CFIm-mediated alternative polyadenylation remodels cellular signaling and miRNA biogenesis

The mammalian cleavage factor I (CFIm) has been implicated in alternative polyadenylation (APA) in a broad range of contexts, from cancers to learning deficits and parasite infections. To determine how the CFIm expression levels are translated into these diverse phenotypes, we carried out a multi-omics analysis of cell lines in which the CFIm25 (NUDT21) or CFIm68 (CPSF6) subunits were either repressed by siRNA-mediated knockdown or over-expressed from stably integrated constructs. We established that >800 genes undergo coherent APA in response to changes in CFIm levels, and they cluster in distinct functional classes related to protein metabolism. The activity of the ERK pathway traces the CFIm concentration, and explains some of the fluctuations in cell growth and metabolism that are observed upon CFIm perturbations. Furthermore, multiple transcripts encoding proteins from the miRNA pathway are targets of CFIm-dependent APA. This leads to an increased biogenesis and repressive activity of miRNAs at the same time as some 3′ UTRs become shorter and presumably less sensitive to miRNA-mediated repression. Our study provides a first systematic assessment of a core set of APA targets that respond coherently to changes in CFIm protein subunit levels (CFIm25/CFIm68). We describe the elicited signaling pathways downstream of CFIm, which improve our understanding of the key role of CFIm in integrating RNA processing with other cellular activities.

Author Correction: Analysis of human metabolism by reducing the complexity of the genome-scale models using redHUMAN

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Analysis of human metabolism by reducing the complexity of the genome-scale models using redHUMAN

Altered metabolism is associated with many human diseases. Human genome-scale metabolic models (GEMs) were reconstructed within systems biology to study the biochemistry occurring in human cells. However, the complexity of these networks hinders a consistent and concise physiological representation. We present here redHUMAN, a workflow for reconstructing reduced models that focus on parts of the metabolism relevant to a specific physiology using the recently established methods redGEM and lumpGEM. The reductions include the thermodynamic properties of compounds and reactions guaranteeing the consistency of predictions with the bioenergetics of the cell. We introduce a method (redGEMX) to incorporate the pathways used by cells to adapt to the medium. We provide the thermodynamic curation of the human GEMs Recon2 and Recon3D and we apply the redHUMAN workflow to derive leukemia-specific reduced models. The reduced models are powerful platforms for studying metabolic differences between phenotypes, such as diseased and healthy cells.

pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis

Summary

pyTFA and matTFA are the first published implementations of the original TFA paper. Specifically, they include explicit formulation of Gibbs energies and metabolite concentrations, which enables straightforward integration of metabolite concentration measurements.

Motivation

High-throughput analytic technologies provide a wealth of omics data that can be used to perform thorough analyses for a multitude of studies in the areas of Systems Biology and Biotechnology. Nevertheless, most studies are still limited to constraint-based Flux Balance Analyses (FBA), neglecting an important physicochemical constraint: thermodynamics. Thermodynamics-based Flux Analysis (TFA) in metabolic models enables the integration of quantitative metabolomics data to study their effects on the net-flux directionality of reactions in the network. In addition, it allows us to estimate how far each reaction operates from thermodynamic equilibrium, which provides critical information for guiding metabolic engineering decisions.

Results

We present a Python package (pyTFA) and a Matlab toolbox (matTFA) that implement TFA. We show an example of application on both a reduced and a genome-scale model of E. coli., and demonstrate TFA and data integration through TFA reduce the feasible flux space with respect to FBA.

Availability and implementation

Documented implementation of TFA framework both in Python (pyTFA) and Matlab (matTFA) are available on www.github.com/EPFL-LCSB/.

Supplementary information

Supplementary data are available at Bioinformatics online.

Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations

Large-scale kinetic models are used for designing, predicting, and understanding the metabolic responses of living cells. Kinetic models are particularly attractive for the biosynthesis of target molecules in cells as they are typically better than other types of models at capturing the complex cellular biochemistry. Using simpler stoichiometric models as scaffolds, kinetic models are built around a steady-state flux profile and a metabolite concentration vector that are typically determined via optimization. However, as the underlying optimization problem is underdetermined, even after incorporating available experimental omics data, one cannot uniquely determine the operational configuration in terms of metabolic fluxes and metabolite concentrations. As a result, some reactions can operate in either the forward or reverse direction while still agreeing with the observed physiology. Here, we analyze how the underlying uncertainty in intracellular fluxes and concentrations affects predictions of constructed kinetic models and their design in metabolic engineering and systems biology studies. To this end, we integrated the omics data of optimally grown Escherichia coli into a stoichiometric model and constructed populations of non-linear large-scale kinetic models of alternative steady-state solutions consistent with the physiology of the E. coli aerobic metabolism. We performed metabolic control analysis (MCA) on these models, highlighting that MCA-based metabolic engineering decisions are strongly affected by the selected steady state and appear to be more sensitive to concentration values rather than flux values. To incorporate this into future studies, we propose a workflow for moving towards more reliable and robust predictions that are consistent with all alternative steady-state solutions. This workflow can be applied to all kinetic models to improve the consistency and accuracy of their predictions. Additionally, we show that, irrespective of the alternative steady-state solution, increased activity of phosphofructokinase and decreased ATP maintenance requirements would improve cellular growth of optimally grown E. coli.

Discovery and Evaluation of Biosynthetic Pathways for the Production of Five Methyl Ethyl Ketone Precursors

The limited supply of fossil fuels and the establishment of new environmental policies shifted research in industry and academia toward sustainable production of the second generation of biofuels, with methyl ethyl ketone (MEK) being one promising fuel candidate. MEK is a commercially valuable petrochemical with an extensive application as a solvent. However, as of today, a sustainable and economically viable production of MEK has not yet been achieved despite several attempts of introducing biosynthetic pathways in industrial microorganisms. We used BNICE.ch as a retrobiosynthesis tool to discover all novel pathways around MEK. Out of 1325 identified compounds connecting to MEK with one reaction step, we selected 3-oxopentanoate, but-3-en-2-one, but-1-en-2-olate, butylamine, and 2-hydroxy-2-methylbutanenitrile for further study. We reconstructed 3 679 610 novel biosynthetic pathways toward these 5 compounds. We then embedded these pathways into the genome-scale model of E. coli, and a set of 18 622 were found to be the most biologically feasible ones on the basis of thermodynamics and their yields. For each novel reaction in the viable pathways, we proposed the most similar KEGG reactions, with their gene and protein sequences, as candidates for either a direct experimental implementation or as a basis for enzyme engineering. Through pathway similarity analysis we classified the pathways and identified the enzymes and precursors that were indispensable for the production of the target molecules. These retrobiosynthesis studies demonstrate the potential of BNICE.ch for discovery, systematic evaluation, and analysis of novel pathways in synthetic biology and metabolic engineering studies.

redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models

Genome-scale metabolic reconstructions have proven to be valuable resources in enhancing our understanding of metabolic networks as they encapsulate all known metabolic capabilities of the organisms from genes to proteins to their functions. However the complexity of these large metabolic networks often hinders their utility in various practical applications. Although reduced models are commonly used for modeling and in integrating experimental data, they are often inconsistent across different studies and laboratories due to different criteria and detail, which can compromise transferability of the findings and also integration of experimental data from different groups. In this study, we have developed a systematic semi-automatic approach to reduce genome-scale models into core models in a consistent and logical manner focusing on the central metabolism or subsystems of interest. The method minimizes the loss of information using an approach that combines graph-based search and optimization methods. The resulting core models are shown to be able to capture key properties of the genome-scale models and preserve consistency in terms of biomass and by-product yields, flux and concentration variability and gene essentiality. The development of these “consistently-reduced” models will help to clarify and facilitate integration of different experimental data to draw new understanding that can be directly extendable to genome-scale models.

