Transcriptional Regulation of Human and Rat Hepatic Lipid Metabolism by the Grapefruit Flavonoid Naringenin: Role of PPARα, PPARγ and LXRα

Disruption of lipid and carbohydrate homeostasis is an important factor in the development of prevalent metabolic diseases such as diabetes, obesity, and atherosclerosis. Therefore, small molecules that could reduce insulin dependence and regulate dyslipidemia could have a dramatic effect on public health. The grapefruit flavonoid naringenin has been shown to normalize lipids in diabetes and hypercholesterolemia, as well as inhibit the production of HCV. Here, we demonstrate that naringenin regulates the activity of nuclear receptors PPARα, PPARγ, and LXRα. We show it activates the ligand-binding domain of both PPARα and PPARγ, while inhibiting LXRα in GAL4-fusion reporters. Using TR-FRET, we show that naringenin is a partial agonist of LXRα, inhibiting its association with Trap220 co-activator in the presence of TO901317. In addition, naringenin induces the expression of PPARα co-activator, PGC1α. The flavonoid activates PPAR response element (PPRE) while suppressing LXRα response element (LXRE) in human hepatocytes, translating into the induction of PPAR-regulated fatty acid oxidation genes such as CYP4A11, ACOX, UCP1 and ApoAI, and inhibition of LXRα-regulated lipogenesis genes, such as FAS, ABCA1, ABCG1, and HMGR. This effect results in the induction of a fasted-like state in primary rat hepatocytes in which fatty acid oxidation increases, while cholesterol and bile acid production decreases. Our findings explain the myriad effects of naringenin and support its continued clinical development. Of note, this is the first description of a non-toxic, naturally occurring LXRα inhibitor

Real-time monitoring of metabolic function in liver-on-chip microdevices tracks the dynamics of mitochondrial dysfunction

Microfluidic organ-on-a-chip technology aims to replace animal toxicity testing, but thus far has demonstrated few advantages over traditional methods. Mitochondrial dysfunction plays a critical role in the development of chemical and pharmaceutical toxicity, as well as pluripotency and disease processes. However, current methods to evaluate mitochondrial activity still rely on end-point assays, resulting in limited kinetic and prognostic information. Here, we present a liver-on-chip device capable of maintaining human tissue for over a month in vitro under physiological conditions. Mitochondrial respiration was monitored in real time using two-frequency phase modulation of tissue-embedded phosphorescent microprobes. A computer-controlled microfluidic switchboard allowed contiguous electrochemical measurements of glucose and lactate, providing real-time analysis of minute shifts from oxidative phosphorylation to anaerobic glycolysis, an early indication of mitochondrial stress. We quantify the dynamics of cellular adaptation to mitochondrial damage and the resulting redistribution of ATP production during rotenone-induced mitochondrial dysfunction and troglitazone (Rezulin)-induced mitochondrial stress. We show troglitazone shifts metabolic fluxes at concentrations previously regarded as safe, suggesting a mechanism for its observed idiosyncratic effect. Our microfluidic platform reveals the dynamics and strategies of cellular adaptation to mitochondrial damage, a unique advantage of organ-on-chip technology

Efficient Recombinase-Mediated Cassette Exchange in hPSCs to Study the Hepatocyte Lineage Reveals AAVS1 Locus-Mediated Transgene Inhibition

Tools for rapid and efficient transgenesis in "safe harbor" loci in an isogenic context remain important to exploit the possibilities of human pluripotent stem cells (hPSCs). We created hPSC master cell lines suitable for FLPe recombinase-mediated cassette exchange (RMCE) in the AAVS1 locus that allow generation of transgenic lines within 15 days with 100% efficiency and without random integrations. Using RMCE, we successfully incorporated several transgenes useful for lineage identification, cell toxicity studies, and gene overexpression to study the hepatocyte lineage. However, we observed unexpected and variable transgene expression inhibition in vitro, due to DNA methylation and other unknown mechanisms, both in undifferentiated hESC and differentiating hepatocytes. Therefore, the AAVS1 locus cannot be considered a universally safe harbor locus for reliable transgene expression in vitro, and using it for transgenesis in hPSC will require careful assessment of the function of individual transgenes

Efficacy and safety of metabolic interventions for the treatment of severe COVID-19: in vitro, observational, and non-randomized open-label interventional study

