Updates in metabolomics tools and resources: 2014-2015

Data processing and interpretation represent the most challenging and time-consuming steps in high-throughput metabolomic experiments, regardless of the analytical platforms (MS or NMR spectroscopy based) used for data acquisition. Improved machinery in metabolomics generates increasingly complex datasets that create the need for more and better processing and analysis software and in silico approaches to understand the resulting data. However, a comprehensive source of information describing the utility of the most recently developed and released metabolomics resources—in the form of tools, software, and databases—is currently lacking. Thus, here we provide an overview of freely-available, and open-source, tools, algorithms, and frameworks to make both upcoming and established metabolomics researchers aware of the recent developments in an attempt to advance and facilitate data processing workflows in their metabolomics research. The major topics include tools and researches for data processing, data annotation, and data visualization in MS and NMR-based metabolomics. Most in this review described tools are dedicated to untargeted metabolomics workflows; however, some more specialist tools are described as well. All tools and resources described including their analytical and computational platform dependencies are summarized in an overview Table

novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model

To increase the number of value-added chemicals that can be produced by metabolic engineering and synthetic biology, constructing metabolic space with novel reactions/pathways is crucial. However, with the large number of reactions that existed in the metabolic space and complicated metabolisms within hosts, identifying novel pathways linking two molecules or heterologous pathways when engineering a host to produce a target molecule is an arduous task. Hence, we built a user-friendly web server, novoPathFinder, which has several features: (i) enumerate novel pathways between two specified molecules without considering hosts; (ii) construct heterologous pathways with known or putative reactions for producing target molecule within Escherichia coli or yeast without giving precursor; (iii) estimate novel pathways with considering several categories, including enzyme promiscuity, Synthetic Complex Score (SCScore) and LD50 of intermediates, overall stoichiometric conversions, pathway length, theoretical yields and thermodynamic feasibility. According to the results, novoPathFinder is more capable to recover experimentally validated pathways when comparing other rule-based web server tools. Besides, more efficient pathways with novel reactions could also be retrieved for further experimental exploration. novoPathFinder is available at http://design.rxnfinder.org/novopathfinder/

Perfil metabolómico de los tumores neuroendocrinos de origen gastrointestinal y pulmonar : papel pronóstico y relevancia biológica

Tesis inédita de la Universidad Complutense de Madrid, Facultad de Medicina, leída el 11-02-2022Reprogrammed metabolism encompasses the capacity of cells to respond or adapt their metabolic signalling to support and enable cell survival in unfavourable or hostile conditions. This ability is enhanced in cancer cells to improve their adaptive phenotype and maintain both viability and uncontrolled proliferation. Metabolic flexibility is therefore one of the key hallmarks of cancer, although pathways involved in the metabolic plasticity of each cancer type remain to be elucidated. Metabolites are the final products of this adaptation, reflecting the aberrant changes in the genomic, transcriptomic and proteomic variability of tumors, and therefore provide useful biological and clinical information on cancer biology. This, together with the fact that metabolomics can be easily performed in readily accessible biological samples (i.e. plasma, urine), makes metabolic profiling of cancer patients a promising tool to characterize the tumor phenotype and identify novel biomarkers of potential clinical use...La reprogramación del metabolismo permite a las células para responder o adaptar su regulación metabólica para permitir la supervivencia celular en condiciones desfavorables u hostiles. Esta capacidad aumenta en las células cancerosas para mejorar su fenotipo adaptativo y mantener tanto la viabilidad como la proliferación incontrolada. Así, la flexibilidad metabólica es una de las características distintivas del cáncer, aunque todavía quedan por dilucidar las vías implicadas en la plasticidad metabólica de cada tipo de tumor. Los metabolitos son los productos finales de esta adaptación, que en último término reflejan los cambios aberrantes que sufren los tumores reflejando la variabilidad genómica, transcriptómica y proteómica de los mismos y, por lo tanto, proporcionando información relevante sobre la biología del cáncer. Además, el estudio de los perfiles de metabolitos (metabolómica) puede realizarse fácilmente en muestras biológicas de fácil acceso (plasma, orina), constituyendo así una herramienta prometedora para caracterizar el fenotipo tumoral e identificar nuevos biomarcadores de potencial utilidad clínica...Fac. de MedicinaTRUEunpu

