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Valenti A, Falcone I, Valenti F, Ricciardi E, Di Martino S, Maccallini MT, Cerro M, Desiderio F, Miseo L, Russillo M, Guerrisi A. Biobanks as an Indispensable Tool in the "Era" of Precision Medicine: Key Role in the Management of Complex Diseases, Such as Melanoma. J Pers Med 2024; 14:731. [PMID: 39063985 PMCID: PMC11278009 DOI: 10.3390/jpm14070731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 07/02/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024] Open
Abstract
In recent years, medicine has undergone profound changes, strongly entering a new phase defined as the "era of precision medicine". In this context, patient clinical management involves various scientific approaches that allow for a comprehensive pathology evaluation: from preventive processes (where applicable) to genetic and diagnostic studies. In this scenario, biobanks play an important role and, over the years, have gained increasing prestige, moving from small deposits to large collections of samples of various natures. Disease-oriented biobanks are rapidly developing as they provide useful information for the management of complex diseases, such as melanoma. Indeed, melanoma, given its highly heterogeneous characteristics, is one of the oncologic diseases with the greatest clinical and therapeutic management complexity. So, the possibility of extrapolating tissue, genetic and imaging data from dedicated biobanks could result in more selective study approaches. In this review, we specifically analyze the several biobank types to evaluate their role in technology development, patient monitoring and research of new biomarkers, especially in the melanoma context.
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Affiliation(s)
- Alessandro Valenti
- Radiology and Diagnostic Imaging Unit, Department of Clinical and Dermatological Research, San Gallicano Dermatological Institute IRCCS, 00144 Rome, Italy; (F.D.); (L.M.); (A.G.)
| | - Italia Falcone
- SAFU, Department of Research, Advanced Diagnostics, and Technological Innovation, IRCCS-Regina Elena National Cancer Institute, 00144 Rome, Italy;
| | - Fabio Valenti
- UOC Oncological Translational Research, IRCCS-Regina Elena National Cancer Institute, 00144 Rome, Italy; (F.V.); (E.R.)
| | - Elena Ricciardi
- UOC Oncological Translational Research, IRCCS-Regina Elena National Cancer Institute, 00144 Rome, Italy; (F.V.); (E.R.)
| | - Simona Di Martino
- UOC Pathology Unit, Biobank IRCCS-Regina Elena National Cancer Institute, 00144 Rome, Italy;
| | - Maria Teresa Maccallini
- Department of Clinical and Molecular Medicine, Università La Sapienza di Roma, 00185 Rome, Italy; (M.T.M.); (M.C.)
| | - Marianna Cerro
- Department of Clinical and Molecular Medicine, Università La Sapienza di Roma, 00185 Rome, Italy; (M.T.M.); (M.C.)
| | - Flora Desiderio
- Radiology and Diagnostic Imaging Unit, Department of Clinical and Dermatological Research, San Gallicano Dermatological Institute IRCCS, 00144 Rome, Italy; (F.D.); (L.M.); (A.G.)
| | - Ludovica Miseo
- Radiology and Diagnostic Imaging Unit, Department of Clinical and Dermatological Research, San Gallicano Dermatological Institute IRCCS, 00144 Rome, Italy; (F.D.); (L.M.); (A.G.)
| | - Michelangelo Russillo
- Division of Medical Oncology, IRCCS-Regina Elena National Cancer Institute, 00144 Rome, Italy;
| | - Antonino Guerrisi
- Radiology and Diagnostic Imaging Unit, Department of Clinical and Dermatological Research, San Gallicano Dermatological Institute IRCCS, 00144 Rome, Italy; (F.D.); (L.M.); (A.G.)
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Maggo S, North LY, Ozuna A, Ostrow D, Grajeda YR, Hakimjavadi H, Cotter JA, Judkins AR, Levitt P, Gai X. A method for measuring mitochondrial DNA copy number in pediatric populations. Front Pediatr 2024; 12:1401737. [PMID: 38938506 PMCID: PMC11208623 DOI: 10.3389/fped.2024.1401737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 05/31/2024] [Indexed: 06/29/2024] Open
Abstract
The mitochondrion is a multifunctional organelle that modulates multiple systems critical for homeostasis during pathophysiological stress. Variation in mitochondrial DNA (mtDNA) copy number (mtDNAcn), a key mitochondrial change associated with chronic stress, is an emerging biomarker for disease pathology and progression. mtDNAcn can be quantified from whole blood samples using qPCR to determine the ratio of mtDNA to nuclear DNA. However, the collection of blood samples in pediatric populations, particularly in infants and young children, can be technically challenging, yield much smaller volume samples, and can be distressing for the patients and their caregivers. Therefore, we have validated a mtDNAcn assay utilizing DNA from simple buccal swabs (Isohelix SK-2S) and report here it's performance in specimens from infants (age = <12 months). Utilizing qPCR to amplify ∼200 bp regions from two mitochondrial (ND1, ND6) and two nuclear (BECN1, NEB) genes, we demonstrated absolute (100%) concordance with results from low-pass whole genome sequencing (lpWGS). We believe that this method overcomes key obstacles to measuring mtDNAcn in pediatric populations and creates the possibility for development of clinical assays to measure mitochondrial change during pathophysiological stress.
