33 results on '"Uygun, Korkut"'
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2. Effect of Donor Age and Liver Steatosis on Potential of Decellularized Liver Matrices to be used as a Platform for iPSC‐Hepatocyte Culture
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Acun, Aylin, Fan, Letao, Oganesyan, Ruben, Uygun, Korkut M., Yeh, Heidi, Yarmush, Martin L., and Uygun, Basak E.
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Decellularization of discarded whole livers and their recellularization with patient‐specific induced pluripotent stem cells (iPSCs) to develop a functional organ is a promising approach to increasing the donor pool. The effect of extracellular matrix (ECM) of marginal livers on iPSC‐hepatocyte differentiation and function has not been shown. To test the effect of donor liver ECM age and steatosis, young and old, as well as no, low, and high steatosis livers, are decellularized. All livers are decellularized successfully. High steatosis livers have fat remaining on the ECM after decellularization. Old donor liver ECM induces lower marker expression in early differentiation stages, compared to young liver ECM, while this difference is closed at later stages and do not affect iPSC‐hepatocyte function significantly. High steatosis levels of liver ECM lead to higher albumin mRNA expression and secretion while at later stages of differentiation expression of major cytochrome (CYP) 450 enzymes is highest in low steatosis liver ECM. Both primary human hepatocytes and iPSC‐hepatocytes show an increase in fat metabolism marker expression with increasing steatosis levels most likely induced by excess fat remaining on the ECM. Overall, removal of excess fat from liver ECM may be needed for inducing proper hepatic function after recellularization. Human livers from young and old donors, as well as donor livers with no, low, and high steatosis, are decellularized and the resulting matrix is used as a hydrogel (human decellularized liver matrix, hDLM) for induced pluripotent stem cell culture and differentiation. Differentiation efficiency for all groups at different stages and fat metabolism markers of cells cultured with hDLM with varying levels of steatosis are analyzed.
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- 2024
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3. Optimal Temperature Protocols for Liver Machine Perfusion Using a Monte Carlo Method
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Lucia, Angelo and Uygun, Korkut
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Monte Carlo simulation with a novel acceptance procedure is used to find optimal temperature profiles for liver machine perfusion. Numerical results for MC simulation are compared to a greedy approach and to current practice in machine perfusion research. Results show that the proposed Monte Carlo simulation approach finds optimal temperature profiles that agree with current clinical research practice.
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- 2022
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4. Multiorgan Metabolomics and Lipidomics Provide New Insights Into Fat Infiltration in the Liver, Muscle Wasting, and Liver–Muscle Crosstalk Following Burn Injury
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Mert, Safak, Bulutoglu, Beyza, Chu, Christopher, Dylewski, Maggie, Lin, Florence M, Yu, Yong-Ming, Yarmush, Martin L, Sheridan, Robert L, and Uygun, Korkut
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Burn injury mediated hypermetabolic syndrome leads to increased mortality among severe burn victims, due to liver failure and muscle wasting. Metabolic changes may persist up to 2 years following the injury. Thus, understanding the underlying mechanisms of the pathology is crucially important to develop appropriate therapeutic approaches. We present detailed metabolomic and lipidomic analyses of the liver and muscle tissues in a rat model with a 30% body surface area burn injury located at the dorsal skin. Three hundred and thirty-eight of 1587 detected metabolites and lipids in the liver and 119 of 1504 in the muscle tissue exhibited statistically significant alterations. We observed excessive accumulation of triacylglycerols, decreased levels of S-adenosylmethionine, increased levels of glutamine and xenobiotics in the liver tissue. Additionally, the levels of gluconeogenesis, glycolysis, and tricarboxylic acid cycle metabolites are generally decreased in the liver. On the other hand, burn injury muscle tissue exhibits increased levels of acyl-carnitines, alpha-hydroxyisovalerate, ophthalmate, alpha-hydroxybutyrate, and decreased levels of reduced glutathione. The results of this preliminary study provide compelling observations that liver and muscle tissues undergo distinctly different changes during hypermetabolism, possibly reflecting liver–muscle crosstalk. The liver and muscle tissues might be exacerbating each other’s metabolic pathologies, via excessive utilization of certain metabolites produced by each other.