Background: Viral infection is associated with a significant rewire of the host metabolic pathways, presenting attractive metabolic targets for intervention. Methods: We chart the metabolic response of lung epithelial cells to SARS-CoV-2 infection in primary cultures and COVID-19 patient samples and perform in vitro metabolism-focused drug screen on primary lung epithelial cells infected with different strains of the virus. We perform observational analysis of Israeli patients hospitalized due to COVID-19 and comparative epidemiological analysis from cohorts in Italy and the Veteran's Health Administration in the United States. In addition, we perform a prospective non-randomized interventional open-label study in which 15 patients hospitalized with severe COVID-19 were given 145 mg/day of nanocrystallized fenofibrate added to the standard of care. Results: SARS-CoV-2 infection produced transcriptional changes associated with increased glycolysis and lipid accumulation. Metabolism-focused drug screen showed that fenofibrate reversed lipid accumulation and blocked SARS-CoV-2 replication through a PPARα-dependent mechanism in both alpha and delta variants. Analysis of 3233 Israeli patients hospitalized due to COVID-19 supported in vitro findings. Patients taking fibrates showed significantly lower markers of immunoinflammation and faster recovery. Additional corroboration was received by comparative epidemiological analysis from cohorts in Europe and the United States. A subsequent prospective non-randomized interventional open-label study was carried out on 15 patients hospitalized with severe COVID-19. The patients were treated with 145 mg/day of nanocrystallized fenofibrate in addition to standard-of-care. Patients receiving fenofibrate demonstrated a rapid reduction in inflammation and a significantly faster recovery compared to patients admitted during the same period. Conclusions: Taken together, our data suggest that pharmacological modulation of PPARα should be strongly considered as a potential therapeutic approach for SARS-CoV-2 infection and emphasizes the need to complete the study of fenofibrate in large randomized controlled clinical trials. Funding: Funding was provided by European Research Council Consolidator Grants OCLD (project no. 681870) and generous gifts from the Nikoh Foundation and the Sam and Rina Frankel Foundation (YN). The interventional study was supported by Abbott (project FENOC0003). Clinical trial number: NCT04661930

Enhancement of Naringenin Bioavailability by Complexation with Hydroxypropoyl-β-Cyclodextrin

The abundant flavonoid aglycone, naringenin, which is responsible for the bitter taste in grapefruits, has been shown to possess hypolipidemic and anti-inflammatory effects both in vitro and in vivo. Recently, our group demonstrated that naringenin inhibits hepatitis C virus (HCV) production, while others demonstrated its potential in the treatment of hyperlipidemia and diabetes. However, naringenin suffers from low oral bioavailability critically limiting its clinical potential. In this study, we demonstrate that the solubility of naringenin is enhanced by complexation with β-cyclodextrin, an FDA approved excipient. Hydroxypropoyl-β-cyclodextrin (HPβCD), specifically, increased the solubility of naringenin by over 400-fold, and its transport across a Caco-2 model of the gut epithelium by 11-fold. Complexation of naringenin with HPβCD increased its plasma concentrations when fed to rats, with AUC values increasing by 7.4-fold and Cmax increasing 14.6-fold. Moreover, when the complex was administered just prior to a meal it decreased VLDL levels by 42% and increased the rate of glucose clearance by 64% compared to naringenin alone. These effects correlated with increased expression of the PPAR co-activator, PGC1α in both liver and skeletal muscle. Histology and blood chemistry analysis indicated this route of administration was not associated with damage to the intestine, kidney, or liver. These results suggest that the complexation of naringenin with HPβCD is a viable option for the oral delivery of naringenin as a therapeutic entity with applications in the treatment of dyslipidemia, diabetes, and HCV infection.National Institute of Diabetes and Digestive and Kidney Diseases (U.S.) (K01DK080241)Harvard Clinical Nutrition Research Center (P30-DK040561)European Research Council (Starting Grant (TMIHCV 242699))Massachusetts General Hospital (BioMEMS Resource Center (P41 EB-002503))Alexander Silberman Institute of Life Science

Outcomes in patients with gunshot wounds to the brain.