Estudo da resposta metabólica de células de osteossarcoma a agentes anticancerígenos convencionais e novos por metabolómica de RMN

Doutoramento em QuímicaThe main scope of this work was to evaluate the metabolic effects of anticancer agents (three conventional and one new) in osteosarcoma (OS) cells and osteoblasts, by measuring alterations in the metabolic profile of cells by nuclear magnetic resonance (NMR) spectroscopy metabolomics. Chapter 1 gives a theoretical framework of this work, beginning with the main metabolic characteristics that globally describe cancer as well as the families and mechanisms of action of drugs used in chemotherapy. The drugs used nowadays to treat OS are also presented, together with the Palladium(II) complex with spermine, Pd2Spm, potentially active against cancer. Then, the global strategy for cell metabolomics is explained and the state of the art of metabolomic studies that analyze the effect of anticancer agents in cells is presented. In Chapter 2, the fundamentals of the analytical techniques used in this work, namely for biological assays, NMR spectroscopy and multivariate and statistical analysis of the results are described. A detailed description of the experimental procedures adopted throughout this work is given in Chapter 3. The biological and analytical reproducibility of the metabolic profile of MG-63 cells by high resolution magic angle spinning (HRMAS) NMR is evaluated in Chapter 4. The metabolic impact of several factors (cellular integrity, spinning rate, temperature, time and acquisition parameters) on the 1H HRMAS NMR spectral profile and quality is analysed, enabling the definition of the best acquisition parameters for further experiments. The metabolic consequences of increasing number of passages in MG-63 cells as well as the duration of storage are also investigated. Chapter 5 describes the metabolic impact of drugs conventionally used in OS chemotherapy, through NMR metabolomics studies of lysed cells and aqueous extracts analysis. The results show that MG-63 cells treated with cisplatin (cDDP) undergo a strong up-regulation of lipid contents, alterations in phospholipid constituents (choline compounds) and biomarkers of DNA degradation, all associated with cell death by apoptosis. Cells exposed to doxorubicin (DOX) or methotrexate (MTX) showed much slighter metabolic changes, without any relevant alteration in lipid contents. However, metabolic changes associated with altered Krebs cycle, oxidative stress and nucleotides metabolism were detected and were tentatively interpreted at the light of the known mechanisms of action of these drugs. The metabolic impact of the exposure of MG-63 cells and osteoblasts to cDDP and the Pd2Spm complex is described in Chapter 6. Results show that, despite the ability of the two agents to bind DNA, the metabolic consequences that arise from exposure to them are distinct, namely in what concerns to variation in lipid contents (absent for Pd2Spm). Apoptosis detection assays showed that, differently from what was seen for MG-63 cells treated with cDDP, the decreased number of living cells upon exposure to Pd2Spm was not due to cell death by apoptosis or necrosis. Moreover, the latter agent induces more marked alterations in osteoblasts than in cancer cells, while the opposite seemed to occur upon cDDP exposure. Nevertheless, the results from MG-63 cells exposure to combination regimens with cDDP- or Pd2Spm-based cocktails, described in Chapter 7, revealed that, in combination, the two agents induce similar metabolic responses, arising from synergy mechanisms between the tested drugs. Finally, the main conclusions of this thesis are summarized in Chapter 8, and future perspectives in the light of this work are presented.Este trabalho teve como principal objetivo estudar os efeitos