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- 2021
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5. Twenty-four hour ex-vivo normothermic machine perfusion in rat livers
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Haque, Omar, Pendexter, Casie A., Cronin, Stephanie E. J., Raigani, Siavash, de Vries, Reiner J., Yeh, Heidi, Markmann, James F., and Uygun, Korkut
- Abstract
Ex-vivo liver perfusion (EVLP) is an ideal platform to study liver disease, therapeutic interventions, and pharmacokinetic properties of drugs without any patient risk. Rat livers are an ideal model for EVLP due to less organ quality variability, ease of hepatectomy, well-defined molecular pathways, and relatively low costs compared to large animal or human perfusions. However, the major limitation with rat liver normothermic machine perfusion (NMP) is maintaining physiologic liver function on an ex-vivo machine perfusion system. To address this need, our research demonstrates 24-hour EVLP in rats under normothermic conditions. Early (6 hour) perfusate transaminase levels and oxygen consumption of the liver graft are shown to be good markers of perfusion success and correlate with viable 24-hour post-perfusion histology. Finally, we address overcoming challenges in long-term rat liver perfusions such as rising intrahepatic pressures and contamination, and offer future directions necessary to build upon our work.
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- 2020
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6. Synthetic hemoglobin-based oxygen carriers are an acceptable alternative for packed red blood cells in normothermic kidney perfusion
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Aburawi, Mohamed M., Fontan, Fermin M., Karimian, Negin, Eymard, Corey, Cronin, Stephanie, Pendexter, Casie, Nagpal, Sonal, Banik, Peony, Ozer, Sinan, Mahboub, Paria, Delmonico, Francis L., Yeh, Heidi, Uygun, Korkut, and Markmann, James F.
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Normothermic machine perfusion presents a novel platform for pretransplant assessment and reconditioning of kidney grafts. Maintaining the metabolic activity of a preserved graft at physiologic levels requires an adequate oxygen supply, typically delivered by crystalloid solutions supplemented with red blood cells. In this study, we explored the feasibility of using a synthetic hemoglobin-based oxygen carrier (HBOC) in human kidney normothermic perfusion. Fourteen discarded human kidneys were perfused for 6 hours at a mean temperature of 37°C using a pressure-controlled system. Kidneys were perfused with a perfusion solution supplemented with either HBOC (n = 7) or packed red blood cells (PRBC) (n = 7) to increase oxygen-carrying capacity. Renal artery resistance, oxygen extraction, metabolic activity, energy stores, and histological features were evaluated. Throughout perfusion, kidneys from both groups exhibited comparable behavior regarding vascular flow (P= .66), oxygen consumption (P= .88), and reconstitution of tissue adenosine triphosphate (P= .057). Lactic acid levels were significantly higher in kidneys perfused with PRBC (P= .007). Histological findings were comparable between groups, and there was no evidence of histological damage caused by the HBOC. This feasibility experiment demonstrates that a HBOC solution can offer a logistically more convenient off-the-shelf alternative to PRBC in normothermic machine perfusion of human kidneys.
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- 2019
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7. Synthetic hemoglobin‐based oxygen carriers are an acceptable alternative for packed red blood cells in normothermic kidney perfusion
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Aburawi, Mohamed M., Fontan, Fermin M., Karimian, Negin, Eymard, Corey, Cronin, Stephanie, Pendexter, Casie, Nagpal, Sonal, Banik, Peony, Ozer, Sinan, Mahboub, Paria, Delmonico, Francis L., Yeh, Heidi, Uygun, Korkut, and Markmann, James F.
- Abstract
Normothermic machine perfusion presents a novel platform for pretransplant assessment and reconditioning of kidney grafts. Maintaining the metabolic activity of a preserved graft at physiologic levels requires an adequate oxygen supply, typically delivered by crystalloid solutions supplemented with red blood cells. In this study, we explored the feasibility of using a synthetic hemoglobin‐based oxygen carrier (HBOC) in human kidney normothermic perfusion. Fourteen discarded human kidneys were perfused for 6 hours at a mean temperature of 37°C using a pressure‐controlled system. Kidneys were perfused with a perfusion solution supplemented with either HBOC (n = 7) or packed red blood cells (PRBC) (n = 7) to increase oxygen‐carrying capacity. Renal artery resistance, oxygen extraction, metabolic activity, energy stores, and histological features were evaluated. Throughout perfusion, kidneys from both groups exhibited comparable behavior regarding vascular flow (P= .66), oxygen consumption (P= .88), and reconstitution of tissue adenosine triphosphate (P= .057). Lactic acid levels were significantly higher in kidneys perfused with PRBC (P= .007). Histological findings were comparable between groups, and there was no evidence of histological damage caused by the HBOC. This feasibility experiment demonstrates that a HBOC solution can offer a logistically more convenient off‐the‐shelf alternative to PRBC in normothermic machine perfusion of human kidneys. An acellular oxygen carrier performs similarly to packed red blood cells during normothermic machine perfusion of human kidneys.