Introduction:Gunshot wounds to the brain (GSWB) confer high lethality and uncertain recovery. It is unclear which patients benefit from aggressive resuscitation, and furthermore whether patients with GSWB undergoing cardiopulmonary resuscitation (CPR) have potential for survival or organ donation. Therefore, we sought to determine the rates of survival and organ donation, as well as identify factors associated with both outcomes in patients with GSWB undergoing CPR. Methods:We performed a retrospective, multicenter study at 25 US trauma centers including dates between June 1, 2011 and December 31, 2017. Patients were included if they suffered isolated GSWB and required CPR at a referring hospital, in the field, or in the trauma resuscitation room. Patients were excluded for significant torso or extremity injuries, or if pregnant. Binomial regression models were used to determine predictors of survival/organ donation. Results:825 patients met study criteria; the majority were male (87.6%) with a mean age of 36.5 years. Most (67%) underwent CPR in the field and 2.1% (n=17) survived to discharge. Of the non-survivors, 17.5% (n=141) were considered eligible donors, with a donation rate of 58.9% (n=83) in this group. Regression models found several predictors of survival. Hormone replacement was predictive of both survival and organ donation. Conclusion:We found that GSWB requiring CPR during trauma resuscitation was associated with a 2.1% survival rate and overall organ donation rate of 10.3%. Several factors appear to be favorably associated with survival, although predictions are uncertain due to the low number of survivors in this patient population. Hormone replacement was predictive of both survival and organ donation. These results are a starting point for determining appropriate treatment algorithms for this devastating clinical condition. Level of evidence:Level II

A conceptual framework for crop-based agri-food supply chain characterization under uncertainty

