeostasis. Instead, they significantly reduced synthesis and levels of another downstream product, the mitochondrial electron carrier coenzyme Q, both in cultured cancer cells and tumors. This compromised oxidative phosphorylation, causing severe oxidative stress. To compensate, cancer cells upregulated antioxidant metabolic pathways, including reductive carboxylation, proline synthesis, and cystine import. Targeting cystine import with an xCT transporter-lowering MEK inhibitor, in combination with statins, caused profound tumor cell death. Thus, statin-induced ROS production in cancer cells can be exploited in a combinatorial regimen.

Formate induces a metabolic switch in nucleotide and energy metabolism

Abstract: Formate is a precursor for the de novo synthesis of purine and deoxythymidine nucleotides. Formate also interacts with energy metabolism by promoting the synthesis of adenine nucleotides. Here we use theoretical modelling together with metabolomics analysis to investigate the link between formate, nucleotide and energy metabolism. We uncover that endogenous or exogenous formate induces a metabolic switch from low to high adenine nucleotide levels, increasing the rate of glycolysis and repressing the AMPK activity. Formate also induces an increase in the pyrimidine precursor orotate and the urea cycle intermediate argininosuccinate, in agreement with the ATP-dependent activities of carbamoyl-phosphate and argininosuccinate synthetase. In vivo data for mouse and human cancers confirms the association between increased formate production, nucleotide and energy metabolism. Finally, the in vitro observations are recapitulated in mice following and intraperitoneal injection of formate. We conclude that formate is a potent regulator of purine, pyrimidine and energy metabolism.

Metabolite AutoPlotter - an application to process and visualise metabolite data in the web browser.

Abstract: Metabolomics is gaining popularity as a standard tool for the investigation of biological systems. Yet, parsing metabolomics data in the absence of in-house computational scientists can be overwhelming and time-consuming. As a consequence of manual data processing, the results are often not analysed in full depth, so potential novel findings might get lost. To tackle this problem, we developed Metabolite AutoPlotter, a tool to process and visualise quantified metabolite data. Other than with bulk data visualisations, such as heat maps, the aim of the tool is to generate single plots for each metabolite. For this purpose, it reads as input pre-processed metabolite-intensity tables and accepts different experimental designs, with respect to the number of metabolites, conditions and replicates. The code was written in the R-scripting language and wrapped into a shiny application that can be run online in a web browser on https://mpietzke.shinyapps.io/autoplotter . We demonstrate the main features and the ease of use with two different metabolite datasets, for quantitative experiments and for stable isotope tracing experiments. We show how the plots generated by the tool can be interactively modified with respect to plot type, colours, text labels and the shown statistics. We also demonstrate the application towards 13C-tracing experiments and the seamless integration of natural abundance correction, which facilitates the better interpretation of stable isotope tracing experiments. The output of the tool is a zip-file containing one single plot for each metabolite as well as restructured tables that can be used for further analysis. With the help of Metabolite AutoPlotter, it is now possible to simplify data processing and visualisation for a wide audience. High-quality plots from complex data can be generated in a short time by pressing a few buttons. This offers dramatic improvements over manual analysis. It is significantly faster and allows researchers to spend more time interpreting the results or to perform follow-up experiments. Further, this eliminates potential copy-and-paste errors or tedious repetitions when things need to be changed. We are sure that this tool will help to improve and speed up scientific discoveries.

Amino acid dependent formaldehyde metabolism in mammals

Abstract: Aldehyde dehydrogenase class 3, encoded by ADH5 in humans, catalyzes the glutathione dependent detoxification of formaldehyde. Here we show that ADH5 deficient cells turn over formaldehyde using alternative pathways starting from the reaction of formaldehyde with free amino acids. When mammalian cells are exposed to formaldehyde, the levels of the reaction products of formaldehyde with the amino acids cysteine and histidine - timonacic and spinacine - are increased. These reactions take place spontaneously and the formation of timonacic is reversible. The levels of timonacic are higher in the plasma of Adh5−/− mice relative to controls and they are further increased upon administration of methanol. We conclude that mammals possess pathways of cysteine and histidine dependent formaldehyde metabolism and that timonacic is a formaldehyde reservoir. Formaldehyde is known to react with nucleophilic amino acids in solution but its in vivo nonenzymatic reactivity is poorly understood. Here LC/MS and isotopic labeling studies suggest nonenzymatic formaldehyde metabolism may occur in living mice through the direct reactivity of formaldehyde with amino acids, including a possible role of timonacic, a product of formaldehyde and cysteine, as a reservoir.