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- 2019
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8. Bulk Droplet Vitrification: An Approach to Improve Large-Scale Hepatocyte Cryopreservation Outcome
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de Vries, Reinier J., Banik, Peony D., Nagpal, Sonal, Weng, Lindong, Ozer, Sinan, van Gulik, Thomas M., Toner, Mehmet, Tessier, Shannon N., and Uygun, Korkut
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Loss of hepatocyte viability and metabolic function after cryopreservation is still a major issue. Although vitrification is a promising alternative, it has generally been proven to be unsuitable for vitrification of large cell volumes which is required for clinical applications. Here, we propose a novel bulk droplet (3–5 mm diameter) vitrification method which allows high throughput volumes (4 mL/min), while using a low preincubated CPA concentration (15% v/v) to minimize toxicity and loss of cell viability and function. We used rapid (1.25 s) osmotic dehydration to concentrate a low preincubated intracellular CPA concentration ahead of vitrification, without the need of fully equilibrating toxic CPA concentrations. We compared direct postpreservation viability, long-term viability, and metabolic function of bulk droplet vitrified, cryopreserved, and fresh hepatocytes. Simulations and cooling rate measurements confirmed an adequate concentration of the intracellular CPA concentration (up to 8.53 M) after dehydration in combination with high cooling rates (960–1320 °C/min) for successful vitrification. In comparison to cryopreserved hepatocytes, bulk droplet vitrified hepatocytes had a significantly higher viability, directly after preservation and after 1 day in culture. Moreover, bulk droplet vitrified hepatocytes had evidently better morphology and showed significantly higher metabolic activity than cryopreserved hepatocytes in long-term collagen sandwich cultures. In conclusion, we developed a novel bulk droplet vitrification method of which we validated the theoretical background and demonstrated the feasibility to use this method to vitrify large cell volumes. Moreover, we showed that this method results in improved hepatocyte viability and metabolic function as compared to cryopreservation.
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- 2019
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9. Specific Patterns of Postoperative Temperature Elevations Predict Blood Infection in Pediatric Burn Patients
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Poster, Jonah, Chu, Chris, Weber, Joan M, Lydon, Martha, Dylewski, Maggie, Uygun, Korkut, and Sheridan, Robert L
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Using readily available temperature data, we seek to propose a scoring criteria that can facilitate accurate and immediate prediction of blood infection. The standard in diagnosing blood infection is a positive blood culture result that may take up to 3 days to process, requiring providers to make a prediction about which febrile patient is actually bacteremic. This prediction is difficult in burned children as systemic inflammation can cause fever in the absence of infection. An ability to make this prediction more accurate using readily available information would be useful. A retrospective chart review was performed for 28 pediatric patients, with a burn size 20% or greater, admitted to the burn unit between 2010 and 2014. All children had blood cultures drawn. They were divided into either infection (positive blood cultures) or control (negative blood cultures) groups. Median temperature and mean number of temperature elevations were compared between the two groups. We evaluated the predictive accuracy of using temperature elevation, pattern, and timing to predict blood infection. A significant difference was seen in the mean number of temperature elevations above 39°C. This was significant for each time stage, especially in the 0- to 24-hour post-surgery period. We found the most predictive accuracy in the 0- to 12-, 12- to 38-, and 12- to 48-hour time periods. We found a strong association between mean number of fever spikes above 39°C and blood infection, especially 12 to 24 hours after surgery. This readily available data can be useful to clinicians as they access children with burns.
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- 2019
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10. Exploring donor demographics effects on hepatocyte yield and viability: Results of whole human liver isolation from one center
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Geerts, Sharon, Ozer, Sinan, Chu, Chris, Fuchs, Bryan C., Tanabe, Kenneth K., Yeh, Heidi, and Uygun, Korkut
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Due to the growth of cell-based therapeutic alternatives addressing the shortage of livers for transplant, there is necessity for a reliable source of human hepatocytes. In addition, pharmaceutical research often requires human hepatocytes to assess new drug therapies during development or to achieve FDA approval. Whole human livers producing large quantities of cells from the same donor are ideal, enhancing reproducibility for all purposes, while also allowing for capturing variances in drug-metabolism across different demographics for pharmaceutical testing and development but are limited in availability and quality for research purposes. The present study investigates the effect of donor and liver procurement factors of 16 human livers on cell viability and yield, showing that typical exclusion criteria for transplant still produce viable hepatocytes with significant yields. Although limited in number of data points, which should be taken into consideration, the conclusions of this study could be utilized as indications, allowing for expansion of liver selection criteria for hepatocyte isolation and provide the necessary quality hepatocytes in large quantities for the growing pharmaceutical, biomedical, and therapeutic research fields.
