Activation Of Metabolic Pathways Research Articles

The landscape of metabolic pathway dependencies in cancer cell lines

The metabolic reprogramming of cancer cells creates metabolic vulnerabilities that can be therapeutically targeted. However, our understanding of metabolic dependencies and the pathway crosstalk that creates these vulnerabilities in cancer cells remains incomplete. Here, by integrating gene expression data with genetic loss-of-function and pharmacological screening data from hundreds of cancer cell lines, we identified metabolic vulnerabilities at the level of pathways rather than individual genes. This approach revealed that metabolic pathway dependencies are highly context-specific such that cancer cells are vulnerable to inhibition of one metabolic pathway only when activity of another metabolic pathway is altered. Notably, we also found that the no single metabolic pathway was universally essential, suggesting that cancer cells are not invariably dependent on any metabolic pathway. In addition, we confirmed that cell culture medium is a major confounding factor for the analysis of metabolic pathway vulnerabilities. Nevertheless, we found robust associations between metabolic pathway activity and sensitivity to clinically approved drugs that were independent of cell culture medium. Lastly, we used parallel integration of pharmacological and genetic dependency data to confidently identify metabolic pathway vulnerabilities. Taken together, this study serves as a comprehensive characterization of the landscape of metabolic pathway vulnerabilities in cancer cell lines.

A guide to interrogating immunometabolism.

The metabolic charts memorized in early biochemistry courses, and then later forgotten, have come back to haunt many immunologists with new recognition of the importance of these pathways. Metabolites and the activity of metabolic pathways drive energy production, macromolecule synthesis, intracellular signalling, post-translational modifications and cell survival. Immunologists who identify a metabolic phenotype in their system are often left wondering where to begin and what does it mean? Here, we provide a framework for navigating and selecting the appropriate biochemical techniques to explore immunometabolism. We offer recommendations for initial approaches to develop and test metabolic hypotheses and how to avoid common mistakes. We then discuss how to take things to the next level with metabolomic approaches, such as isotope tracing and genetic approaches. By proposing strategies and evaluating the strengths and weaknesses of different methodologies, we aim to provide insight, note important considerations and discuss ways to avoid common misconceptions. Furthermore, we highlight recent studies demonstrating the power of these metabolic approaches to uncover the role of metabolism in immunology. By following the framework in this Review, neophytes and seasoned investigators alike can venture into the emerging realm of cellular metabolism and immunity with confidence and rigour.

Control of T Cell Metabolism by Cytokines and Hormones.

Dynamic, coordinated changes in metabolic pathway activity underpin the protective and inflammatory activity of T cells, through provision of energy and biosynthetic precursors for effector functions, as well as direct effects of metabolic enzymes, intermediates and end-products on signaling pathways and transcriptional mechanisms. Consequently, it has become increasingly clear that the metabolic status of the tissue microenvironment directly influences T cell activity, with changes in nutrient and/or metabolite abundance leading to dysfunctional T cell metabolism and interlinked immune function. Emerging evidence now indicates that additional signals are integrated by T cells to determine their overall metabolic phenotype, including those arising from interaction with cytokines and hormones in their environment. The impact of these on T cell metabolism, the mechanisms involved and the pathological implications are discussed in this review article.

Identification of the Roles of a Stemness Index Based on mRNA Expression in the Prognosis and Metabolic Reprograming of Pancreatic Ductal Adenocarcinoma.

