Research Catalyst
​
JOURNAL CLUB
Presentations and other Teaching material
From our conference presentations, lab meetings, teaching​ (click on pdf icon to download)
To enjoy these slides, please download the free font Oswald Regular (we really love that here!)
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
-
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.
-
Nemkov et al. High-Throughput Metabolomics: Isocratic and Gradient Mass Spectrometry-Based Methods. Methods Mol Biol. 2019;1978:13-26. doi: 10.1007/978-1-4939-9236-2_2.
-
Reisz et al. Untargeted and Semi-targeted Lipid Analysis of Biological Samples Using Mass Spectrometry-Based Metabolomics. Methods Mol Biol . 2019;1978:121-135. doi: 10.1007/978-1-4939-9236-2_8.
-
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.
-
Reisz et al. Blood and Plasma Proteomics: Targeted Quantitation and Posttranslational Redox Modifications. Methods Mol Biol. 2017;1619:353-371.
-
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.
-
D'Alessandro et al. Biological and Clinical Factors Contributing to the Metabolic Heterogeneity of Hospitalized Patients with and without COVID-19 Cells. 2021 Sep 2;10(9):2293. doi: 10.3390/cells10092293.
-
Buescher et. A roadmap for interpreting (13)C metabolite labeling patterns from cells. Curr Opin Biotechnol. 2015 Aug;34:189-201
-
Pang et al. MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights. Nucleic Acids Res. 2021 Jul 2;49(W1):W388-W396. doi: 10.1093/nar/gkab382.
Red Blood Cell Aging in vivo and in vitro (storage in the blood bank)
-
Yoshida et al. Red blood cell storage lesion: causes and potential clinical consequences. Blood Transfus. 2019 Jan;17(1):27-52. doi: 10.2450/2019.0217-18.
-
Nemkov et al. Blood donor exposome and impact of common drugs on red blood cell metabolism. JCI Insight 2021; 6(3):e146175. doi: 10.1172/jci.insight.146175.
-
Issaian et al. The interactome of the N-terminus of band 3 regulates red blood cell metabolism and storage quality. Haematologica. 2021 Nov 1;106(11):2971-2985. doi: 10.3324/haematol.2020.278252.
-
D'Alessandro et al. Donor sex, age and ethnicity impact stored red blood cell antioxidant metabolism through mechanisms in part explained by glucose 6-phosphate dehydrogenase levels and activity. Haematologica. 2021 May 1;106(5):1290-1302. doi: 10.3324/haematol.2020.246603.
-
D'Alessandro et al. Protein-L-isoaspartate O-methyltransferase is required for in vivo control of oxidative damage in red blood cells. Haematologica. 2021 Oct 1;106(10):2726-2739. doi: 10.3324/haematol.2020.266676.
-
D'Alessandro et al. Hematologic and systemic metabolic alterations due to Mediterranean class II G6PD deficiency in mice. JCI Insight 2021 Jul 22;6(14):e147056. doi: 10.1172/jci.insight.147056.
-
Francis et al. Donor glucose-6-phosphate dehydrogenase deficiency decreases blood quality for transfusion. J Clin Invest
. 2020 May 1;130(5):2270-2285. doi: 10.1172/JCI133530. -
Roussel et al. Rapid clearance of storage-induced microerythrocytes alters transfusion recovery. Blood. 2021 Apr 29;137(17):2285-2298. doi: 10.1182/blood.2020008563.
-
Roubinian et al. Effect of donor, component, and recipient characteristics on hemoglobin increments following red blood cell transfusion. Blood . 2019 Sep 26;134(13):1003-1013. doi: 10.1182/blood.2019000773. Epub 2019 Jul 26.
-
D'Alessandro et al. Hypoxic storage of red blood cells improves metabolism and post-transfusion recovery. Transfusion. 2020 Apr;60(4):786-798. doi: 10.1111/trf.15730.