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- 2019
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11. Oxygenated UW Solution Decreases ATP Decay and Improves Survival After Transplantation of DCD Liver Grafts
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Martins, Paulo N., Berendsen, Timothy A., Yeh, Heidi, Bruinsma, Bote G., Izamis, Maria-Louisa, Op den Dries, Sanna, Gillooly, Andrew R., Porte, Robert, Yarmush, Martin L., Uygun, Korkut, and Markmann, James F.
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The authors explore the protective effect of additional oxygen provided by Perfluorocarbons during static cold preservation of donation after cardiac death livers in a rat model. It is demonstrated that Oxygenated University of Wisconsin solution may attenuate ischemia reperfusion injury and improve graft survival.
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- 2019
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12. Effect of Ice Nucleation and Cryoprotectants during High Subzero-Preservation in Endothelialized Microchannels
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Tessier, Shannon N., Weng, Lindong, Moyo, Will D., Au, Sam H., Wong, Keith H. K., Angpraseuth, Cindy, Stoddard, Amy E., Lu, Chenyue, Nieman, Linda T., Sandlin, Rebecca D., Uygun, Korkut, Stott, Shannon L., and Toner, Mehmet
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Cryopreservation is of significance in areas including tissue engineering, regenerative medicine, and organ transplantation. We investigated endothelial cell attachment and membrane integrity in a microvasculature model at high subzero temperatures in the presence of extracellular ice. The results show that in the presence of heterogeneous extracellular ice formation induced by ice nucleating bacteria, endothelial cells showed improved attachment at temperature minimums of −6 °C. However, as temperatures decreased below −6 °C, endothelial cells required additional cryoprotectants. The glucose analog, 3-O-methyl-d-glucose (3-OMG), rescued cell attachment optimally at 100 mM (cells/lane was 34, as compared to 36 for controls), while 2% and 5% polyethylene glycol (PEG) were equally effective at −10 °C (88% and 86.4% intact membranes). Finally, endothelialized microchannels were stored for 72 h at −10 °C in a preservation solution consisting of the University of Wisconsin (UW) solution, Snomax, 3-OMG, PEG, glycerol, and trehalose, whereby cell attachment was not significantly different from unfrozen controls, although membrane integrity was compromised. These findings enrich our knowledge about the direct impact of extracellular ice on endothelial cells. Specifically, we show that, by controlling the ice nucleation temperature and uniformity, we can preserve cell attachment and membrane integrity. Further, we demonstrate the strength of leveraging endothelialized microchannels to fuel discoveries in cryopreservation of thick tissues and solid organs.
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- 2018
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13. 710 Specific Patterns of Vital Sign Fluctuations Predict Bloodstream Infection in Pediatric Burn Patients
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Sadeq, Farzin, Poster, Jonah, Weber, Joan M, Begis, Maggie D, Sheridan, Robert L, and Uygun, Korkut
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- 2022
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14. Multi-omic network-based interrogation of rat liver metabolism following gastric bypass surgery featuring SWATH proteomics
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Sridharan, Gautham Vivek, D’Alessandro, Matthew, Bale, Shyam Sundhar, Bhagat, Vicky, Gagnon, Hugo, Asara, John M., Uygun, Korkut, Yarmush, Martin L., and Saeidi, Nima
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Morbidly obese patients often elect for Roux-en-Y gastric bypass (RYGB), a form of bariatric surgery that triggers a remarkable 30% reduction in excess body weight and reversal of insulin resistance for those who are type II diabetic. A more complete understanding of the underlying molecular mechanisms that drive the complex metabolic reprogramming post-RYGB could lead to innovative non-invasive therapeutics that mimic the beneficial effects of the surgery, namely weight loss, achievement of glycemic control, or reversal of non-alcoholic steatohepatitis (NASH). To facilitate these discoveries, we hereby demonstrate the first multi-omic interrogation of a rodent RYGB model to reveal tissue-specific pathway modules implicated in the control of body weight regulation and energy homeostasis. In this study, we focus on and evaluate liver metabolism three months following RYGB in rats using both SWATH proteomics, a burgeoning label free approach using high resolution mass spectrometry to quantify protein levels in biological samples, as well as MRM metabolomics. The SWATH analysis enabled the quantification of 1378 proteins in liver tissue extracts, of which we report the significant down-regulation of Thrsp and Acot13 in RYGB as putative targets of lipid metabolism for weight loss. Furthermore, we develop a computational graph-based metabolic network module detection algorithm for the discovery of non-canonical pathways, or sub-networks, enriched with significantly elevated or depleted metabolites and proteins in RYGB-treated rat livers. The analysis revealed a network connection between the depleted protein Baat and the depleted metabolite taurine, corroborating the clinical observation that taurine-conjugated bile acid levels are perturbed post-RYGB.