metabólicos de alguns fármacos (três fármacos convencionais e um em desenvolvimento) em células de osteossarcoma (OS) e osteoblastos, através da medição de alterações dos perfis metabólicos celulares por metabolómica usando espectroscopia de Ressonância Magnética Nuclear (RMN). O Capítulo 1 apresenta um enquadramento teórico deste trabalho, começando por identificar as principais características metabólicas que descrevem o cancro em geral, assim como as famílias e mecanismos de ação dos fármacos usados no seu tratamento. São ainda apresentados os fármacos usados atualmente na quimioterapia do OS, bem como o complexo de Paládio (II) com espermina, Pd2Spm, com potencial atividade anticancerígena. Seguidamente, é explicada a estratégia da metabolómica celular e apresentado o estado da arte de estudos metabolómicos do efeito de agentes anticancerígenos em células. No Capítulo 2, apresentam-se os princípios das técnicas analíticas usadas neste trabalho, nomeadamente ensaios biológicos, espectroscopia de RMN e análise multivariada e estatística dos resultados. Os detalhes e procedimentos experimentais relativos aos métodos usados são descritos no Capítulo 3. O estudo da reprodutibilidade analítica e biológica do perfil metabólico de células MG-63 medido por RMN de alta resolução e rotação segundo o ângulo mágico (HRMAS) é apresentado no Capítulo 4. Avalia-se o impacto de vários fatores (integridade celular, velocidade de rotação da amostra, temperatura, duração e parâmetros de aquisição) nas características e qualidade do espectro de RMN HRMAS de 1H, definindo-se então os parâmetros de aquisição dos espectros a adquirir subsequentemente. Avaliam-se também os efeitos do nº de passagens celulares e do tempo de armazenamento no perfil metabólico de células MG-63. O Capítulo 5 descreve o impacto metabólico de fármacos convencionais usados atualmente na quimioterapia do OS, estudado por metabolómica por RMN de células lisadas e análise de extratos celulares aquosos. Os resultados mostram que as células MG-63 tratadas com cisplatina (cDDP) sofrem um aumento dramático do teor de lípidos, alterações dos níveis de constituintes dos fosfolípidos (compostos de colina) e de indicadores de degradação do DNA, associados a fenómenos de apoptose. Nas células expostas a doxorrubicina (DOX) ou a metotrexato (MTX) foram identificadas alterações metabólicas mais ténues, com a quase total ausência de alterações no teor de lípidos. Foram também detetadas alterações em metabolitos relacionados com o ciclo de Krebs, stress oxidativo e metabolismo de nucleótidos, interpretadas tentativamente à luz dos mecanismos de ação de cada um dos fármacos. O impacto metabólico da exposição de células MG-63 e osteoblastos a cDDP e ao complexo de Pd2Spm é apresentado no Capítulo 6. Os resultados mostram que, apesar de ambos os fármacos poderem ligar ao DNA, as alterações metabólicas que decorrem da sua ação são muito distintas, nomeadamente no que respeita às variações nos teores de lípidos (ausentes para Pd2Spm). Ensaios de medição de apoptose mostraram que, contrariamente ao verificado para células MG-63 expostas a cDDP, a redução do número de células por exposição a Pd2Spm não se deve a fenómenos de morte celular por apoptose ou necrose. Além disso, este último complexo exerce um efeito mais marcado em osteoblastos do que nas células cancerígenas, o inverso parecendo acontecer com a exposição a cDDP. Contudo, os resultados da exposição de células MG-63 a regimes de tratamento combinado com base em cocktails de cDDP ou Pd2Spm, descritos no Capítulo 7, mostram que, em combinação, os dois agentes induzem respostas metabólicas semelhantes entre si, decorrentes de mecanismos de sinergia entre fármacos. Finalmente, sumariam-se no Capítulo 8 as conclusões deste trabalho e apontam-se perspetivas de trabalho futuro