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Affiliation(s)
- Simran Maggo
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - Liam Y. North
- The Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - Aime Ozuna
- The Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - Dejerianne Ostrow
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - Yander R. Grajeda
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - Hesamedin Hakimjavadi
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - Jennifer A. Cotter
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Alexander R. Judkins
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Pat Levitt
- The Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA, United States
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Xiaowu Gai
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
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Patel MA, Daley M, Van Nynatten LR, Slessarev M, Cepinskas G, Fraser DD. A reduced proteomic signature in critically ill Covid-19 patients determined with plasma antibody micro-array and machine learning. Clin Proteomics 2024; 21:33. [PMID: 38760690 PMCID: PMC11100131 DOI: 10.1186/s12014-024-09488-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 05/06/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND COVID-19 is a complex, multi-system disease with varying severity and symptoms. Identifying changes in critically ill COVID-19 patients' proteomes enables a better understanding of markers associated with susceptibility, symptoms, and treatment. We performed plasma antibody microarray and machine learning analyses to identify novel proteins of COVID-19. METHODS A case-control study comparing the concentration of 2000 plasma proteins in age- and sex-matched COVID-19 inpatients, non-COVID-19 sepsis controls, and healthy control subjects. Machine learning was used to identify a unique proteome signature in COVID-19 patients. Protein expression was correlated with clinically relevant variables and analyzed for temporal changes over hospitalization days 1, 3, 7, and 10. Expert-curated protein expression information was analyzed with Natural language processing (NLP) to determine organ- and cell-specific expression. RESULTS Machine learning identified a 28-protein model that accurately differentiated COVID-19 patients from ICU non-COVID-19 patients (accuracy = 0.89, AUC = 1.00, F1 = 0.89) and healthy controls (accuracy = 0.89, AUC = 1.00, F1 = 0.88). An optimal nine-protein model (PF4V1, NUCB1, CrkL, SerpinD1, Fen1, GATA-4, ProSAAS, PARK7, and NET1) maintained high classification ability. Specific proteins correlated with hemoglobin, coagulation factors, hypertension, and high-flow nasal cannula intervention (P < 0.01). Time-course analysis of the 28 leading proteins demonstrated no significant temporal changes within the COVID-19 cohort. NLP analysis identified multi-system expression of the key proteins, with the digestive and nervous systems being the leading systems. CONCLUSIONS The plasma proteome of critically ill COVID-19 patients was distinguishable from that of non-COVID-19 sepsis controls and healthy control subjects. The leading 28 proteins and their subset of 9 proteins yielded accurate classification models and are expressed in multiple organ systems. The identified COVID-19 proteomic signature helps elucidate COVID-19 pathophysiology and may guide future COVID-19 treatment development.
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Affiliation(s)
- Maitray A Patel
- Epidemiology and Biostatistics, Western University, London, ON, N6A 3K7, Canada
| | - Mark Daley
- Epidemiology and Biostatistics, Western University, London, ON, N6A 3K7, Canada
- Computer Science, Western University, London, ON, N6A 3K7, Canada
| | | | - Marat Slessarev
- Medicine, Western University, London, ON, N6A 3K7, Canada
- Lawson Health Research Institute, London, ON, N6C 2R5, Canada
| | - Gediminas Cepinskas
- Lawson Health Research Institute, London, ON, N6C 2R5, Canada
- Medical Biophysics, Western University, London, ON, N6A 3K7, Canada
| | - Douglas D Fraser
- Lawson Health Research Institute, London, ON, N6C 2R5, Canada.
- Children's Health Research Institute, London, ON, N6C 4V3, Canada.
- Pediatrics, Western University, London, ON, N6A 3K7, Canada.
- Clinical Neurological Sciences, Western University, London, ON, N6A 3K7, Canada.