[EN] Crop-based Agri-food Supply Chains (AFSCs) are complex systems that face multiple sources of uncertainty that can cause a significant imbalance between supply and demand in terms of product varieties, quantities, qualities, customer requirements, times and prices, all of which greatly complicate their management. Poor management of these sources of uncertainty in these AFSCs can have negative impact on quality, safety, and sustainability by reducing the logistic efficiency and increasing the waste. Therefore, it becomes crucial to develop models in order to deal with the key sources of uncertainty. For this purpose, it is necessary to precisely understand and define the problem under study. Even, the characterisation process of this domains is also a difficult and time-consuming task, especially when the right directions and standards are not in place. In this chapter, a Conceptual Framework is proposed that systematically collects those aspects that are relevant for an adequate crop-based AFSC management under uncertainty.Authors of this publication acknowledge the contribution of the Project 691249, RUC-APS "Enhancing and implementing Knowledge based ICT solutions within high Risk and Uncertain Conditions for Agriculture Production Systems" (www.ruc-aps.eu), funded by the European Union under their funding scheme H2020-MSCA-RISE-2015Alemany Díaz, MDM.; Esteso, A.; Ortiz Bas, Á.; Hernández Hormazabal, JE.; Fernández, A.; Garrido, A.; Martin, J.... (2021). A conceptual framework for crop-based agri-food supply chain characterization under uncertainty. Studies in Systems, Decision and Control. 280:19-33. https://doi.org/10.1007/978-3-030-51047-3_2S1933280Taylor, D.H., Fearne, A.: Towards a framework for improvement in the management of demand in agri-food supply chains. Supply Chain Manage. 11, 379–384 (2006)Matopoulos, A., Vlachopoulou, M., Manthou, V., Manos, B.: A conceptual framework for supply chain collaboration: empirical evidence from the agri-food industry. Supply Chain Manage. 12, 177–186 (2007)Ahumada, O., Villalobos, J.R.: Application of planning models in the agri-food supply chain: a review. Eur. J. Oper. Res. 196, 1–20 (2009)Iakovou, E., Vlachos, D., Achillas, C., Anastasiadis, F.: A methodological framework for the design of green supply chains for the agrifood sector. Paper presented at the 2nd international conference on supply chains, Katerini, 5–7 Oct 2012Manzini, R., Accorsi, R.: The new conceptual framework for food supply chain assessment. J. Food Eng. 115, 251–263 (2013)Shukla, M., Jharkharia, S.: Agri-fresh produce supply chain management: a state-of-the-art literature review. Int. J. Oper. Prod. Manage. 33, 114–158 (2013)Lemma, Y., Kitaw, D., Gatew, G.: Loss in perishable food supply chain: an optimization approach literature review. Int. J. Sci. Eng. Res. 5, 302–311 (2014)Tsolakis, N.K., Keramydas, C.A., Toka, A.K., Aidonis, D.A., Iakovou, E.T.: Agrifood supply chain management: a comprehensive hierarchical decision-making framework and a critical taxonomy. Biosyst. Eng. 120, 47–64 (2014)Van der Vorst, J.G., Da Silva, C.A., Trienekens, J.H.: Agro-industrial Supply Chain Management: Concepts and Applications. FAO (2007)Hernandez, J., Mortimer, M., Patelli, E., Liu, S., Drummond, C., Kehr, E., Calabrese, N., Iannacone, R., Kacprzyk, J., Alemany, M.M.E., Gardner, D.: RUC-APS: enhancing and implementing knowledge based ICT solutions within high risk and uncertain conditions for agriculture production systems. In: 11th International Conference on Industrial Engineering and Industrial Management, Valencia, Spain (2017)Miles, M.B., Huberman, A.M.: Qualitative Data Analysis: An Expanded Sourcebook. Sage Publications, Thousand Oaks (1994)Alemany, M.M.E., Alarcón, F., Lario, F.C., Boj, J.J.: An application to support the temporal and spatial distributed decision-making process in supply chain collaborative planning. Comput. Ind. 62, 519–540 (2011)Teimoury, E., Nedaei, H., Ansari, S., Sabbaghi, M.: A multi-objective analysis for import quota policy making in a perishable fruit and vegetable supply chain: a system dynamics approach. Comput. Electron. Agric. 93, 37–45 (2013)Kusumastuti, R.D., van Donk, D.P., Teunter, R.: Crop-related harvesting and processing planning: a review. Int. J. Prod. Econ. 174, 76–92 (2016)Zhang, W., Wilhelm, W.E.: OR/MS decision support models for the specialty crops industry: a literature review. Ann. Oper. Res. 190, 131–148 (2011)Grillo, H., Alemany, M.M.E., Ortiz, A.: A review of mathematical models for supporting the order promising process under lack of homogeneity in product and other sources of uncertainty. Comput. Ind. Eng. 91, 239–261 (2016)Blanco, A.M., Masini, G., Petracci, N., Bandoni, J.A.: Operations management of a packaging plant in the fruit industry. J. Food Eng. 70, 299–307 (2005)Grillo, H., Alemany, M.M.E., Ortiz, A., Fuertes-Miquel, V.S.: Mathematical modelling of the order-promising process for fruit supply chains considering the perishability and subtypes of products. Appl. Math. Model. 49, 255–278 (2017)Verdouw, C.N., Beulens, A.J.M., Trienekens, J.H., Wolferta, J.: Process modelling in demand-driven supply chains: a reference model for the fruit industry. Comput. Electron. Agric. 73, 174–187 (2010)Amorim, P., Günther, H., Almada-Lobo, B.: Multi-objective integrated production and distribution planning of perishable products. Int. J. Prod. Econ. 138, 89–101 (2012)Nahmias, S.: Perishable inventory theory: a review. Oper. Res. 30, 680–708 (1982)Mowat, A., Collins, R.: Consumer behavior and fruit quality: supply chain management in an emerging industry. Supply Chain Manage. 5, 45–54 (2000)Kazaz, B., Webster, S.: The impact of yield-dependent trading costs on pricing and production planning under supply uncertainty. M&SOM Manuf. Serv. Oper. Manage. 13, 404–417 (2011)Van der Vorst, J.G.: Effective food supply chains: generating, modelling and evaluating supply chain scenarios (2000)Fuertes-Miquel, V.S., Cuenca, L., Boza, A., Guyon, C., Alemany, M.M.E.: Conceptual framework for the characterization of vegetable breton supply chain sustainability in an uncertain context. In: 12th International Conference on Industrial Engineering and Industrial Management, XXII Congreso de Ingeniería de Organización, Girona, Spain, 12–13 July 2018Kummu, M., de Moel, H., Porkka, M., Siebert, S., Varis, O., Ward, P.J.: Lost food, wasted resources: global food supply chain losses and their impacts on freshwater, cropland, and fertiliser use. Sci. Total Environ. 438, 477–489 (2012)Hoekstra, S., Romme, J.: Integral Logistic Structures: Developing Customer-Oriented Goods Flow. Industrial Press Inc., New York (1992)Borodin, V., Bourtembourg, J., Hnaien, F., Labadie, N.: Handling uncertainty in agricultural supply chain management: a state of the art. Eur. J. Oper. Res. 254, 348–359 (2016)Handayati, Y., Simatupang, T.M., Perdana, T.: Agri-food supply chain coordination: the state-of-the-art and recent developments. Logist. Res. 8, 1–15 (2015)Mintzberg, H.: The Structuring of Organisations. Prentice-Hall, Upper Saddle River (1979)Keuning, D.: Grondslagen Van Het Management. Stenfert Kroese, Houten (1995) (in Dutch)Esteso, A., Alemany, M.M.E., Ortiz, A.: Conceptual framework for designing agri-food supply chains under uncertainty by mathematical programming models. Int. J. Prod. Res. (2018)Backus, G.B.C., Eidman, V.R., Dijkhuizen, A.A.: Farm decision making under risk and uncertainty. Neth. J. Agr. Sci. 45, 307–328 (1997)Esteso, A., Alemany, M.M.E., Ortiz, A.: Conceptual framework for managing uncertainty in a collaborative agri-food supply chain context. In: IFIP Advances in Information and Communication Technology, vol. 506, pp. 715–724 (2017)Mundi, I., Alemany, M.M.E., Poler, R., Fuertes-Miquel, V.S.: Review of mathematical models for production planning under uncertainty due to lack of homogeneity: proposal of a conceptual model. Int. J. Prod. Res. (2019)Grillo, H., Alemany, M.M.E., Ortiz, A., De Baets, B.: Possibilistic compositions and state functions: application to the order promising process for perishables. Int. J. Prod. Res. (2019)Soto-Silva, W.E., Nadal-Roig, E., González-Araya, M.C., Pla-Aragones, L.M.: Operational research models applied to the fresh fruit supply chain. Eur. J. Oper. Res. 251, 345–355 (2016)Farahani, R.Z., Rezapour, S., Drezner, T., Fallah, S.: Competitive supply chain network design: an overview of classifications, models, solution techniques and applications. Omega 45, 92–118 (2014)Banasik, A., Bloemhof-Ruwaard, J.M., Kanellopoulos, A., Claassen, G.D.H., van der Vorst, J.G.: Multi-criteria decision making approaches for green supply chains: a review. Flex. Serv. Manuf. J. 1–31 (2016)Paam, P., Berretta, R., Heydar, M., Middleton, R.H., García-Flores, R., Juliano, P.: Planning models to optimize the agri-fresh food supply chain for loss minimization: a review. In: Reference Module in Food Science (2016)Soysal, M., Bloemhof-Ruwaard, J.M., Meuwissen, M.P., van der Vorst, J.G.: A review on quantitative models for sustainable food logistics management. Int. J. Food Syst. Dyn. 3, 136–155 (2012