Superspreaders and lockdown timing explain the power-law dynamics of COVID-19

Abstract: Infectious disease outbreaks are expected to grow exponentially in time when left unchecked. Containment measures such as lockdown and social distancing can drastically alter the growth dynamics of the outbreak. This is the case for the 2019-2020 COVID-19 outbreak, which is characterized by a power-law growth. Strikingly however, the power-law exponent is different across countries. Here I illustrate the relationship between these two extreme scenarios, exponential and power-law growth, based on the impact of superspreaders and lockdown strategies to contain the outbreak. The theory predicts a relationship between the power- law exponent and the time interval between the first case and lockdown that is validated by the observed COVID-19 data across different countries.

Exact solution of infection dynamics with gamma distribution of generation intervals

Abstract: Infectious disease outbreaks are expected to grow exponentially in time but their initial dynamics is less known. Here I derive analytical expressions for the infectious disease dynamics with a gamma distribution of generation intervals. Excluding the exponential distribution, the outbreak grows as a power law at short times. At long times the dynamics is exponential with a growth rate determined by the basic reproductive number and the parameters of the generation interval distribution. These analytical expressions can be deployed to do better estimates of infectious disease parameters.

The conversion of formate into purines stimulates mTORC1 leading to CAD-dependent activation of pyrimidine synthesis

Abstract: Mitochondrial serine catabolism to formate induces a metabolic switch to a hypermetabolic state with high rates of glycolysis, purine synthesis and pyrimidine synthesis. While formate is a purine precursor, it is not clear how formate induces pyrimidine synthesis. Here we combine phospho-proteome and metabolic profiling to determine how formate induces pyrimidine synthesis. We discover that formate induces phosphorylation of carbamoyl phosphate synthetase (CAD), which is known to increase CAD enzymatic activity. Mechanistically, formate induces mechanistic target of rapamycin complex 1 (mTORC1) activity as quantified by phosphorylation of its targets S6, 4E-BP1, S6K1 and CAD. Treatment with the allosteric mTORC1 inhibitor rapamycin abrogates CAD phosphorylation and pyrimidine synthesis induced by formate. Furthermore, we show that the formate-dependent induction of mTOR signalling and CAD phosphorylation is dependent on an increase in purine synthesis. We conclude that formate activates mTORC1 and induces pyrimidine synthesis via the mTORC1-dependent phosphorylation of CAD.

Multi-type branching and graph product theory of infectious disease outbreaks

Abstract: The heterogeneity of human populations is a major challenge to mathematical descriptions of infectious disease outbreaks. Numerical simulations are therefore deployed to account for the many factors influencing the disease spreading dynamics. Yet, the results from numerical simulations are often as complicated as the reality, leaving us with a sense of confusion about how the different factors account for the simulation results. Here, using a multi-type branching together with a graph tensor product approach, I derive a single equation for the effective reproductive number of an infectious disease outbreak. Using this equation I deconvolute the impact of crowd management, contact heterogeneity, testing, vaccination, mask use and smartphone tracing app use. This equation can be used to gain a basic understanding of infectious disease outbreaks and their simulations.