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- 2017
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15. Peritransplant Energy Changes and Their Correlation to Outcome After Human Liver Transplantation
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Bruinsma, Bote G., Avruch, James H., Sridharan, Gautham V., Weeder, Pepijn D., Jacobs, Marie Louise, Crisalli, Kerry, Amundsen, Beth, Porte, Robert J., Markmann, James F., Uygun, Korkut, and Yeh, Heidi
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Considering the importance of energy status during transplantation, the authors aimed to correlate peritransplant energy cofactors to posttransplant outcome and subsequently modelled this in an ex vivo setting. Supplemental digital content is available in the text.
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- 2017
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16. Subzero organ preservation: the dawn of a new ice age?
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Bruinsma, Bote G. and Uygun, Korkut
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- 2017
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17. Role of Machine Perfusion in Liver Transplantation.
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Longchamp, Alban, Nakamura, Tsukasa, Uygun, Korkut, and Markmann, James F.
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Given the current severe shortage of available livers for transplantation, there is an urgent need to maximize the utilization of donor organs. One of the strategies to increase the number of available livers for transplantation is to improve organ utilization through the use of elderly, overweight, or organs donated after circulatory death (DCD). However, the utilization of these “marginal” organs was associated with an increased risk of early allograft dysfunction, primary non-function, ischemic biliary complications or even re-transplantation. Ischemia–reperfusion (IR) injury is a key mechanism in the pathogenesis of these complication. Although conventional static cold preservation provides some protection against IR injury, more-advanced preservation methods are needed to improve outcomes after transplantation of marginal livers or obtained after circulatory death. Among the most promising strategies is the utilization of ex-vivo machine perfusion. Recently, a variety of perfusion machines have received approval for clinical use, each differing in terms of perfusion temperature and oxygenation capabilities. Overall, clinical trials have demonstrated that these devices have resulted in superior posttransplant outcomes and increased utilization of marginal livers, leading to their widespread adoption. In this review, we aim to provide both the rationale and up-to-date clinical evidence for machine perfusion, along with its potential future applications.
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- 2023
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18. Nuclear receptors control pro-viral and antiviral metabolic responses to hepatitis C virus infection
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Levy, Gahl, Habib, Naomi, Guzzardi, Maria Angela, Kitsberg, Daniel, Bomze, David, Ezra, Elishai, Uygun, Basak E, Uygun, Korkut, Trippler, Martin, Schlaak, Joerg F, Shibolet, Oren, Sklan, Ella H, Cohen, Merav, Timm, Joerg, Friedman, Nir, and Nahmias, Yaakov
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A metabolomics analysis finds that host glycolysis, fatty acid oxidation, the urea cycle, cholesterol biosynthesis and oxidative phosphorylation are modified by hepatitis C virus infection. These effects are mediated through nuclear receptor transcription factors HNF4α, PPARα and FXR.
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- 2016
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19. Subnormothermic Ex Vivo Porcine Kidney Perfusion Improves Energy Metabolism: Analysis Using 31P Magnetic Resonance Spectroscopic Imaging
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Agius, Thomas, Songeon, Julien, Klauser, Antoine, Allagnat, Florent, Longchamp, Grégoire, Ruttimann, Raphael, Lyon, Arnaud, Ivaniesevic, Julijana, Meier, Raphael, Déglise, Sébastien, Markmann, James F., Uygun, Korkut, Buhler, Leo, Toso, Christian, Corpataux, Jean-Marc, Lazeyras, Francois, and Longchamp, Alban
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- 2022
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20. A Novel Digital Algorithm for Identifying Liver Steatosis Using Smartphone-Captured Images
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Xu, Katherine, Raigani, Siavash, Shih, Angela, Baptista, Sofia G., Rosales, Ivy, Parry, Nicola M., Shroff, Stuti G., Misdraji, Joseph, Uygun, Korkut, Yeh, Heidi, Fairchild, Katherine, and Anne Dageforde, Leigh
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- 2022
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21. Surgical models of Roux-en-Y gastric bypass surgery and sleeve gastrectomy in rats and mice
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Bruinsma, Bote G, Uygun, Korkut, Yarmush, Martin L, and Saeidi, Nima
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Bariatric surgery is the only definitive solution currently available for the present obesity pandemic. These operations typically involve reconfiguration of gastrointestinal tract anatomy and impose profound metabolic and physiological benefits, such as substantially reducing body weight and ameliorating type II diabetes. Therefore, animal models of these surgeries offer unique and exciting opportunities to delineate the underlying mechanisms that contribute to the resolution of obesity and diabetes. Here we describe a standardized procedure for mouse and rat models of Roux-en-Y gastric bypass (80–90 min operative time) and sleeve gastrectomy (30–45 min operative time), which, to a high degree, resembles operations in humans. We also provide detailed protocols for both pre- and postoperative techniques that ensure a high success rate in the operations. These protocols provide the opportunity to mechanistically investigate the systemic effects of the surgical interventions, such as regulation of body weight, glucose homeostasis and gut microbiome.