-
Reisz et al. Methylation of protein aspartates and deamidated asparagines as a function of blood bank storage and oxidative stress in human red blood cells. Transfusion . 2018 Dec;58(12):2978-2991. doi: 10.1111/trf.14936. Epub 2018 Oct 12.
-
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.
-
D'Alessandro et al. Red blood cell proteomics update- is there more to discover? Blood Transfusion 2017; 15(2):182-187.
-
D'Alessandro et al. Citrate metabolism in red blood cells stored in additive solution-3. Transfusion. 2017 Feb;57(2):325-336.
-
Paglia et al. Biomarkers defining the metabolic age of red blood cells during cold storage. Blood 2016; 128(13):e43-50
-
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.
-
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.
-
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.
-
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
-
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
-
D'Alessandro et al. Hallmarks of pulmonary hypertension.Antioxidant Redox Signaling 2017; doi: 10.1089/ars.2017.7217.
-
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
-
Sun et al. Erythrocyte sphingosine 1 phosphate: a key intracellular modulator for adaptation to high altitude hypoxia. Nature Comm 2016; 7:12086.
-
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.
-
Song et al. Erythrocytes retain “hypoxic purinergic memory” for faster acclimatization upon re-ascent. Nat Comm 2017; 8:14108
-
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
-
Sciacovelli et al. Fumarate is an epigenetic modifier that elicits epithelial-to-mesenchymal transition.. Nature 2016; 537(7261):544-547
-
.Tannahill et al. Succinate is an inflammatory signal that induces IL-1β through HIF-1α. Nature. 2013;496(7444):238-42
-
Kerr et al. Mutant Kras copy number defines metabolic reprogramming and therapeutic susceptibilities.Nature. 2016;531(7592):110-3.
-
Chouchani et al. Ischaemic accumulation of succinate controls reperfusion injury through mitochondrial ROS. Nature. 201420;515(7527):431-435.
-
Chaneton et al. Serine is a natural ligand and allosteric activator of pyruvate kinase M2. Nature. 2012 ;491(7424):458-462.
-
Frezza et al. Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase.Nature. 2011;477(7363):225-8.
Trauma/Hemorrhagic Shock
-
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.
-
Slaughter et al. The Metabolopathy of Tissue Injury, Hemorrhagic Shock and Resuscitation in a Rat Model. Shock 2017; doi: 10.1097/SHK.0000000000000948
-
Clendenen et al. Hemorrhagic Shock, not Poly-Trauma, Drives the Plasma Metabolome Derangement in Pigs. J Trauma 2017; 83(4):635-642
-
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.
-
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
Metabolomics and Proteomics
An introduction to Metabolomics
High-throughput metabolomics
Metabolomics Core at UC Denver
Expected isotopolgue distributions in tracing experiments
Freeze thaw effect on Metabolite levels
Metabolic Tracing Experiments
Overview of Metabolomics and Proteomics
Proteomics services
Metabolomics services
Metabolomics in COVID-19
Red Blood Cell aging in vivo and storage lesion
High-Throughput Metabolomics: Towards personalized Transfusion Medicine
AABB 2017 - Hypoxanthine and PTR
Alternative RBC storage strategies
Hypoxic Metabolic Reprogramming in sickle cell disease and high altitude
RBC Hypoxic metabolic reprogramming
RBC responses to high altitude hypoxia
Scott Murphy Lecture - BEST 2015
EHA 2013 - RBC aging in vivo and in vitro
Anaerobic storage of RBCs
Down Syndrome
RBC metabolism in Down syndrome
RBC metabolism in Down syndrome - Rachel
Hypoxia: Pulmonary hypertension, trauma/hemorrhagic shock and hibernation
Sleeping squirrel hiking students and trauma patients
miR-124 and pulmonary hypertension
Other
Small molecules, big data and something in between
Love me tender - an omics view on meat tenderization biochemistry
Omics and blood doping
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