BackgroundCancer stem cells (CSCs) are widely thought to contribute to the dismal prognosis of pancreatic ductal adenocarcinoma (PDAC). CSCs share biological features with adult stem cells, such as longevity, self-renewal capacity, differentiation, drug resistance, and the requirement for a niche; these features play a decisive role in cancer progression. A prominent characteristic of PDAC is metabolic reprogramming, which provides sufficient nutrients to support rapid tumor cell growth. However, whether PDAC stemness is correlated with metabolic reprogramming remains unknown.MethodRNA sequencing data of PDAC, including read counts and fragments per kilobase of transcript per million mapped reads (FPKM), were collected from The Cancer Genome Atlas-Pancreatic Adenocarcinoma (TCGA-PAAD) database. Single-sample gene set enrichment analysis (GSEA) was used to calculate the relative activities of metabolic pathways in each PDAC sample. Quantitative real-time PCR was performed to validate the expression levels of genes of interest.ResultsThe overall survival (OS) of patients with high mRNA expression-based stemness index (mRNAsi) values was significantly worse than that of their counterparts with low mRNAsi values (P = 0.003). This survival disadvantage was independent of baseline clinical characteristics. Gene ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and GSEA showed that the differentially expressed genes between patients with high and low mRNAsi values were mainly enriched in oncogenic and metabolic pathways. Weighted gene coexpression network analysis (WGCNA) revealed 8 independent gene modules that were significantly associated with mRNAsi and 12 metabolic pathways. Unsupervised clustering based on the key genes in each module identified two PDAC subgroups characterized by different mRNAsi values and metabolic activities. Univariate Cox regression analysis identified 14 genes beneficial to OS from 95 key genes selected from the eight independent gene modules from WGCNA. Among them, MAGEH1, MAP3K3, and PODN were downregulated in both pancreatic tissues and cell lines.ConclusionThe present study showed that PDAC samples with high mRNAsi values exhibited aberrant activation of multiple metabolic pathways, and the patients from whom these samples were obtained had a poor prognosis. Future studies are expected to investigate the underlying mechanism based on the crosstalk between PDAC stemness and metabolic rewiring.

Enhanced anti-cancer activity of andrographis with oligomeric proanthocyanidins through activation of metabolic and ferroptosis pathways in colorectal cancer

The high degree of morbidity and mortality in colorectal cancer (CRC) patients is largely due to the development of chemoresistance against conventional chemotherapeutic drugs. In view of the accumulating evidence that various dietary botanicals offer a safe, inexpensive and multi-targeted treatment option, herein, we hypothesized that a combination of Andrographis paniculata and Oligomeric Proanthocyanidins (OPCs) might interact together with regard to anti-tumorigenic activity in CRC. As a result, we demonstrated the enhanced anti-cancer activity between these two botanical extracts in terms of their ability to inhibit cancer cell growth, suppress colony formation and induce apoptosis. Furthermore, we validated these findings in subcutaneous xenograft model and in patient derived primary epithelial 3D organoids. Transcriptomic profiling identified involvement of metabolic pathways and ferroptosis-associated genes, including HMOX1, GCLC and GCLM, that may be responsible for the increased anti-tumorigenic activity by the two compounds. Collectively, our study provides novel evidence in support of the combinatorial use of andrographis and OPCs as a potential therapeutic option, perhaps as an adjunctive treatment to classical drugs, in patients with colorectal cancer.

Gut microbiome differences between amyotrophic lateral sclerosis patients and spouse controls

Objective: Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease that is incurable and ultimately fatal. Few therapeutic options are available to patients. In this study, we explored differences in microbiome composition associated with ALS. Methods: We compared the gut microbiome and inflammatory marker profiles of ALS patients (n = 10) to those of their spouses (n = 10). Gut microbiome profiles were determined by 16S rRNA gene sequencing. Results: The gut microbial communities of the ALS patients were more diverse and were deficient in Prevotella spp. compared with those of their spouses. In contrast, healthy couples (n = 10 couples of the opposite sex) recruited from the same geographic region as the patient population did not exhibit these differences. Stool and plasma inflammatory markers were similar between ALS patients and their spouses. Predictive analysis of microbial enzymes revealed that ALS patients had decreased activity in several metabolic pathways, including carbon metabolism, butyrate metabolism, and systems involving histidine kinase and response regulators. Conclusions: ALS patients exhibit differences in their gut microbial communities compared with spouse controls. Our findings suggest that modifying the gut microbiome, such as via amelioration of Prevotella spp. deficiency, and/or altering butyrate metabolism may have translational value for ALS treatment.