- Physiology & Pharmacology, Western University, London, ON, N6A 3K7, Canada.
- London Health Sciences Centre, 800 Commissioners Road East, London, ON, N6A 5W9, Canada.
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Kremer S, Shakhnovich V, Riffel AK, Harvey L, Borges CR. Delta-S-Cys-Albumin as a Marker of Pediatric Biospecimen Integrity. Biopreserv Biobank 2024. [PMID: 38651617 DOI: 10.1089/bio.2023.0121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Abstract
Blood plasma storage is a crucial element of pediatric biobanking. Improperly stored or handled specimens (e.g., at > -30°C) can result in altered biomolecular compositions that no longer reflects in vivo reality. We report application of a previously developed assay in adults-the ΔS-Cys-Albumin assay, which facilitates estimation of plasma and serum exposure to thawed conditions-to a population of pediatric EDTA plasma samples from patients aged 3-18 years to determine the assay's applicability, estimate its reference range for pediatric samples, and assess the impact of pre-centrifugation delay at 0°C. In addition, the effect of plasma thawed-state exposure to a range of times at 23°C, 4°C, and -20°C on ΔS-Cys-Albumin was evaluated. Using 98 precollected and processed pediatric EDTA plasma specimens, no difference was found in ΔS-Cys-Albumin under conditions of pre-centrifugation delay for up to 10 hours at 0°C. This lack of change allowed us to estimate a pediatric reference range for ΔS-Cys-Albumin of 7.0%-22.5% (mean of 12.8%) with a modest Pearson correlation between ΔS-Cys-Albumin and age (p = 0.0037, R2 = 0.29). ΔS-Cys-Albumin stability in six specimens at 23°C, 4°C, and -20°C was also evaluated. Plateaus in the decay curves were reached by 1 day, 7 days, and 14-28 days at these respective temperatures. The estimated pediatric reference range observed in children was lower than that previously observed in 180 adults of 12.3%-30.6% (mean of 20.0%), and the slope of the age correlation in children was twice as steep as that from adults. ΔS-Cys-Albumin decay curves at 23°C, 4°C, and -20°C were similar to those previously observed in adults. The data reported here support the use of ΔS-Cys-Albumin in evaluating the integrity and overall exposure of pediatric EDTA plasma specimens to thawed conditions. In doing so, they add an important quality control tool to the biobanker's arsenal.
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Affiliation(s)
- Schuyler Kremer
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- The Biodesign Institute at Arizona State University, Tempe, Arizona, USA
| | - Valentina Shakhnovich
- Children's Mercy Hospital, Kansas City, Missouri, USA
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
- Ironwood Pharmaceuticals, Boston, Massachusetts, USA
| | | | - Lisa Harvey
- Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Chad R Borges
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- The Biodesign Institute at Arizona State University, Tempe, Arizona, USA
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Patel MA, Fraser DD, Daley M, Cepinskas G, Veraldi N, Grazioli S. The plasma proteome differentiates the multisystem inflammatory syndrome in children (MIS-C) from children with SARS-CoV-2 negative sepsis. Mol Med 2024; 30:51. [PMID: 38632526 PMCID: PMC11022403 DOI: 10.1186/s10020-024-00806-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 03/09/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND The Multi-System Inflammatory Syndrome in Children (MIS-C) can develop several weeks after SARS-CoV-2 infection and requires a distinct treatment protocol. Distinguishing MIS-C from SARS-CoV-2 negative sepsis (SCNS) patients is important to quickly institute the correct therapies. We performed targeted proteomics and machine learning analysis to identify novel plasma proteins of MIS-C for early disease recognition. METHODS A case-control study comparing the expression of 2,870 unique blood proteins in MIS-C versus SCNS patients, measured using proximity extension assays. The 2,870 proteins were reduced in number with either feature selection alone or with a prior COMBAT-Seq batch effect adjustment. The leading proteins were correlated with demographic and clinical variables. Organ system and cell type expression patterns were analyzed with Natural Language Processing (NLP). RESULTS The cohorts were well-balanced for age and sex. Of the 2,870 unique blood proteins, 58 proteins were identified with feature selection (FDR-adjusted P < 0.005, P < 0.0001; accuracy = 0.96, AUC = 1.00, F1 = 0.95), and 15 proteins were identified with a COMBAT-Seq batch effect adjusted feature selection (FDR-adjusted P < 0.05, P < 0.0001; accuracy = 0.92, AUC = 1.00, F1 = 0.89). All of the latter 15 proteins were present in the former 58-protein model. Several proteins were correlated with illness severity scores, length of stay, and interventions (LTA4H, PTN, PPBP, and EGF; P < 0.001). NLP analysis highlighted the multi-system nature of MIS-C, with the 58-protein set expressed in all organ systems; the highest levels of expression were found in the digestive system. The cell types most involved included leukocytes not yet determined, lymphocytes, macrophages, and platelets. CONCLUSIONS The plasma proteome of MIS-C patients was distinct from that of SCNS. The key proteins demonstrated expression in all organ systems and most cell types. The unique proteomic signature identified in MIS-C patients could aid future diagnostic and therapeutic advancements, as well as predict hospital length of stays, interventions, and mortality risks.