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- 2015
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22. Determination and Extension of the Limits to Static Cold Storage using Subnormothermic Machine Perfusion
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Bruinsma, Bote G., Berendsen, Tim A., Izamis, Maria-Louisa, Yarmush, Martin L., and Uygun, Korkut
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Background/Aims Static cold storage (SCS) of the liver for transplantation is limited by time. Continuation of metabolic activity leads to depletion of energy stores and loss of cellular function, which results in poor post-transplant function. Machine perfusion (MP) applied at the end of preservation may improve the viability of marginal liver grafts and provides information on the quality of the organ. We attempt to define the limits to SCS in terms of easily measurable perfusion parameters and investigate whether MP can improve liver viability.Methods Rat livers were cold-stored for 0, 24, 48, 72, and 120 h, after which they were treated with subnormothermic machine perfusion (SNMP). Livers cold-stored for 48 and 72 h were transplanted orthotopically with or without SNMP. During SNMP easily measurable parameters were monitored and adenosine triphosphate (ATP) content was measured following preservation and SNMP.Results ATP increased significantly during SNMP, but the recovered ATP content deteriorated with increased duration of SCS, with minimal improvement after 72 h of SCS. Vascular resistance during SNMP increased with extended preservation. After 48 h of SCS, orthotopic transplantation survival increased significantly from 50% to 100% with SNMP, but did not improve after 72 h.MConclusions Vascular resistance and ATP recovery suggest a decrease in viability after 48 h of SCS. Survival data confirms the loss of post-transplant graft function and supports the use of ATP and vascular resistance as useful indicators. Further, we show that the recoverability of a liver using SNMP is limited to 48 h of SCS.
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- 2013
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23. Application of whole-organ tissue engineering in hepatology
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Uygun, Basak E., Yarmush, Martin L., and Uygun, Korkut
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Initially hailed as the ultimate solution to organ failure, engineering of vascularized tissues such as the liver has stalled because of the need for a well-structured circulatory system that can maintain the cells seeded inside the construct. A new approach has evolved to overcome this obstacle. Whole-organ decellularization is a method that retains most of the native vascular structures of the organ, providing microcirculatory support and structure, which can be anastomosed with the recipient circulation. The technique was first applied to the heart and then adapted for the liver. Several studies have shown that cells can be eliminated, the extracellular matrix and vasculature are reasonably preserved and, after repopulation with hepatocytes, these grafts can perform hepatic functions in vitro and in vivo. Progress is rapidly being made as researchers are addressing several key challenges to whole-organ tissue engineering, such as ensuring correct cell distribution, nonparenchymal cell seeding, blood compatibility, immunological concerns, and the source of cells and matrices.
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- 2012
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24. Cell Delivery: From Cell Transplantation to Organ Engineering
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Soto-Gutierrez, Alejandro, Yagi, Hiroshi, Uygun, Basak E., Navarro-Alvarez, Nalu, Uygun, Korkut, Kobayashi, Naoya, Yang, Yong-Guang, and Yarmush, Martin L.
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Cell populations derived from adult tissue and stem cells possess a great expectation for the treatment of several diseases. Great efforts have been made to generate cells with therapeutic impact from stem cells. However, it is clear that the development of systems to deliver such cells to induce efficient engraftment, growth, and function is a real necessity. Biologic and artificial scaffolds have received significant attention for their potential therapeutic application when use to form tissues in vitro and facilitate engraftment in vivo. Ultimately more sophisticated methods for decellularization of organs have been successfully used in tissue engineering and regenerative medicine applications. These decellularized tissues and organs appear to provide bioactive molecules and bioinductive properties to induce homing, differentiation, and proliferation of cells. The combination of decellularized organs and stem cells may dramatically improve the survival, engraftment, and fate control of transplanted stem cells and their ultimate clinical utility, opening the doors to a new era of organ engineering.