SIRT1/NFκB pathway mediates anti-inflammatory and anti-apoptotic effects of rosmarinic acid on in a mouse model of nonalcoholic steatohepatitis (NASH)

Nonalcoholic steatohepatitis (NASH) is considered as a common liver disease. SIRT1, a pivotal sensor, controls activation of metabolic, inflammatory and apoptotic pathways. Rosmarinic acid (RA) has positive effects on the liver injuries; nevertheless, its mechanisms are not completely studied. The aim of this study was to explore the role of rosmarinic acid on the pathways involved by SIRT1 for amelioration of a mouse model of NASH. To do this, C57/BL6 mice were divided into four equal groups (6 in each group). Animals received saline and rosmarinic acid as the control groups. NASH was induced by methionine-choline-deficient (MCD) diet. In the NASH + RA group, Rosmarinic acid was injected daily in mice fed on an MCD diet. Rosmarinic acid decreased plasma triglyceride, cholesterol, liver Steatosis and oxidative stress. Rosmarinic acid administration also increased SIRT1, Nrf2 and PPARα and decreased SREBP1c, FAS, NFκB and caspase3 expressions. Moreover, TNFα, IL6, P53, Bax/Bcl2 ratio and caspase3 expressions decreased. Our study demonstrated that remarkable effects of rosmarinic acid on the mice with NASH might be due to activation of SIRT1/Nrf2, SIRT1/NFκB and SIRT1/PPARα pathways, which alleviate hepatic steatosis, oxidative stress, inflammation and apoptosis.

The Metabolic Fates of Pyruvate in Normal and Neoplastic Cells.

Pyruvate occupies a central metabolic node by virtue of its position at the crossroads of glycolysis and the tricarboxylic acid (TCA) cycle and its production and fate being governed by numerous cell-intrinsic and extrinsic factors. The former includes the cell’s type, redox state, ATP content, metabolic requirements and the activities of other metabolic pathways. The latter include the extracellular oxygen concentration, pH and nutrient levels, which are in turn governed by the vascular supply. Within this context, we discuss the six pathways that influence pyruvate content and utilization: 1. The lactate dehydrogenase pathway that either converts excess pyruvate to lactate or that regenerates pyruvate from lactate for use as a fuel or biosynthetic substrate; 2. The alanine pathway that generates alanine and other amino acids; 3. The pyruvate dehydrogenase complex pathway that provides acetyl-CoA, the TCA cycle’s initial substrate; 4. The pyruvate carboxylase reaction that anaplerotically supplies oxaloacetate; 5. The malic enzyme pathway that also links glycolysis and the TCA cycle and generates NADPH to support lipid bio-synthesis; and 6. The acetate bio-synthetic pathway that converts pyruvate directly to acetate. The review discusses the mechanisms controlling these pathways, how they cross-talk and how they cooperate and are regulated to maximize growth and achieve metabolic and energetic harmony.

De novo transcriptome reveals blood coagulation/antithrombin factors and infection mechanisms in Angiostrongylus cantonensis adult worms.

Angiostrongylus cantonensis is the main aetiological agent of eosinophilic meningoencephalitis in humans. Several outbreaks have been documented around the world, cementing its status as an emerging global public health concern. As a result, new strategies for the diagnosis, prophylaxis and treatment of cerebral angiostrongyliasis are urgently needed. In this study, we report on the de novo assembly of the A. cantonensis transcriptome, its full functional annotation and a reconstruction of complete metabolic pathways. All results are available at AngiostrongylusDB (http://angiostrongylus.lad.pucrs.br/admin/welcome). The aim of this study was to identify the active genes and metabolic pathways involved in the mechanisms of infection and survival inside Rattus norvegicus. Among 389 metabolic mapped pathways, the blood coagulation/antithrombin pathways of heparan sulphate/heparin are highlighted. Moreover, we identified genes codified to GP63 (leishmanolysin), CALR (calreticulin), ACE (peptidyl-dipeptidase A), myoglobin and vWD (von Willebrand factor type D domain protein) involved in the infection invasion and survival of the parasite. The large dataset of functional annotations provided and the full-length transcripts identified in this research may facilitate future functional genomics studies and provides a basis for the development of new techniques for the diagnosis, prevention and treatment of cerebral angiostrongyliasis.