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Affiliation(s)
- Maitray A Patel
- Epidemiology and Biostatistics, Western University, N6A 3K7, London, ON, Canada
| | - Douglas D Fraser
- Lawson Health Research Institute, N6C 2R5, London, ON, Canada.
- Children's Health Research Institute, N6C 4V3, London, ON, Canada.
- Pediatrics, Western University, N6A 3K7, London, ON, Canada.
- Clinical Neurological Sciences, Western University, N6A 3K7, London, ON, Canada.
- Physiology & Pharmacology, Western University, N6A 3K7, London, ON, Canada.
- London Health Sciences Centre, Room C2-C82, 800 Commissioners Road East, N6A 5W9, London, ON, Canada.
| | - Mark Daley
- Epidemiology and Biostatistics, Western University, N6A 3K7, London, ON, Canada
- Computer Science, Western University, N6A 3K7, London, ON, Canada
| | - Gediminas Cepinskas
- Lawson Health Research Institute, N6C 2R5, London, ON, Canada
- Medical Biophysics, Western University, N6A 3K7, London, ON, Canada
| | - Noemi Veraldi
- Department of Pediatrics, Gynaecology and Obstetrics, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Serge Grazioli
- Department of Pediatrics, Gynaecology and Obstetrics, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of Neonatal and Pediatric Intensive Care, Department of Child, Woman, and Adolescent Medicine, Geneva University Hospitals, Geneva, Switzerland
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Mielke N, Lee R, Bahl A. Pediatric hemolysis in emergency departments: Prevalence, risk factors, and clinical implications. PLoS One 2024; 19:e0299692. [PMID: 38512885 PMCID: PMC10956767 DOI: 10.1371/journal.pone.0299692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 02/15/2024] [Indexed: 03/23/2024] Open
Abstract
OBJECTIVE This study aimed to analyze the prevalence, risk factors, and clinical implications of hemolyzed laboratory samples in the pediatric emergency department (ED), a subject on which existing data remains scarce. METHODS We conducted a multi-site observational cohort analysis of pediatric ED encounters in Metro Detroit, Michigan, United States. The study included participants below 18 years of age who had undergone peripheral intravenous catheter (PIVC) placement and laboratory testing. The primary outcome was the presence of hemolysis, and secondary outcomes included identifying risk factors for hemolysis and assessing the impact of hemolysis on PIVC failure. RESULTS Between January 2021 and May 2022, 10,462 ED encounters met inclusion criteria, of which 14.0% showed laboratory evidence of hemolysis. The highest proportion of hemolysis occurred in the infant (age 0-1) population (20.1%). Multivariable regression analysis indicated higher odds of hemolysis for PIVCs placed in the hand/wrist in the toddler (age 2-5) and child (age 6-11) subgroups. PIVCs placed in the hand/wrist also demonstrated higher odds of failure in infants. CONCLUSIONS Hemolysis in the pediatric ED population is a frequent complication that occurs at similar rates as in adults. PIVCs placed in the hand/wrist were associated with higher odds of hemolysis compared to those placed in the antecubital fossa. Clinicians should consider alternative locations for PIVC placement if clinically appropriate. Further research is needed to better understand the clinical implications of pediatric hemolysis.