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- 2010
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25. Effects of Burn Injury on Markers of Hypermetabolism in Rats
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Izamis, Maria-Louisa, Uygun, Korkut, Uygun, Basak, Yarmush, Martin L., and Berthiaume, François
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The basic metrics of hypermetabolism have not been thoroughly characterized in rat burn injury models. We examined three models expected to differ in sensitivity to burn injury to identify that which group(s) exhibited the most clinically relevant metabolic response. Six and 12 weeks old male CD (6 week mCD and 12 week mCD) rats, and 12 weeks old female Fischer (12 week fFI) rats received a 20% total body surface area burn, followed by saline resuscitation. Activity, core body temperature, heart rate (via implanted telemetry devices), body weight, food and water intake, and fecal output were measured daily for 1 week before and after burn. Rats lost weight initially postburn but resumed weight gain by 1 week, except for 12 week mCD rats. Core body temperature increased above normal 2 days postburn and returned to baseline by 1 week. Food intake, normalized to body weight, remained unchanged postburn for 12 week mCD rats, but decreased in 6 week mCD rats and increased in 12 week fFI rats. Heart rate in the 12 week mCD and 12 week fFI rats remained at 10 to 15% above baseline, whereas, in 6 week mCD, heart rates returned to baseline after 4 days. Activity levels were unchanged for 12 week fFI and 6 week mCD rats postburn, but decreased for 12 week mCD rats. Postburn hypermetabolism was most significant and sustained in 12 week mCD rats, of least consequence and brief in 6 week mCD rats, and intermediate in 12 week fFI rats. The disparate responses indicate that the choice of animal model should be carefully considered in hypermetabolism studies.
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- 2009
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26. Tissue Growth Modeling in a Wavy-Walled Bioreactor
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Bilgen, Bahar, Uygun, Korkut, Bueno, Ericka M., Sucosky, Philippe, and Barabino, Gilda A.
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Bioreactors have played a crucial role in recent approaches to cartilage tissue engineering, providing an environment that promotes efficient cell seeding, nutrient and waste transport, and essential physical stimuli. This study employed a wavy-walled bioreactor to investigate the effects of the hydrodynamic environment on the properties of engineered cartilage. Its unique design provides multiple hydrodynamic environments within one setting. A tissue growth model was developed to characterize the tissue growth and extracellular matrix synthesis by chondrocytes seeded and cultivated on polyglycolic acid scaffolds in the wavy-walled bioreactor for a period of 4 weeks. This model consists of four components: 1) a computational fluid dynamics model, 2) a kinetic growth model, 3) an artificial neural network that empirically correlates hydrodynamic parameters with kinetic constants, and 4) a second artificial neural network that correlates the biochemical composition of constructs with their material properties. In tandem, these components enable the prediction of the dynamics of tissue growth, as well as the final compositional and mechanical properties of engineered cartilage. The growth model methodology developed in this study serves as a tool to predict the optimal bioprocessing conditions required to achieve desired tissue properties.
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- 2009
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27. Recovery of Warm Ischemic Rat Liver Grafts by Normothermic Extracorporeal Perfusion
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Tolboom, Herman, Pouw, Roos E., Izamis, Maria-Louisa, Milwid, Jack M., Sharma, Nripen, Soto-Gutierrez, Alejandro, Nahmias, Yaakov, Uygun, Korkut, Berthiaume, François, and Yarmush, Martin L.
- Abstract
Liver transplantation is currently the only established treatment of end-stage liver disease, but it is limited by a severe shortage of viable donor livers. Donors after cardiac death (DCD) are an untapped source that could significantly increase the pool of available livers. Preservation of these DCD livers by conventional static cold storage (SCS) is associated with an unacceptable risk of primary nonfunction and delayed graft failure. Normothermic extracorporeal liver perfusion (NELP) has been suggested as an improvement over SCS. Livers recovered from male Lewis rats were subjected to 1 hr of warm ischemia and preserved with 5 hr of SCS or NELP, and transplanted into syngeneic recipients. As additional controls, non-ischemic livers preserved with 6 hr of SCS or NELP and unpreserved ischemic livers were transplanted. After NELP, ischemically damaged livers could be orthotopically transplanted into syngeneic recipients with 92% survival (n13) after 4 weeks, which was comparable with control animals that received healthy livers preserved by SCS (n9) or NELP (n11) for 6 hr. On the other hand, animals from ischemia/SCS control group all died within 12 hr postoperatively (n6). Similarly, animals that received ischemic livers without preservation all died within 24 hr after transplantation (n6). These results suggest that NELP has the potential to reclaim warm ischemic livers that would not be transplantable otherwise. The rat model in this study is a useful platform to further optimize NELP as a method of recovery and preservation of DCD livers.