Active metabolic pathways of anaerobic methane oxidation in paddy soils

Anaerobic oxidation of methane (AOM) is a globally important CH4 sink. However, the AOM pathways in paddy soils, the largest agricultural source of methane emissions (31 Mio tons per year) are not yet well described. Here, a combination of 13C isotope tracer, phospholipid fatty acids (PLFA) analyses, and microbial community analysis was used to identify AOM pathways in fertilized (pig manure, biochar, NPK, and the control) paddy soils amended with alternative electron acceptors (AEAs) (NO3−, Fe3+, SO42−, humic acids, and the reference without AEAs addition). After 84 days of anaerobic incubation, the microbial co-occurrence network got tightened and became more complex relative to unincubated samples. Fertilization and AEAs addition led to a strong divergence of the microbial community structure as indicated by abundances of AOM-related microbiota and 13C incorporation into microbial PLFA, thus suggesting an environmental niche differentiation of AOM-involved microorganisms. Comparative analyses revealed a set of major and minor AOM pathways with synergistic relations to complementary anaerobic microbial groups. NO3−-driven AOM, performed by members of the candidate group ANME-2d, was the major AOM pathway. Minor AOM pathways involved NO2− reduction by NC10, reduction of humic acids and Fe3+ by Geobacter species, and SO42− reduction by sulfate-reducing bacteria linked with anaerobic methanotrophs. As identified by the network analysis, these active AOM pathways compensated a fraction of CH4 produced during ongoing methanogenesis. From a broader ecological perspective, nitrogen-driven AOM will become a more important methane sink in the future with the increases of nitrogen fertilization and deposition.

The microbial population structure and function of peanut peanut and their effects on aflatoxin contamination

Aflatoxin is a strong carcinogenic and toxic fungal toxin produced by Aspergillus flavus and other Aspergillus species, and can seriously threaten the health of consumers, thus becoming a global concern. Aflatoxin in agricultural products are closely related to biogeography and symbiotic microorganisms. It is not fully clear that how biogeography affects the assembly process of A. flavus and symbiotic microorganisms on plant. In this study, we analyzed the structure and assembly process of fungi and bacteria on the peanut. We also performed metagenome analysis to assess the relationships between functional genes and metabolic pathways in the microorganisms, aflatoxin and biogeography. Finally, our data showed that inoculation of beneficial microorganisms isolated from the healthy peanut-associated microbiome could significantly inhibit the enrichment of A. flavus and the production of aflatoxin in inoculated plants. Our results indicate that biogeography can significantly influence the assembly process of microorganisms, the activation of functional genes and metabolic pathways, the enrichment of aflatoxin-producing fungi. Manipulation of the peanut-associated microbiome, for instance, by inoculating peanut with beneficial strains, has potential to promote plant health. This will provide us with new ideas and perspectives on the early warning and effective prevention and control of aflatoxin contamination in agricultural products.

Life-Long Hyperbilirubinemia Exposure and Bilirubin Priming Prevent In Vitro Metabolic Damage

Background: Unconjugated bilirubin (UCB) is more than the final product of heme catabolism. Mildly elevated systemic bilirubin concentrations, such as in Gilbert syndrome (GS), protect against various oxidative stress-mediated and metabolic diseases, including cardiovascular disease, type 2 diabetes mellitus, metabolic syndrome, cancer, and age-related disease. The Gunn rat is an animal model of hereditary hyperbilirubinemia widely used in assessing the effect of high serum bilirubin concentration in various organs. The present work aims to understand if life-long hyperbilirubinemia and bilirubin-priming might contribute to protection against atherosclerosis and diabetic nephropathy (DN) at the cellular level. Methods: Primary aortic endothelial cells and podocytes obtained from hyperbilirubinemic homozygous jj and normobilirubinemic heterozygous Nj Gunn rats were exposed to Palmitic Acid (PA) and Angiotensin II (Ang II), respectively, and the effects on cell viability and the activation of damage-related metabolic pathways evaluated. Results were validated on immortalized H5V and HK2 cells exposed to damage after UCB pretreatment. Results: In both primary cell models, cells obtained from jj Gunn rats showed as significantly higher than Nj Gunn rats at any dose of the toxic agent. Reduction in CHOP expression and IL-6 release was observed in jj primary aortic endothelial cells exposed to PA compared to Nj cells. The same occurred on H5V pretreated with Unconjugated bilirubin. Upon Ang II treatment, primary podocytes from jj Gunn rats showed lower DNA fragmentation, cleaved caspase-3, and cleaved PARP induction than primary podocytes from Nj Gunn rats. In HK2 cells, the induction by Ang II of HIF-1α and LOXl2 was significantly reduced by UCB pretreatment. Conclusion: Our data suggest that in models of atherosclerosis and DN life–long hyperbilirubinemia exposure or bilirubin-priming significantly contribute to decrease the injury by enhancing thecellular defensive response,