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Affiliation(s)
- Nicholas Mielke
- Creighton University School of Medicine, Omaha, Nebraska, United States of America
| | - Ray Lee
- Corewell Health Research Institute, Royal Oak, Michigan, United States of America
| | - Amit Bahl
- Corewell Health William Beaumont University Hospital, Royal Oak, Michigan, United States of America
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Leonard S, Guertin H, Odoardi N, Miller MR, Patel MA, Daley M, Cepinskas G, Fraser DD. Pediatric sepsis inflammatory blood biomarkers that correlate with clinical variables and severity of illness scores. J Inflamm (Lond) 2024; 21:7. [PMID: 38454423 PMCID: PMC10921642 DOI: 10.1186/s12950-024-00379-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 02/19/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Sepsis is a dysregulated systemic inflammatory response triggered by infection, resulting in organ dysfunction. A major challenge in clinical pediatrics is to identify sepsis early and then quickly intervene to reduce morbidity and mortality. As blood biomarkers hold promise as early sepsis diagnostic tools, we aimed to measure a large number of blood inflammatory biomarkers from pediatric sepsis patients to determine their predictive ability, as well as their correlations with clinical variables and illness severity scores. METHODS Pediatric patients that met sepsis criteria were enrolled, and clinical data and blood samples were collected. Fifty-eight inflammatory plasma biomarker concentrations were determined using immunoassays. The data were analyzed with both conventional statistics and machine learning. RESULTS Twenty sepsis patients were enrolled (median age 13 years), with infectious pathogens identified in 75%. Vasopressors were administered to 85% of patients, while 55% received invasive ventilation and 20% were ventilated non-invasively. A total of 24 inflammatory biomarkers were significantly different between sepsis patients and age/sex-matched healthy controls. Nine biomarkers (IL-6, IL-8, MCP-1, M-CSF, IL-1RA, hyaluronan, HSP70, MMP3, and MMP10) yielded AUC parameters > 0.9 (95% CIs: 0.837-1.000; p < 0.001). Boruta feature reduction yielded 6 critical biomarkers with their relative importance: IL-8 (12.2%), MCP-1 (11.6%), HSP70 (11.6%), hyaluronan (11.5%), M-CSF (11.5%), and IL-6 (11.5%); combinations of 2 biomarkers yielded AUC values of 1.00 (95% CI: 1.00-1.00; p < 0.001). Specific biomarkers strongly correlated with illness severity scoring, as well as other clinical variables. IL-3 specifically distinguished bacterial versus viral infection (p < 0.005). CONCLUSIONS Specific inflammatory biomarkers were identified as markers of pediatric sepsis and strongly correlated to both clinical variables and sepsis severity.
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Affiliation(s)
- Sean Leonard
- Pediatrics, Western University, London, ON, Canada
| | | | - Natalya Odoardi
- Emergency Medicine, Lakeridge Health, Ajax/Oshawa, ON, Canada
| | | | - Maitray A Patel
- Epidemiology and Biostatistics, Western University, London, ON, Canada
| | - Mark Daley
- Epidemiology and Biostatistics, Western University, London, ON, Canada
- Computer Science, Western University, London, ON, Canada
| | - Gediminas Cepinskas
- Medical Biophysics, Western University, London, ON, Canada
- Lawson Health Research Institute, London, ON, Canada
| | - Douglas D Fraser
- Pediatrics, Western University, London, ON, Canada.
- Lawson Health Research Institute, London, ON, Canada.
- Clinical Neurological Sciences, Western University, London, ON, Canada.
- Physiology & Pharmacology, Western University, London, ON, Canada.
- Room C2-C82, London Health Sciences Centre, 800 Commissioners Road East, London, ON, N6A 5W9, Canada.
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Maity S, Aakriti J, Manandhar S, Anchan SB, Bhat A, Shetty MU, Nayak Y. Emvolio - A battery operated portable refrigerator preserves biochemical and haematological integrity of biological samples in preclinical studies. F1000Res 2023; 11:223. [PMID: 37771720 PMCID: PMC10523100 DOI: 10.12688/f1000research.109134.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/19/2023] [Indexed: 09/30/2023] Open
Abstract
Background: Emvolio is a non-medical device, indigenously developed portable refrigeration for maintaining the internal temperature 2-8˚C. The Indian Patent Office has granted patent for applications such as preservation and transport of medicines, vaccines, food, beverages, dairy etc. Further, use of Emvolio can be utilized in transport and store biologicals to preserve their biochemical and cellular integrity. The objective of this study was to evaluate the biochemical and haematological integrity of biological samples such as rat blood, serum and liver. Methods: The steady temperature was maintained inside the Emvolio, and it was compared to that of thermocol and polypropylene boxes aided with frozen gel packs. The blood and liver samples were isolated from Wistar rats and kept in Emvolio, thermocol and polypropylene boxes for 10 hrs, and the temperature was monitored. The blood parameters, namely red blood cells (RBC), white blood cells (WBC), platelets, haematocrit, haemoglobin, mean corpuscular volume (MCV), mean corpuscular haemoglobin concentration (MCHC) and red cell distribution width (RDW), serum parameters like alanine transaminase, alkaline phosphatase, total protein, albumin, creatine kinase, blood urea nitrogen and liver parameters like superoxide dismutase (SOD), glutathione (GSH), catalase were estimated and compared. Results: Emvolio maintained a constant inner temperature range of 2-8˚C, whereas a significant temperature variation was seen in thermocol and polypropylene boxes. There was no significant deviation in the parameters tested when samples were kept in Emvolio for six hours compared to the zero hour readings. In contrast, there was a significant deviation among the parameters for the samples kept in thermocol and polypropylene boxes for six hours compared to zero hour parameters. Conclusions: Emvolio maintained constant temperature and preserved the biological integrity of rat blood, serum and liver. Thus, Emvolio can be efficiently used as a biological sample carrier, especially in preclinical studies.