Trends in Phase II trials for cancer therapies

Abstract: Background Drug combinations are the standard of care in cancer treatment. Identifying effective cancer drug combinations has become more challenging because of the increasing number of drugs. However, a substantial number of cancer drugs stumble at Phase III clinical trials despite exhibiting favourable efficacy in the earlier Phase. Methods We analysed recent Phase II cancer trials comprising 2,165 response rates to uncover trends in cancer therapies and used a null model of non-interacting agents to infer synergistic and antagonistic drug combinations. We compared our latest efficacy dataset with a previous dataset to assess the progress of cancer therapy. Results We demonstrate that targeted therapies should be used in combination with cytotoxic drugs to reach high response rates. We identify 4 synergistic and 10 antagonistic combinations based on the observed and expected response rates. We also demonstrate that recent targeted agents have not significantly increased the response rates. Conclusions We conclude either we are not making progress or response rate measured by tumour shrinkage is not a reliable surrogate endpoint for the targeted agents.

Superspreaders and lockdown timing explain the power law dynamics of COVID-19

Abstract: Infectious disease outbreaks are expected to grow exponentially in time when left unchecked. Containment measures such as lockdown and social distancing can drastically alter the growth dynamics of the outbreak. This is the case for the 2019-2020 COVID-19 outbreak, which is characterized by a power law growth. Strikingly however, the power law exponent is different across countries. Here I illustrate the relationship between these two extreme scenarios, exponential and power law growth, based on the impact of superspreaders and lockdown strategies to contain the outbreak. The theory predicts a relationship between the power law exponent and the time interval between the first case and lockdown that is validated by the observed COVID-19 data across different countries.

Impact of Formate Supplementation on Body Weight and Plasma Amino Acids.

Abstract: Current nutritional recommendations are focused on energy, fat, carbohydrate, protein and vitamins. Less attention has been paid to the nutritional demand of one-carbon units for nucleotide and methionine synthesis. Here, we investigated the impact of sodium formate supplementation as a nutritional intervention to increase the dietary intake of one-carbon units. A cohort of six female and six male mice received 125 mM of sodium formate in the drinking water for three months. A control group of another six female and six male mice was also followed up for the same period of time. Tail vein blood samples were collected once a month and profiled with a haematology analyser. At the end of the study, blood and tissues were collected for metabolomics analysis and immune cell profiling. Formate supplementation had no significant physiological effect on male mice, except for a small decrease in body weight. Formate supplementation had no significant effect on the immune cell counts during the intervention or at the end of the study in either gender. In female mice, however, the body weight and spleen wet weight were significantly increased by formate supplementation, while the blood plasma levels of amino acids were decreased. Formate supplementation also increased the frequency of bifidobacteria, a probiotic bacterium, in the stools of female mice. We conclude that formate supplementation induces physiological changes in a gender-specific manner.

Dietary and pharmacological induction of serine synthesis genes

Abstract: There is an increasing interest in the pathway of L-serine synthesis and its. Although L-serine and downstream products can be obtained from the diet, serine deficiency has been documented in neurological disorders, macular degeneration and aging. This evidence calls for strategies to induce serine synthesis. Here I address this problem taking advantage of the wealth of data deposited in the gene expression omnibus database. I uncover that low protein and ketogenic diets increase the expression of serine synthesis genes in the liver and the brain relative to control diets. I discover oestrogen medications, the antifolate methotrexate and serine synthesis inhibitors as classes of compounds inducing the expression of serine synthesis genes in the liver. Future work is required to investigate the use of these interventions for the management of serine deficiency disorders.

Oxygen dependent mitochondrial formate production and the reverse Pasteur effect

Abstract: The Pasteur effect dictates that oxygen induces respiration and represses fermentation. However, we have shown that oxygen stimulates mitochondrial formate production and excess formate production induces glycolysis in mammalian cells. Our observations suggest the hypothesis that increased respiration induces an increase, rather than a decrease, of fermentation, the reverse Pasteur effect. Using a mathematical model we show that, in the absence of mitochondrial formate production, we should always observe the Pasteur effect, a reduction in fermentation with increasing respiration. However, in cells with active mitochondrial formate production, the rate of fermentation first increases with increasing the rate of respiration, indicating a metabolic sweet spot at moderate oxygen availability that is within the range of tissue oxygen tensions. We provide experimental evidence for the manifestation of the reverse Pasteur effect at such oxygen tension.