Reduced models are used commonly to understand the metabolism of organisms and to integrate experimental data for many different studies such as physiology, fluxomics and metabolomics. Without consistent or clear criteria on how these reduced models are actually developed, it is difficult to ensure that they reflect the detailed knowledge that is kept in genome scale metabolic network models (GEMs). The redGEM algorithm presented here allows us to systematically develop consistently reduced metabolic models from their genome-scale counterparts. We applied redGEM for the construction of a core model for E. coli central carbon metabolism. We constructed the core model irJO1366 based on the latest genome-scale E. coli metabolic reconstruction (iJO1366). irJO1366 contains the central carbon pathways and other immediate pathways that must be connected to them for consistency with the iJO1366. irJO1366 can be used to understand metabolism of the organism and also to provide guidance for metabolic engineering purposes. The algorithm is also designed to be modular so that heterologous reactions or pathways can be appended to the core model akin to a “plug-and-play”, synthetic biology approach. The algorithm is applicable to any compartmentalized or non-compartmentalized GEM.

lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites

In the post-genomic era, Genome-scale metabolic networks (GEMs) have emerged as invaluable tools to understand metabolic capabilities of organisms. Different parts of these metabolic networks are defined as subsystems/pathways, which are sets of functional roles to implement a specific biological process or structural complex, such as glycolysis and TCA cycle. Subsystem/pathway definition is also employed to delineate the biosynthetic routes that produce biomass building blocks. In databases, such as MetaCyc and SEED, these representations are composed of linear routes from precursors to target biomass building blocks. However, this approach cannot capture the nested, complex nature of GEMs. Here we implemented an algorithm, lumpGEM, which generates biosynthetic subnetworks composed of reactions that can synthesize a target metabolite from a set of defined core precursor metabolites. lumpGEM captures balanced subnetworks, which account for the fate of all metabolites along the synthesis routes, thus encapsulating reactions from various subsystems/pathways to balance these metabolites in the metabolic network. Moreover, lumpGEM collapses these subnetworks into elementally balanced lumped reactions that specify the cost of all precursor metabolites and cofactors. It also generates alternative subnetworks and lumped reactions for the same metabolite, accounting for the flexibility of organisms. lumpGEM is applicable to any GEM and any target metabolite defined in the network. Lumped reactions generated by lumpGEM can be also used to generate properly balanced reduced core metabolic models.

Stoichiometric models have been used in the area of metabolic engineering and systems biology for many decades. The early examples of these models include simplified ad hoc built metabolic pathways, and biomass compositions. The development of genome scale models (GEMs) brought a standard to metabolic network modeling. However, the vast amount of detailed biochemistry in GEMs makes it necessary to develop methods to manage the complexity in them. In this study, we developed lumpGEM, a tool that can systematically identify subnetworks from metabolic networks that can perform certain tasks, such as biosynthesis of a biomass building block and any other target metabolite. By generating alternative subnetworks, lumpGEM also accounts for the redundancy in metabolic networks. We applied lumpGEM on latest E. coli GEM iJO1366 and identified subnetworks/lumped reactions for every biomass building block defined in its biomass formulation. We also compared the results from lumpGEM with existing knowledge in the literature. The lumped reactions generated by lumpGEM can be used to generate consistently reduced metabolic network models.

Exploring biochemical pathways for mono-ethylene glycol (MEG) synthesis from synthesis gas

Mono-ethylene glycol (MEG) is an important petrochemical with widespread use in numerous consumer products. The current industrial MEG-production process relies on non-renewable fossil fuel-based feedstocks, such as petroleum, natural gas, and naphtha; hence, it is useful to explore alternative routes of MEG-synthesis from gases as they might provide a greener and more sustainable alternative to the current production methods. Technologies of synthetic biology and metabolic engineering of microorganisms can be deployed for the expression of new biochemical pathways for MEG-synthesis from gases, provided that such promising alternative routes are first identified. We used the BNICE.ch algorithm to develop novel and previously unknown biological pathways to MEG from synthesis gas by leveraging the Wood-Ljungdahl pathway of carbon fixation of acetogenic bacteria. We developed a set of useful pathway pruning and analysis criteria to systematically assess thousands of pathways generated by BNICE.ch. Published genome-scale models of Moorella thermoacetica and Clostridium ljungdahlii were used to perform the pathway yield calculations and in-depth analyses of seven (7) newly developed biological MEG-producing pathways from gases, including CO₂, CO, and H₂. These analyses helped identify not only better candidate pathways, but also superior chassis organisms that can be used for metabolic engineering of the candidate pathways. The pathway generation, pruning, and detailed analysis procedures described in this study can also be used to develop biochemical pathways for other commodity chemicals from gaseous substrates.