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Affiliation(s)
- Swastika Maity
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Jaya Aakriti
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Suman Manandhar
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Sharad B Anchan
- Blackfrog Technologies Private Limited, Manipal, Karnataka, 576104, India
| | - Ashlesh Bhat
- Blackfrog Technologies Private Limited, Manipal, Karnataka, 576104, India
| | - Mayur U Shetty
- Blackfrog Technologies Private Limited, Manipal, Karnataka, 576104, India
| | - Yogendra Nayak
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
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Zhang Q, Inagaki NF, Ito T. Recent advances in micro-sized oxygen carriers inspired by red blood cells. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2023; 24:2223050. [PMID: 37363800 PMCID: PMC10288928 DOI: 10.1080/14686996.2023.2223050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/22/2023] [Accepted: 05/31/2023] [Indexed: 06/28/2023]
Abstract
Supplementing sufficient oxygen to cells is always challenging in biomedical engineering fields such as tissue engineering. Originating from the concept of a 'blood substitute', nano-sized artificial oxygen carriers (AOCs) have been studied for a long time for the optimization of the oxygen supplementation and improvement of hypoxia environments in vitro and in vivo. When circulating in our bodies, micro-sized human red blood cells (hRBCs) feature a high oxygen capacity, a unique biconcave shape, biomechanical and rheological properties, and low frictional surfaces, making them efficient natural oxygen carriers. Inspired by hRBCs, recent studies have focused on evolving different AOCs into microparticles more feasibly able to achieve desired architectures and morphologies and to obtain the corresponding advantages. Recent micro-sized AOCs have been developed into additional categories based on their principal oxygen-carrying or oxygen-releasing materials. Various biomaterials such as lipids, proteins, and polymers have also been used to prepare oxygen carriers owing to their rapid oxygen transfer, high oxygen capacity, excellent colloidal stability, biocompatibility, suitable biodegradability, and long storage. In this review, we concentrated on the fabrication techniques, applied biomaterials, and design considerations of micro-sized AOCs to illustrate the advances in their performances. We also compared certain recent micro-sized AOCs with hRBCs where applicable and appropriate. Furthermore, we discussed existing and potential applications of different types of micro-sized AOCs.
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Affiliation(s)
- Qiming Zhang
- Department of Chemical System Engineering, The University of Tokyo, Tokyo, Japan
| | - Natsuko F. Inagaki
- Center for Disease Biology and Integrative Medicine, The University of Tokyo, Tokyo, Japan
| | - Taichi Ito
- Department of Chemical System Engineering, The University of Tokyo, Tokyo, Japan
- Center for Disease Biology and Integrative Medicine, The University of Tokyo, Tokyo, Japan
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10
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Fraser DD, Patel MA, Van Nynatten LR, Martin C, Seney SL, Miller MR, Daley M, Slessarev M, Cepinskas G, Juneja GK, Sabourin V, Fox-Robichaud A, Yeh CH, Kim PY, Badrnya S, Oehler S, Miholits M, Webb B. Cross-immunity against SARS-COV-2 variants of concern in naturally infected critically ill COVID-19 patients. Heliyon 2023; 9:e12704. [PMID: 36594041 PMCID: PMC9797417 DOI: 10.1016/j.heliyon.2022.e12704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022] Open
Abstract
Critically ill patients infected with SARS-CoV-2 display adaptive immunity, but it is unknown if they develop cross-reactivity to variants of concern (VOCs). We profiled cross-immunity against SARS-CoV-2 VOCs in naturally infected, non-vaccinated, critically ill COVID-19 patients. Wave-1 patients (wild-type infection) were similar in demographics to Wave-3 patients (wild-type/alpha infection), but Wave-3 patients had higher illness severity. Wave-1 patients developed increasing neutralizing antibodies to all variants, as did patients during Wave-3. Wave-3 patients, when compared to Wave-1, developed more robust antibody responses, particularly for wild-type, alpha, beta and delta variants. Within Wave-3, neutralizing antibodies were significantly less to beta and gamma VOCs, as compared to wild-type, alpha and delta. Patients previously diagnosed with cancer or chronic obstructive pulmonary disease had significantly fewer neutralizing antibodies. Naturally infected ICU patients developed adaptive responses to all VOCs, with greater responses in those patients more likely to be infected with the alpha variant, versus wild-type.