Persistente organiske forbindelser og effekter på utviklings- og funksjonsprosesser i mus

Initial exposure to persistent organic pollutants (POPs) occurs by placental and lactational transfer during fetal and neonatal life and continues during the adult stage through ingestion, inhalation and dermal absorption. Many POPs have functional groups that resemble endogenous molecules rendering them with the potential for endocrine disruption during sensitive periods of organ development and function. Thus, adverse health effects may arise from exposure to POPs such as cancer and dysfunction of the endocrine, immune, reproductive, developmental or neurological systems. Mice are extensively used in research related to human health and disease as they are small animals with short generation time and high genetic similarity to humans. In addition, transgenic and knockout technology has led to the development of murine models with high phenotypic similarity to human disease. However, several differences between humans and mice are present in the absorption, distribution, metabolism, excretion, sensitivity and susceptibility to POPs. Furthermore, attention has recently shifted from assessing the toxicity of single compounds or well-defined chemical mixtures to evaluating large and environmentally relevant mixtures of POPs. The present study utilized two mouse models (CD-1 and A/J Min) and two exposure regimes (dietary or perinatal) to explore the effects of a human relevant mixture of POPs on female mammary gland development and ovarian folliculogenesis, liver morphology and function, and colorectal cancer development, intestinal microbiota and metabolome. The mixture composition was based on chemicals present in Scandinavian food products and the individual compound concentrations were adjusted to 0x (Control), 5 000x (Low) or 100 000x (High) human estimated daily intake levels for the general Scandinavian population. As shown previously, the present study also demonstrated gestational and lactational transfer of POPs from mothers to offspring. Furthermore, the results showed absorption, distribution, accumulation and persistence of POPs in murine tissues. The Low dose resulted in human relevant concentrations (for some chemicals) and can be considered at least partly human relevant in both its composition and concentration. Perinatal exposure to the mixture restricted mammary gland development and led to a premature arrest of gland growth in female CD-1 mice. In addition, it decreased ovarian follicle maturation and possibly also increased follicle atresia. Together this indicated potential endocrine disruption. Furthermore, the mixture caused persistent hepatocellular hypertrophy in CD-1 mice, but not in A/J Min mice. Thus, a strain-dependent difference in hepatic sensitivity was illustrated and, together with the induction of cytochrome P450 enzymes, indicated that the mixture may cause hepatotoxicity in sensitive strains. The two exposure regimes, dietary and perinatal, resulted in contradictory effects on colorectal carcinogenesis in A/J Min mice. Dietary exposure moderately increased cancer development while perinatal exposure reduced carcinogenesis. The increase was synergistically enhanced when combined with one injection of azoxymethane. Interestingly, perinatal POP exposure modulated the biochemical and microbial environment of the intestine possibly to reduce colorectal carcinogenesis in the predetermined cancer model. In conclusion, the human relevant mixture of POPs affected several developmental and functional processes in mice. The results of the present study can facilitate future mechanistic investigations into how human relevant chemical mixtures may affect biological development and function.Eksponering for persistente organiske forbindelser (POPs) starter i foster- og neonatalstadiet igjennom morkaken og brystmelk, og fortsetter videre igjennom matinntak, innånding og dermal absorpsjon. Mange POPs har funksjonelle grupper som etterligner endogene molekyler, noe som gir kjemikaliene et potensiale for endokrine forstyrrelser i løpet av sensitive perioder for organutvikling og funksjon. Alvorlige helseeffekter kan dermed oppstå som følge av eksponering, slik som kreft og dysfunksjon av ulike kroppsfunksjoner. Mus er mye brukt i forskning på human helse og sykdommer fordi de er små dyr med kort generasjonstid og har høy genetisk likhet til mennesker. I tillegg har transgen- og knockoutteknologi ført til utvikling av musemodeller med høy fenotypisk likhet til humane sykdommer. Likevel finnes det flere ulikheter mellom mennesker og mus, blant annet når det gjelder absorpsjon, distribusjon, metabolisme og ekskresjon av POPs. Videre har oppmerksomheten skiftet fra å studere toksisiteten av enkeltstoffer eller veldefinerte mikser av kjemikalier til å undersøke store og miljørelevante sammensetninger av POPs. I denne avhandlingen ble det brukt to musemodeller (CD-1 og A/J Min) og to eksponeringsregimer (diett og perinatal) til å undersøke effektene av en humanrelevant miks av POPs på hunnlig brystutvikling og utvikling av follikler i ovariene, levermorfologi og funksjon. Forekomst av tykktarmskreft, sammensetning av tarmmikrobiota og metabolom i tarminnhold og tarmvev ble også undersøkt. Miksen hadde en sammensetning av stoffer basert på kjemikalier som er tilstede i Skandinaviske matprodukter og konsentrasjonene av de individuelle stoffene ble justert til 0x (Kontroll), 5 000x (Lav) eller 100 000x (Høy) nivået av estimert humant daglig inntak for den generelle Skandinaviske populasjonen. I likhet med tidligere studier viste også dette studiet at POPs overføres fra mor til barn igjennom graviditet og amming. Videre viste resultatene absorpsjon, distribusjon, akkumulasjon og persistens av POPs i vev fra mus. Lav eksponeringsdose resulterte i konsentrasjoner (for noen av kjemikaliene) som var humanrelevante og kan delvis vurderes til å være humanrelevant i både sin komposisjon og konsentrasjon. Perinatal eksponering for miksen begrenset brystutviklingen og førte til en prematur stans i kjertelveksten i CD-1 hunnmus. Videre førte eksponeringen til en reduksjon i follikkelmodningen og mulig også en økning av follikkelatresi i ovariene. Til sammen indikerte dette en mulig endokrin forstyrrelse. Miksen førte også til persistent hypertrofi av leverceller i CD-1 mus, men ikke i A/J Min mus. Dette tydet på forskjeller i leversensitivitet mellom musemodeller og, sammen med en induksjon av cytokrom P450 enzymer, indikerte dette at miksen kunne føre til levertoksisitet i høysensitive mus. De to eksponeringsregimene, igjennom diett og perinatal overføring, førte til motstridende effekter på tarmkreft i A/J Min mus. Eksponering igjennom dietten førte til en moderat økning av kreft, mens perinatal eksponering reduserte karsinogenesen. Økningen ble synergistisk forsterket i kombinasjon med én injeksjon av azoxymetan. Perinatal POP-eksponering modulerte det biokjemiske og mikrobielle miljøet i tarmen, noe som mulig reduserte tarmkreftutviklingen i den forutbestemte kreftmodellen. Vi konkluderer med at den humanrelevante miksen av POPs påvirket utviklingen og funksjonen til flere kroppsfunksjoner i mus. Disse resultatene gir et godt grunnlag for videre forskning knyttet til hvordan humanrelevante blandinger av POPs kan påvirke utvikling og helse hos dyr og mennesker