A8 DIETARY TRYPTOPHAN MODULATES KYNURENINE AND INDOLE PRODUCTION IN HEALTHY INDIVIDUALS

Abstract Background Tryptophan is an essential amino acid that is transformed by host and gut microbial enzymes into multiple bioactive metabolites that regulate immunity, mood and circadian rhythms. In particular, indoles, produced by gut bacterial metabolism of tryptophan, have recently gained central attention. Indoles are activators of the aryl hydrocarbon receptor (AhR), which is crucial for the maintenance of intestinal homeostasis and immunity. Tryptophan supplementation in fortified foods have been advocated to prevent chronic inflammatory conditions, from autism to chronic inflammation. However, whether dietary tryptophan supplementation affects immune function, tryptophan metabolic pathways and gastrointestinal symptoms in healthy subjects, is unknown. Aims To assess whether tryptophan supplementation, in healthy subjects on a low tryptophan diet, induces changes in microbiota-derived metabolites (indoles), host cytokine production or gut symptoms. Methods We performed a randomized, double blind, placebo-controlled, crossover study in 20 healthy individuals, between 18 and 75 years old, following a regular diet. Subjects were instructed to start a standardized low tryptophan diet and were randomly assigned to a 3-week tryptophan supplement (3gr/day) or placebo. After a 2-week washout period, subjects were crossed over to the opposite 3-week intervention arm. Self-administered questionnaires (GSRS, DASS21 and HADS) were used to assess gastrointestinal symptoms and mood/anxiety/stress. Stool, urine and blood samples were collected to measure tryptophan metabolites (kynurenine pathway and indoles) and cytokines. Results Supplementation of tryptophan was well tolerated and no changes in gastrointestinal symptoms or mood/anxiety were found. Compared with placebo, tryptophan supplementation increased urinary and plasma levels of indoleamine 2,3-dioxygenase (p= 0.002 and p= 0.02, respectively), a key enzyme in the kynurenine pathway, and of several indoles (p= 0.0008 and p= 0.01, respectively), suggestive of activation of microbial and host metabolic pathways. However, there were no measurable changes in the host cytokine production. There was a positive correlation between fecal kynurenine levels and anxiety and depression scores, suggesting that microbial metabolites may impact host behavior in humans. Conclusions Dietary tryptophan supplementation in healthy individuals was safe and had a measurable effect on microbial and host metabolism, mainly kynurenine and indole pathways, with known immunomodulatory properties. Although no effects on cytokine production were found, further studies are warranted to investigate tryptophan supplementation in disorders with altered AhR pathway, such as inflammatory bowel disease, metabolic syndrome and celiac disease. Funding Agencies None

Host-virus interaction and viral evasion.

With each infectious pandemic or outbreak, the medical community feels the need to revisit basic concepts of immunology to understand and overcome the difficult times brought about by these infections. Regarding viruses, they have historically been responsible for many deaths, and such a peculiarity occurs because they are known to be obligate intracellular parasites that depend upon the host's cell machinery for their replication. Successful infection with the production of essential viral components requires constant viral evolution as a strategy to manipulate the cellular environment, including host internal factors, the host's nonspecific and adaptive immune responses to viruses, the metabolic and energetic state of the infected cell, and changes in the intracellular redox environment during the viral infection cycle. Based on this knowledge, it is fundamental to develop new therapeutic strategies for controlling viral dissemination, by means of antiviral therapies, vaccines, or antioxidants, or by targeting the inhibition or activation of cell signaling pathways or metabolic pathways that are altered during infection. The rapid recovery of altered cellular homeostasis during viral infection is still a major challenge. Here, we review the strategies by which viruses evade the host's immune response and potential tools used to develop more specific antiviral therapies to cure, control, or prevent viral diseases.

Biomarkers of Oxidative Stress for Neonatal Lung Disease.