Discovering compounds mimicking calorie restriction using mammalian gene expression profiles

Abstract: Obesity is a risk factor for cardiovascular diseases, diabetes and cancer. In theory the obesity problem could be solve by the adherence to a calorie restricted diet, but that is not generally achieved in practice. An alternative is a pharmacological approach, using compounds that trigger the same metabolic changes associated with calorie restriction. Here I expand in the pharmacological direction by identifying compounds that induce liver gene signature profiles that mimic those induced by calorie restriction. Using gene expression profiles from mice and rat I identify corticosteroids, PPAR agonists and some antibacterial/antifungal as candidate compounds mimicking the response to calorie restriction in the liver gene signatures. Liver gene signature analysis can be used to identify compounds that mimic calorie restriction.

Identification of putative calorie restriction mimetics using mammalian gene expression profiles.

Abstract: Obesity is a risk factor for cardiovascular diseases, diabetes and cancer. In theory, the obesity problem could be solved by the adherence to a calorie-restricted diet, but that is not generally achieved in practice. An alternative is a pharmacological approach, using compounds that trigger the same metabolic changes associated with calorie restriction. Here, I expand in the pharmacological direction by identifying compounds that induce liver gene signature profiles that mimic those induced by calorie restriction. Using gene expression profiles from mice and rat, I identify corticosteroids, PPAR agonists and some antibacterial/antifungal as candidate compounds mimicking the response to calorie restriction in the liver gene signatures.

The colon-pile

Abstract: Bacteria populate the colon where they replicate and migrate in response to nutrient availability. Here I model the colon bacterial population as a sandpile model, the colon-pile. Sand addition mimics bacterial replication and grains toppling represents bacterial migration coupled to high population density. The numerical simulations reveal a behaviour similar to non-conservative sandpile models, approaching a critical state with system wide avalanches when the death rate becomes negligible. The critical exponents estimation indicates that the colon-pile belongs to a new universality class. This work suggest that the colon microbiome is in a self-organised critical state, where small perturbations can trigger large scale rearrangements, covering an area comparable to the system size and characterised by a 1/f noise spectra

Impact of formate supplementation on body weight and plasma amino acids

Abstract: Current nutritional recommendations are focused on energy, fat, carbohydrate, protein and vitamins. Less attention has been paid to the nutritional demand of one-carbon units for nucleotide and methionine synthesis. Here we investigate the impact of sodium formate supplementation as a nutritional intervention to increase the dietary intake of one-carbon units. A cohort of six female and six male mice received 125 mM sodium formate in the drinking water for three months. A control group of another six female and six male mice was also followed up for the same period of time. Tail vein blood samples were collected once a month and profiled with a haematology Analyser. At the end of the study blood and tissues were collected for metabolomics analysis and immune cell sorting. Formate supplementation has no significant physiological effect on male mice. Formate supplementation has no significant effect on the immune cell counts during the intervention or at the end of the study in either gender. In female mice however, the body weight and spleen wet-weight were significantly increased by formate supplementation, while the blood plasma levels of amino acids were decreased. Formate supplementation also increased the frequency of probiotic bacteria in the stools of female mice. We conclude that formate supplementation induces physiological changes in female mice.

Transition to multi-type mixing in d-dimensional spreading dynamics

Abstract: The spreading dynamics of infectious diseases is determined by the interplay between geography and population mixing. There is homogeneous mixing at the local level and human mobility between distant populations. Here I model spatial location as a type and the population mixing by intra- and inter-type mixing patterns. Using the theory of multi-type branching process, I calculate the expected number of new infections as a function of time. In 1-dimension the analysis is reduced to the eigenvalue problem of a tridiagonal Teoplitz matrix. In d-dimensions I take advantage of the graph cartesian product to construct the eigenvalues and eigenvectors from the eigenvalue problem in 1-dimension. Using numerical simulations I uncover a transition from linear to multi-type mixing exponential growth with increasing the population size. Given that most countries are characterized by a network of cities with more than 100,000 habitants, I conclude that the multi-type mixing approximation should be the prevailing scenario.