Biological Networks

Networks of coordinated interactions among biological entities govern a myriad of biological functions that span a wide range of both length and time scales—from ecosystems to individual cells and from years to milliseconds. For these networks, the concept “the whole is greater than the sum of its parts” applies as a norm rather than an exception. Meanwhile, continued advances in molecular biology and high-throughput technology have enabled a broad and systematic interrogation of whole-cell networks, allowing the investigation of biological processes and functions at unprecedented breadth and resolution—even down to the single-cell level. The explosion of biological data, especially molecular-level intracellular data, necessitates new paradigms for unraveling the complexity of biological networks and for understanding how biological functions emerge from such networks. These paradigms introduce new challenges related to the analysis of networks in which quantitative approaches such as machine learning and mathematical modeling play an indispensable role. The Special Issue on “Biological Networks” showcases advances in the development and application of in silico network modeling and analysis of biological systems

Computational Methods for the Analysis of Genomic Data and Biological Processes

In recent decades, new technologies have made remarkable progress in helping to understand biological systems. Rapid advances in genomic profiling techniques such as microarrays or high-performance sequencing have brought new opportunities and challenges in the fields of computational biology and bioinformatics. Such genetic sequencing techniques allow large amounts of data to be produced, whose analysis and cross-integration could provide a complete view of organisms. As a result, it is necessary to develop new techniques and algorithms that carry out an analysis of these data with reliability and efficiency. This Special Issue collected the latest advances in the field of computational methods for the analysis of gene expression data, and, in particular, the modeling of biological processes. Here we present eleven works selected to be published in this Special Issue due to their interest, quality, and originality