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Key Words
- ACE2, angiotensin-converting enzyme
- AUC, area-under-the-curve
- Adaptive immunity
- Antibodies
- COPD, chronic obstructive pulmonary disease
- COVID-19
- COVID-19, coronavirus disease 2019
- ICU, intensive care unit
- IQR, interquartile range
- Intensive care units
- MFI, median fluorescence intensity
- MODS, multi-organ dysfunction score
- Neutralizing
- P/F, arterial partial pressure to inspired oxygen
- RBD, receptor binding domain
- REB, research ethics board
- ROC, receiver operating characteristic
- SARS-CoV-2
- SARS-CoV-2 alpha variant
- SARS-CoV-2 beta variant
- SARS-CoV-2 delta variant
- SARS-CoV-2 gamma variant
- SOFA, sequential organ failure assessment
- VOC, variants of concern
- VTE, venous thromboembolism
- WT, wild-type
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Affiliation(s)
- Douglas D. Fraser
- Lawson Health Research Institute, London, ON, N6C 2R5, Canada,Pediatrics, Western University, London, ON, N6A 3K7, Canada,Clinical Neurological Sciences, Western University, London, ON, N6A 3K7, Canada,Physiology & Pharmacology, Western University, London, ON, N6A 3K7, Canada,Corresponding author. Lawson Health Research Institute, London, ON, N6C 2R5, Canada
| | | | | | - Claudio Martin
- Lawson Health Research Institute, London, ON, N6C 2R5, Canada,Medicine, Western University, London, ON, N6A 3K7, Canada
| | | | - Michael R. Miller
- Lawson Health Research Institute, London, ON, N6C 2R5, Canada,Pediatrics, Western University, London, ON, N6A 3K7, Canada
| | - Mark Daley
- Epidemiology, Western University, London, ON, N6A 3K7, Canada
| | - Marat Slessarev
- Lawson Health Research Institute, London, ON, N6C 2R5, Canada,Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Gediminas Cepinskas
- Lawson Health Research Institute, London, ON, N6C 2R5, Canada,Medical Biophysics, Western University, London, ON, N6A 3K7, Canada
| | - Ganeem K. Juneja
- Medicine, McMaster University, Hamilton, ON, L8S 4L8, Canada,Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, L8L 2X2, Canada
| | - Vanessa Sabourin
- Medicine, McMaster University, Hamilton, ON, L8S 4L8, Canada,Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, L8L 2X2, Canada
| | - Alison Fox-Robichaud
- Medicine, McMaster University, Hamilton, ON, L8S 4L8, Canada,Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, L8L 2X2, Canada
| | - Calvin H. Yeh
- Medicine, McMaster University, Hamilton, ON, L8S 4L8, Canada,Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, L8L 2X2, Canada
| | - Paul Y. Kim
- Medicine, McMaster University, Hamilton, ON, L8S 4L8, Canada,Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, L8L 2X2, Canada
| | | | | | | | - Brian Webb
- Thermo Fisher Scientific, Rockford, IL, USA
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11
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Van Nynatten LR, Slessarev M, Martin CM, Leligdowicz A, Miller MR, Patel MA, Daley M, Patterson EK, Cepinskas G, Fraser DD. Novel plasma protein biomarkers from critically ill sepsis patients. Clin Proteomics 2022; 19:50. [PMID: 36572854 PMCID: PMC9792322 DOI: 10.1186/s12014-022-09389-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/09/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Despite the high morbidity and mortality associated with sepsis, the relationship between the plasma proteome and clinical outcome is poorly understood. In this study, we used targeted plasma proteomics to identify novel biomarkers of sepsis in critically ill patients. METHODS Blood was obtained from 15 critically ill patients with suspected/confirmed sepsis (Sepsis-3.0 criteria) on intensive care unit (ICU) Day-1 and Day-3, as well as age- and sex-matched 15 healthy control subjects. A total of 1161 plasma proteins were measured with proximal extension assays. Promising sepsis biomarkers were narrowed with machine learning and then correlated with relevant clinical and laboratory variables. RESULTS The