Journal Club
Recommended reads - to catch up with what we work on in the lab
(relevant references to other lab's work are cited/reviewed in these papers)
Metabolomics methods
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Nemkov et al. A three-minute method for high-throughput quantitative metabolomics and quantitative tracing experiments of central carbon and nitrogen pathways. Rapid Commun Mass Spectrom. 2017 Apr 30;31(8):663-673.
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Gehrke et al. Characterization of rapid extraction protocols for high-throughput metabolomics. Rapid Commun Mass Spectrom. 2017 Sep 15;31(17):1445-1452.
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Nemkov et al. Three-minute method for amino acid analysis by UHPLC and high-resolution quadrupole orbitrap mass spectrometry. Amino Acids. 2015 Nov;47(11):2345-57.
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Reisz et al. Blood and Plasma Proteomics: Targeted Quantitation and Posttranslational Redox Modifications. Methods Mol Biol. 2017;1619:353-371.
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Culp-Hill et al. Investigation of the effects of storage and freezing on mixes of heavy-labeled metabolite and amino acid standards. Rapid Commun Mass Spectrom. 2017 Dec 15;31(23):2030-2034.
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Nemkov et al. Metabolism of Citrate and Other Carboxylic Acids in Erythrocytes As a Function of Oxygen Saturation and Refrigerated Storage. Front Med. 2017 Oct 17;4:175.
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Reisz and D'Alessandro. Measurement of metabolic fluxes using stable isotope tracers in whole animals and human patients. Curr Opin Clin Nutr Metab Care. 2017 Sep;20(5):366-374.
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Buescher et. A roadmap for interpreting (13)C metabolite labeling patterns from cells. Curr Opin Biotechnol. 2015 Aug;34:189-201
Red Blood Cell Aging in vivo and in vitro (storage in the blood bank)
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Nemkov T et al. Hypoxia modulates the purine salvage pathway and decreases cell and supernatant levels of hypoxanthine, a predictor of 24h in vivo survival of stored mouse and human red blood cells. Haematologica 2017; doi: 10.3324/haematol.2017.178608.
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Sun K et al. Red blood cell storage and purinergic signaling. Blood Transfuion 2017; 15(6):535-542.
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D’Alessandro A, Zolla L. Red blood cell proteomics for clinical applications. Exp Rev Prot 2017; 14(3):243-252
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D’Alessandro A et al. Metabolomics of outdated red blood cells upon rejuvenation-freezing/thawing/deglycerolization and 4C overnight hold after 24h refrigerated storage. Transfusion 2017; 57(4):1019-1030.
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D'Alessandro et al. Red blood cell proteomics update- is there more to discover? Blood Transfusion 2017; 15(2):182-187.
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D'Alessandro et al. Citrate metabolism in red blood cells stored in additive solution-3. Transfusion. 2017 Feb;57(2):325-336.
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Paglia et al. Biomarkers defining the metabolic age of red blood cells during cold storage. Blood 2016; 128(13):e43-50
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Reisz et al. Oxidative modifications of glyceraldehyde 3-phosphate dehydrogenase regulate metabolic reprogramming of stored red blood cells. Blood. 2016 Sep 22;128(12):e32-42.
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D'Alessandro et al. An update on red blood cell storage lesions, as gleaned through biochemistry and omics technologies. Transfusion 2015; 55(1):205-19.
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D'Alessandro et al. Routine Storage of Red Blood Cell Units in Additive Solution-3: a comprehensive investigation of the RBC metabolome Transfusion 2015; 55(6):1155-68.
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D'Alessandro A et al. Time-course Investigation of SAGM-Stored Erythrocyte Concentrates: from Metabolism to Proteomics. Hematologica 2012 ;97(1):107-15.
Hypoxia, inflammation, Pulmonary Hypertension
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Zhang et al. The role of CTBP1/miR-124/PKM2 signaling axis in metabolic reprogramming of pulmonary hypertension. Circulation 2017; doi: 10.1161/CIRCULATIONAHA.117.028069
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D'Alessandro et al. Hallmarks of pulmonary hypertension.Antioxidant Redox Signaling 2017; doi: 10.1089/ars.2017.7217.