Molecular thermodynamics of metabolism: quantum thermochemical calculations for key metabolites

The present work is the first of a series of papers aiming at a coherent and unified development of the thermodynamics of metabolism and the rationalization of feasibility analysis of metabolic pathways. The focus in this part is on high-level quantum chemical calculations of the thermochemical quantities of relatively heavy metabolites such as amino acids/oligopeptides, nucleosides, saccharides and their derivatives in the ideal gas state. The results of this study will be combined with the corresponding hydration/solvation results in subsequent parts of this work in order to derive the desired thermochemical quantities in aqueous solutions. The above metabolites exist in a vast conformational/isomerization space including rotational conformers, tautomers or anomers exhibiting often multiple or cooperative intramolecular hydrogen bonding. We examine the challenges posed by these features for the reliable estimation of thermochemical quantities. We discuss conformer search, conformer distribution and averaging processes. We further consider neutral metabolites as well as protonated and deprotonated metabolites. In addition to the traditional presentation of gas-phase acidities, basicities and proton affinities, we also examine heats and free energies of ionic species. We obtain simple linear relations between the thermochemical quantities of ions and the formation quantities of their neutral counterparts. Furthermore, we compare our calculations with reliable experimental measurements and predictive calculations from the literature, when available. Finally, we discuss the next steps and perspectives for this work.

Molecular thermodynamics of metabolism: hydration quantities and the equation-of-state approach

Comprehensive and consistent calculations of hydration quantities, including conformational contributions.

Heading in the right direction: thermodynamics-based network analysis and pathway engineering

Thermodynamics-based network analysis through the introduction of thermodynamic constraints in metabolic models allows a deeper analysis of metabolism and guides pathway engineering. The number and the areas of applications of thermodynamics-based network analysis methods have been increasing in the last ten years. We review recent applications of these methods and we identify the areas that such analysis can contribute significantly, and the needs for future developments. We find that organisms with multiple compartments and extremophiles present challenges for modeling and thermodynamics-based flux analysis. The evolution of current and new methods must also address the issues of the multiple alternatives in flux directionalities and the uncertainties and partial information from analytical methods.

Malignant fibrous histiocytoma of the trachea. Case report

Neoplasms of the trachea are rare. The fifth case of malignant fibrous histiocytoma that nearly obliterated the lumen is reported. It is one of the most frequent soft tissue sarcomas particularly in the extremities. It is very rare in the trachea. Treatment is mainly based on local resection. Postoperative radiotherapy seems of little value.

An unusual presentation: primary tuberculosis of the middle ear cleft

Tuberculosis rarely affects the middle ear cleft; therefore, except for those working in close association with respiratory physicians, the disease is a curiosity and not often considered in the differential diagnosis of otorrhea. The diagnosis is thus made too late, with resulting complications such as irreversible hearing loss and facial nerve paralysis. A case report and review of the literature are presented, emphasizing that tuberculosis should be considered in the differential diagnosis of chronic ear infection.

Pleomorphic adenoma of the septum

Pleomorphic adenoma, the most frequently seen tumour of the salivary glands, is extremely rare in the septum. In this publication a case of pleomorphic adenoma of the nasal septum is presented.

Wegener's granulomatosis: case report and review of the literature

The clinical manifestations of Wegener's granulomatosis (WG) may be varied and easily overlooked. Awareness of distinguishing signs and symptoms allows early recognition and appropriate management. The body of literature dealing with the various facets of this disorder has grown in the past few years. Development of new diagnostic markers and successful therapies has rekindled interest in this disease. To assure early diagnosis and optimal prognosis the physician must maintain a high index of suspicion for WG. Although introduction of immunosuppressive therapy has dramatically improved the course of this disorder, treatment-related morbidity is often profound.

Bronchial asthma in a patient with Usher syndrome: case report

The Usher syndrome is a recessively inherited disorder characterized by the associated deficits of sensorineural hearing impairment and a progressive retinal degeneration called retinitis pigmentosa. A case of Usher syndrome is reported in a 22-year-old atopic patient with asthma. To our knowledge, such an association has not been described previously in the literature.

Giant osteoma of the frontal sinus

Osteoma is the most common benign tumour of the nose and paranasal sinuses, and the frontal sinus is its most frequent location. This tumour may be discovered incidentally on radiographs, or may enlarge to produce symptoms and, rarely, complications referable to its location near the orbit and anterior cranial vault. A 61-year-old man presented with right proptosis was found to have a giant osteoma involving frontal sinus. The aetiology, presenting features, and treatment of this tumour are reviewed.