The transition from prenatal to postnatal life causes a significant increase in arterial oxygen tension and the activation of metabolic pathways enabling the newborn's adaptation to the extra-uterine environment. The balance between pro-oxidant and anti-oxidant systems is critical to preserve cellular functions. Indeed, oxidative stress (OS) occurs when the production of free radicals is not balanced by the activity of intracellular antioxidant systems, contributing to cellular and tissue damage. Perinatal OS may have serious health consequences during the postnatal period and later in life. Namely, OS has been recognized as the major cause of lung injury in newborns, especially those preterm born, due to their immature lung and antioxidant systems. The development of OS biomarkers has gained increasing research interest since they may provide useful insights about pathophysiological pathways underlying OS-mediated pulmonary diseases in newborns. Moreover, their implementation in clinical settings may help to early identify high risk-newborns and to provide targeted treatment. Ideally, a biomarker should demonstrate ease of use, biological validity and reproducibility, high sensitivity and specificity. However, none of the clinically validated biomarkers so far have been qualified for neonatal lung disease. Additionally, the complex technical procedures and the high cost of such determinations have hampered the use of OS biomarkers in clinical practice. This review aims to evaluate the current evidence on the application of biomarkers of oxidative stress for neonatal lung disease and exploring the most relevant issues affecting their implementation in practice, as well as the associated evidence gaps and research limitations.

Topography effect on Aspergillus flavus occurrence and aflatoxin B1 contamination associated with peanut.

Aflatoxin B1 is a strong carcinogenic and toxic fungal toxin produced by Aspergillus flavus and other Aspergillus species, and can seriously threaten the health of consumers and the safety and quality of agricultural products. Aspergillus in agricultural products are closely related to topography and symbiotic microbes. It is not fully clear that how topography affects the assembly process of A. flavus and symbiotic fungi on plant. In this study, we analyzed the structure and assembly process of fungi on the peanut. We also performed the metatranscriptome analysis, identified the functional genes and metabolic pathways enriched in both A. flavus and its symbiotic fungi. In our experiment, terrain and soil properties could significantly affect the gene expression of microbiome, A. flavus abundance and infection ability to peanuts. Meanwhile, the Permanova correlation analysis revealed that differentially expressed genes were strongly correlated with the soil physicochemical factors. Furthermore, metabolomic analysis identified the main metabolites associated with A. flavus and aflatoxin B1, the results proved that the terrain significantly affected the microorganisms associated with peanut pods to produce a variety of metabolites. In conclusion, our results indicate that topography can significantly influence the assembly process of A. flavus and microorganisms, the activation of functional genes and metabolic pathways, the enrichment of aflatoxin-producing fungi.

Pathophysiology of sepsis.

To provide a current overview of sepsis pathophysiology. The emphasis on sepsis pathophysiology has moved away from the pathogen - the initiating factor - and instead is focussed upon the abnormal and exaggerated host response. Instead of targeted eradication of the infection, the host response activates or suppresses multiple downstream pathways, leading to multiple organ dysfunction. Sepsis represents a dysregulated host response to infection leading to organ dysfunction. Here, the pathogen triggers an initial exaggerated inflammatory-immune response that leads to activation or suppression of multiple endothelial, hormonal, bioenergetic, metabolic, immune, and other pathways. These, in turn, produce the circulatory and metabolic perturbations resulting in organ dysfunction. This review will provide an overview of underlying mechanisms and propose that these processes, whereas superficially viewed as dysfunctional, may actually be adaptive/protective in the first instance, though spilling over into maladaptation/harm depending on the magnitude of the host response.

Cognitive analysis of metabolomics data for systems biology.

Cognitive computing is revolutionizing the way big data are processed and integrated, with artificial intelligence (AI) natural language processing (NLP) platforms helping researchers to efficiently search and digest the vast scientific literature. Most available platforms have been developed for biomedical researchers, but new NLP tools are emerging for biologists in other fields and an important example is metabolomics. NLP provides literature-based contextualization of metabolic features that decreases the time and expert-level subject knowledge required during the prioritization, identification and interpretation steps in the metabolomics data analysis pipeline. Here, we describe and demonstrate four workflows that combine metabolomics data with NLP-based literature searches of scientific databases to aid in the analysis of metabolomics data and their biological interpretation. The four procedures can be used in isolation or consecutively, depending on the research questions. The first, used for initial metabolite annotation and prioritization, creates a list of metabolites that would be interesting for follow-up. The second workflow finds literature evidence of the activity of metabolites and metabolic pathways in governing the biological condition on a systems biology level. The third is used to identify candidate biomarkers, and the fourth looks for metabolic conditions or drug-repurposing targets that the two diseases have in common. The protocol can take 1-4 h or more to complete, depending on the processing time of the various software used.