- Published
- 2009
- Full Text
- View/download PDF
28. DFBA-LQR:? An Optimal Control Approach to Flux Balance Analysis
- Author
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Uygun, Korkut, W. T. Matthew, Howard, and Huang, Yinlun
- Abstract
Systems biology is becoming an emerging field, as systems science is demonstrated as an essential tool in untangling biocomplexity. While various steady-state-based methods have been developed for study of metabolic networks, the study of the network dynamics is a less explored area, as it is inherently related to the regulatory network. The difficulty of regulatory network inference opens up the possibility of employing control techniques and methods for analysis of metabolic networks. In this work, the potential for application of optimal control theory to metabolic control problems is investigated. Considering that the regulatory network in essence is a cascade control structure, the proposed modeling approach relies on the postulate that evolution is a genetic optimization scheme leading to “optimal” regulatory networks. Thus the approach utilizes a modified linear quadratic regulator formulation to evaluate the optimal regulatory network for a given flux model. Utilizing a homeostasis-type objective, the proposed dynamic flux balance analysis with linear quadratic regulator (DFBA-LQR) approach enables constructing dynamic flux balance analysis models and produces analytical descriptions of the responses of the metabolic fluxes to disturbances. The analytical description can also be used to calculate the flux control coefficients and linearized reaction kinetics for the system. The application potential of the approach is demonstrated by a sample problem of modeling of lipid accumulation in rat hepatocytes cultures.
- Published
- 2006
- Full Text
- View/download PDF
29. Process security analysis: γ‐Analysis and σ‐map
- Author
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Uygun, Korkut, Huang, Yinlun, and Lou, Helen H.
- Abstract
No Abstract.
- Published
- 2003
- Full Text
- View/download PDF
30. HEN optimizations without using logarithmic‐mean‐temperature difference
- Author
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Akman, Uğur, Uygun, Korkut, Uztürk, Derya, and Konukman, Alp Er Ş.
- Abstract
A simple 1‐1 shell‐and‐tube heat‐exchanger model without the logarithmic‐mean‐temperature difference ΔTlm is proposed for heat‐exchanger network (HEN) optimizations. The model consists of two algebraic equations and allows to determine hot and cold outlet temperatures independent of each other. HEN optimization problems are classified as feasible‐ and infeasible‐path formulations, and compared with regard to problems originating from the use of ΔTlm in exchanger energy‐balance equations. The ΔTlm‐free model eliminates numerical failures in computing the logarithmic terms with negative arguments due to possible inconsistent initialization/progress of exchanger interconnection temperatures during HEN optimizations. The ΔTlm‐free model does not require inclusion of approach‐temperature inequality constraints since positive approach temperatures are guaranteed. It also eliminates iterative solution of nonlinear energy‐balance equations in feasible‐path formulations and is represented as linear equality constraints in infeasible‐path formulations for fixed areas, heat‐capacity‐flow rates, and bypass flows. As demonstrated with two representative HEN optimization problems, the ΔTlm‐free model significantly reduces numerical difficulties and decreases computation time in the optimization phase of synthesis/design, retrofit, and flexibility‐analysis of HENs. Thus, it permits handling large HEN problems.
- Published
- 2002
- Full Text
- View/download PDF
31. Caspase Inhibition: Optimizing Grafts for Transplantation
- Author
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Detelich, Danielle, Yeh, Heidi, and Uygun, Korkut
- Abstract
The authors summarize the protective roles of caspase inhibitors during kidney preservation. Targeting at caspase-dependent cell death pathway by administering graft-protective intervention during ex vivo cold storage may improve the graft function.
- Published
- 2018
- Full Text
- View/download PDF
32. 2517: Ex-vivo subnormothermic oxygenated machine perfusion of swine forelimbs enables prolonged graft preservation prior to transplantation
- Author
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Lellouch, Alexandre Gaston, Karimian, Negin, Ng, Zhi Yang, Mert, Safak, Geerts, Sharon, Uygun, Korkut, and Cetrulo, Curtis L.
- Published
- 2016
- Full Text
- View/download PDF
33. Addressing the Donor Liver Shortage with EX VIVO Machine Perfusion
- Author
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Izamis, Maria-Louisa, a. Berendsen, Tim, Uygun, Korkut, and L. Yarmush, Martin
- Abstract
Despite a critical shortage of viable donor livers for transplantation, only a fraction of the available organs are used. Donor organ defects, which in the majority of cases are caused by extensive exposure to ischemia, cannot be reversed by static cold storage, the current gold standard of organ preservation. In this review, the role of machine perfusion (MP) in the recovery of non-transplantable ischemic donor organs is discussed. Though still in the experimental phase, various models of MP have consistently demonstrated that ischemic donor organs can be recovered to a transplantable state through continuous perfusion. MP can also provide dynamic quantitative assessments of the extent of ischemia, in addition to predicting the likelihood of organ recovery. Continued endeavors to translate MP into clinical use and eventually incorporate it into routine donor organ care will have a significant impact on the quality and availability of transplantable donor organs.
- Published
- 2012
- Full Text
- View/download PDF
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