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Li et al. Glycolytic reprogramming regulates the proliferative and inflammatory phenotype of adventitial fibroblasts in pulmonary hypertension through the transcriptional co-repressor C-terminal Binding Protein-1. Circulation 2016; 134(15):1105-1121
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Sun et al. Erythrocyte sphingosine 1 phosphate: a key intracellular modulator for adaptation to high altitude hypoxia. Nature Comm 2016; 7:12086.
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Sun et al . Structural and functional mechanisms of Sphingosine 1 Phosphate-Mediated Pathogenic Metabolic Reprogramming in Sickle Cell Disease. Scientific Reports 2017; doi: 10.1038/s41598-017-13667-8.
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Song et al. Erythrocytes retain “hypoxic purinergic memory” for faster acclimatization upon re-ascent. Nat Comm 2017; 8:14108
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Liu et al. Adenosine signaling via AMPK-induced erythrocyte oxygen release: a key mechanism for human hypoxia adaptation and novel therapy. Circulation 2016; ;134(5):405-21.
Cancer Metabolism
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Sciacovelli et al. Fumarate is an epigenetic modifier that elicits epithelial-to-mesenchymal transition.. Nature 2016; 537(7261):544-547
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.Tannahill et al. Succinate is an inflammatory signal that induces IL-1β through HIF-1α. Nature. 2013;496(7444):238-42
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Kerr et al. Mutant Kras copy number defines metabolic reprogramming and therapeutic susceptibilities.Nature. 2016;531(7592):110-3.
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Chouchani et al. Ischaemic accumulation of succinate controls reperfusion injury through mitochondrial ROS. Nature. 201420;515(7527):431-435.
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Chaneton et al. Serine is a natural ligand and allosteric activator of pyruvate kinase M2. Nature. 2012 ;491(7424):458-462.
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Frezza et al. Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase.Nature. 2011;477(7363):225-8.
Trauma/Hemorrhagic Shock
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Reisz et al. All animals are equal but some animals are more equal than others: Plasma lactate and succinate in hemorrhaged rats, pigs, non-human primates and clinical patients. J Trauma 2017; doi: 10.1097/TA.0000000000001721.
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Slaughter et al. The Metabolopathy of Tissue Injury, Hemorrhagic Shock and Resuscitation in a Rat Model. Shock 2017; doi: 10.1097/SHK.0000000000000948
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Clendenen et al. Hemorrhagic Shock, not Poly-Trauma, Drives the Plasma Metabolome Derangement in Pigs. J Trauma 2017; 83(4):635-642
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Reisz et al. Red Blood Cells in hemorrhagic shock: a critical role for glutaminolysis in fueling alanine transamination reactions in rats. Blood Advances 2017; 1:1296-1305.
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D'Alessandro et al. Early hemorrhage triggers metabolic responses that build up during prolonged shock. Am J Physiol Reg Integr Comp Physiol 2015; ;308(12):R1034-44
Protocols
A list of our protocols for metabolomics sample preparation to share with collaborators
Metabolomics sample preparation
*All amounts listed are "per sample" or "per replicate"
Blood processing for Red Blood Cell separation from whole blood for metabolomics analyses (from packed RBCs that have already been leukoreduced by filtration - log4 WBC and log2.5 PLT reduced)
Preparation of cellular samples:
1) Collect 0.1 mL of supernatants and freeze (-80 degree C) immediately, while discarding residual supernatants.
2) Trypsinize cultured cells (~2 x million cells - please provide specific counts as lysis buffer volume is normalized according to cell counts) and spin down in 1.5-2 mL Eppendorf tubes in cold(4 oC) PBS at 10,000 rpm for 10min at 4 degree C.
3) After removing PBS, immediately freeze cell pellets by flash freezing or storing at -80 degree C.
4) Transport samples to core on dry ice.
Shipping instructions:
Samples should be stored in tightly capped tubes and the tubes directly labeled with a distinct and simple number or letter (e.g., 1 through 85 or A through M). We encourage you to include a sample list with more information about replicates and groupings in the box. Please do not parafilm tubes or use sticky labels as these often fall off or move during transit. Please ship samples overnight on dry ice to the address below and email tracking information to your contact person:
D'Alessandro Lab
University of Colorado Denver - Anschutz Medical Campus
12801 E. 17th Ave, Room L18-9118
Aurora, CO 80045
or to
Biological Mass Spectrometry Facility - Metabolomics
University of Colorado Denver - Anschutz Medical Campus
12801 E. 17th Ave, Room 1303
Aurora, CO 80045