Integrating transposable elements in the 3D genome

Chromosome organisation is increasingly recognised as an essential component of genome regulation, cell fate and cell health. Within the realm of transposable elements (TEs) however, the spatial information of how genomes are folded is still only rarely integrated in experimental studies or accounted for in modelling. Whilst polymer physics is recognised as an important tool to understand the mechanisms of genome folding, in this commentary we discuss its potential applicability to aspects of TE biology. Based on recent works on the relationship between genome organisation and TE integration, we argue that existing polymer models may be extended to create a predictive framework for the study of TE integration patterns. We suggest that these models may offer orthogonal and generic insights into the integration profiles (or "topography") of TEs across organisms. In addition, we provide simple polymer physics arguments and preliminary molecular dynamics simulations of TEs inserting into heterogeneously flexible polymers. By considering this simple model, we show how polymer folding and local flexibility may generically affect TE integration patterns. The preliminary discussion reported in this commentary is aimed to lay the foundations for a large-scale analysis of TE integration dynamics and topography as a function of the three-dimensional host genome

Modulation of pain perception by transcranial magnetic stimulation of left prefrontal cortex

Evidence by functional imaging studies suggests the role of left dorsolateral prefrontal cortex (DLPFC) in the inhibitory control of nociceptive transmission system. Repetitive transcranial magnetic stimulation (rTMS) is able to modulate pain response to capsaicin. In the present study, we evaluated the effect of DLPFC activation (through rTMS) on nociceptive control in a model of capsaicin-induced pain. The study was performed on healthy subjects that underwent capsaicin application on right or left hand. Subjects judged the pain induced by capsaicin through a 0–100 VAS scale before and after 5 Hz rTMS over left and right DLPFC at 10 or 20 min after capsaicin application in two separate groups (8 subjects each). Left DLPFC-rTMS delivered either at 10 and 20 min after capsaicin application significantly decreased spontaneous pain in both hands. Right DLPFC rTMS showed no significant effect on pain measures. According to these results, stimulation of left DLPFC seems able to exert a bilateral control on pain system, supporting the critical antinociceptive role of such area. This could open new perspectives to non-invasive brain stimulation protocols of alternative target area for pain treatment