Myxoma of the mandible

Myxoma is a rare bone tumor of the jaws. The exact aetiology and pathogenesis of this tumor still remains obscure. The tumor is frequently seen in young adults and in the mandible. Enucleation or local curetting have been recommended in the literature as the treatments of choice, although some authors have suggested more radical procedures because of the recurrences. In this paper a case of myxoma of the mandible and a review of the literature is presented.

Blindness after intranasal ethmoidectomy

Orbital haemorrhage is an unusual and frustrating complication of ethmoid surgery. A case of reversible blindness which was due to intra-operative orbital haemorrhage occurring after intranasal ethmoidectomy is presented. Prevention and management of this kind of blindness can be reversed, if treated aggressively.

An endodermal sinus tumor of the head and neck region

A 2-year-old patient with a recurrent endodermal sinus tumor of the nasopharynx is presented. After the first attempt to surgically excise the tumor it recurred, causing upper airway obstruction within 2 months. Combined treatment with surgery, radiotherapy and chemotherapy resulted in a disease-free survival of four years.

Ameloblastic fibrosarcoma

A case of an ameloblastic fibrosarcoma in the mandible is described. The primary tumor was seen in a 5-year-old child. In spite of repeated surgical interventions, the tumor recurred three times within a one and a half year period, but not metastases have been observed. The difficulties in arriving at a correct diagnosis for this rare tumor involving the mandible are discussed. The treatment of choice seems to be radical surgery.

Biotinidase deficiency: a rare cause of laryngeal stridor

A case of a child with a biotinidase deficiency who had a laryngeal stridor as a leading symptom is presented. This rare disease is distressing for diagnosis but easily treatable, if recognized. This condition, unless suspect clinically, could easily be overlooked and unnecessary tracheotomy could be done.

Tuberculosis of the parotid salivary gland

An interesting and rare case of tuberculosis involving a parotid gland is discussed. Although pulmonary tuberculosis is not uncommon in Turkey, primary parotid gland involvement is rare. The patient was treated by parotidectomy and antituberculous chemotherapy.

Quantitative 99mTc-DTPA scintigraphy for determination of maxillary sinus drainage following Caldwell-Luc surgery

Nine maxillary sinuses of 8 patients who had undergone Caldwell-Luc surgery (CWL) were injected with 100-125 microCi 99mTc-DTPA in 0.2 ml from the gingivo-buccal sulcus, passing through the canine fossa window. Sinus half-emptying times and percent contribution of the natural ostium (NO) and the naso-antral window (NA) to the clearance from the sinus were calculated, using time-activity curves as well as the activity of cotton wool plugs placed into the middle and lower conchae. Mean half-emptying times in patients in whom the mucosa had been removed were shorter than those in patients in whom it had been left in place. In the former group percent drainage through the NO was higher than that through the NA whereas in the latter group the opposite was the case. These findings are consistent with the thesis that if the mucosa is retained, the cilia continue their sweeping action towards the NO but if it is removed the NA gains importance in the drainage. This method is promising for the evaluation of maxillary sinus drainage following CWL.

Quantitative 99mTc-DTPA Scintigraphy for Determination of Maxillary Sinus Drainage following Caldwell-Luc Surgery

Nine maxillary sinuses of 8 patients who had undergone Caldwell-Luc surgery (CWL) were injected with 100-125 µCi 99mTc-DTPA in 0.2 ml from the gingivobuccal sulcus, passing through the canine fossa window. Sinus half-emptying times and percent contribution of the natural ostium (NO) and the nasoantral window (NA) to the clearance from the sinus were calculated, using time-activity curves as well as the activity of cotton wool plugs placed into the middle and lower conchae. Mean half-emptying times in patients in whom the mucosa had been removed were shorter than those in patients in whom it had been left in place. In the former group percent drainage through the NO was higher than that through the NA whereas in the latter group the opposite was the case. These findings are consistent with the thesis that if the mucosa is retained, the ciliae continue their sweeping action towards the NO but if it is removed the NA gains importance in the drainage. This method is promising for the evaluation of maxillary sinus drainage following CWL.