IDENTIFYING RELEVANT PATHWAYS AND BIOMARKERS IN CROHN’S DISEASE USING CONTEXTUALIZED METABOLIC NETWORK MODEL

Abstract Background Candidate markers for Crohn’s Disease (CD) may be identified via gene expression-based construction of metabolic networks (MN). These can computationally describe gene-protein-reaction associations for entire tissues and also predict the flux of reactions (rate of turnover of specific molecules via a metabolic pathway). Recon3D is the most comprehensive human MN to date. We used publicly available CD transcriptomic data along with Recon3D to identify metabolites as potential diagnostic and prognostic biomarkers. Methods Terminal ileal gene expression profiles (36,372 genes; 218 CD. 42 controls) from the RISK cohort (Risk Stratification and Identification of Immunogenetic and Microbial Markers of Rapid Disease Progression in Children with Crohn’s Disease) and their transcriptomic abundances were used. Recon3D was pruned to only include RISK dataset transcripts which determined metabolic reaction linkage with transcriptionally active genes. Flux balance analysis (FBA) was then run using RiPTiDe with context specific transcriptomic data to further constrain genes (Figure 1). RiPTiDe was independently run on transcriptomic data from both CD and controls. From the pruned and constricted MN obtained, reactions were extracted for further analysis. Results After applying the necessary constraints to modify Recon3D, 527 CD and 537 control reactions were obtained. Reaction comparison with a publicly available list of healthy small intestinal epithelial reactions (n=1282) showed an overlap of 80 CD and 84 control reactions. These were then further grouped based on their metabolic pathways. RiPTiDe identified context specific metabolic pathway activity without supervision and the percentage of forward, backward, and balanced reactions for each metabolic pathway (Figure 2). The metabolite concentrations in the small intestine was altered among CD patients. Notably, the citric acid cycle and malate-aspartate shuttle were affected, highlighting changes in mitochondrial metabolic pathways. This is illustrated by changes in the number of reactions at equilibrium between CD and control. Conclusions The results are relevant as cytosolic acetyl-CoA is needed for fatty acid synthesis and is obtained by removing citrate from the citric acid cycle. An intermediate removal from the cycle has significant cataplerotic effects. The malate-aspartate shuttle also allows electrons to move across the impermeable membrane in the mitochondria (fatty acid synthesis location). These findings are reported by previously published studies where gene expression for fatty acid synthesis is altered in CD patients along with mitochondrial metabolic pathway changes, resulting in altered cell homeostasis. In-depth analysis is currently underway with our work supporting the utility of potential metabolic biomarkers for CD diagnosis, management and improved care.

Comparing Stable Isotope Enrichment by Gas Chromatography with Time-of-Flight, Quadrupole Time-of-Flight, and Quadrupole Mass Spectrometry.

Stable isotope tracers are applied for in vivo and in vitro studies to reveal the activity of enzymes and intracellular metabolic pathways. Most often, such tracers are used with gas chromatography coupled to mass spectrometry (GC-MS) owing to its ease of operation and reproducible mass spectral databases. Differences in isotope tracer performance of the classic GC-quadrupole MS instrument and newer time-of-flight instruments are not well studied. Here, we used three commercially available instruments for the analysis of identical samples from a stable isotope labeling study that used [U-13C6] d-glucose to investigate the metabolism of the bacterium Rothia mucilaginosa with respect to 29 amino acids and hydroxyl acids involved in primary metabolism. The prokaryote R. mucilaginosa belongs to the family of Micrococcaceae and is present and metabolically active in the airways and sputum of cystic fibrosis patients. Overall, all three GC-MS instruments (low-resolution GC-SQ MS, low-resolution GC-TOF MS, and high-resolution GC-QTOF MS) can be used to perform stable isotope tracing studies for glycolytic intermediates, tricarboxylic acid (TCA) metabolites, and amino acids, yielding similar biological results, with high-resolution GC-QTOF MS offering additional capabilities to identify the chemical structures of unknown compounds that might show significant isotope enrichments in biological studies.