median age for critically ill sepsis patients was 56 (IQR 51-61) years. The median MODS and SOFA values were 7 (IQR 5.0-8.0) and 7 (IQR 5.0-9.0) on ICU Day-1, and 4 (IQR 3.5-7.0) and 6 (IQR 3.5-7.0) on ICU Day-3, respectively. Targeted proteomics, together with feature selection, identified the leading proteins that distinguished sepsis patients from healthy control subjects with ≥ 90% classification accuracy; 25 proteins on ICU Day-1 and 26 proteins on ICU Day-3 (6 proteins overlapped both ICU days; PRTN3, UPAR, GDF8, NTRK3, WFDC2 and CXCL13). Only 7 of the leading proteins changed significantly between ICU Day-1 and Day-3 (IL10, CCL23, TGFα1, ST2, VSIG4, CNTN5, and ITGAV; P < 0.01). Significant correlations were observed between a variety of patient clinical/laboratory variables and the expression of 15 proteins on ICU Day-1 and 14 proteins on ICU Day-3 (P < 0.05). CONCLUSIONS Targeted proteomics with feature selection identified proteins altered in critically ill sepsis patients relative to healthy control subjects. Correlations between protein expression and clinical/laboratory variables were identified, each providing pathophysiological insight. Our exploratory data provide a rationale for further hypothesis-driven sepsis research.
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Affiliation(s)
| | - Marat Slessarev
- grid.39381.300000 0004 1936 8884Medicine, Western University, London, ON Canada ,grid.415847.b0000 0001 0556 2414Lawson Health Research Institute, London, ON Canada
| | - Claudio M. Martin
- grid.39381.300000 0004 1936 8884Medicine, Western University, London, ON Canada ,grid.415847.b0000 0001 0556 2414Lawson Health Research Institute, London, ON Canada
| | - Aleks Leligdowicz
- grid.39381.300000 0004 1936 8884Medicine, Western University, London, ON Canada ,grid.415847.b0000 0001 0556 2414Lawson Health Research Institute, London, ON Canada
| | - Michael R. Miller
- grid.415847.b0000 0001 0556 2414Lawson Health Research Institute, London, ON Canada ,grid.39381.300000 0004 1936 8884Pediatrics, Western University, London, ON Canada
| | - Maitray A. Patel
- grid.39381.300000 0004 1936 8884Computer Science, Western University, London, ON N6A 3K7 Canada
| | - Mark Daley
- grid.415847.b0000 0001 0556 2414Lawson Health Research Institute, London, ON Canada ,grid.39381.300000 0004 1936 8884Computer Science, Western University, London, ON N6A 3K7 Canada ,grid.494618.6The Vector Institute for Artificial Intelligence, Toronto, ON M5G 1M1 Canada
| | - Eric K. Patterson
- grid.415847.b0000 0001 0556 2414Lawson Health Research Institute, London, ON Canada
| | - Gediminas Cepinskas
- grid.415847.b0000 0001 0556 2414Lawson Health Research Institute, London, ON Canada ,grid.39381.300000 0004 1936 8884Medical Biophysics, Western University, London, ON N6A 3K7 Canada
| | - Douglas D. Fraser
- grid.415847.b0000 0001 0556 2414Lawson Health Research Institute, London, ON Canada ,grid.39381.300000 0004 1936 8884Pediatrics, Western University, London, ON Canada ,grid.39381.300000 0004 1936 8884Clinical Neurological Sciences, Western University, London, ON Canada ,grid.39381.300000 0004 1936 8884Physiology and Pharmacology, Western University, London, ON Canada ,grid.412745.10000 0000 9132 1600London Health Sciences Centre, Room C2-C82, 800 Commissioners Road East, London, ON N6A 5W9 Canada
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12
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Patel MA, Knauer MJ, Nicholson M, Daley M, Van Nynatten LR, Martin C, Patterson EK, Cepinskas G, Seney SL, Dobretzberger V, Miholits M, Webb B, Fraser DD. Elevated vascular transformation blood biomarkers in Long-COVID indicate angiogenesis as a key pathophysiological mechanism. Mol Med 2022; 28:122. [PMID: 36217108 PMCID: PMC9549814 DOI: 10.1186/s10020-022-00548-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/17/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Long-COVID is characterized by prolonged, diffuse symptoms months after acute COVID-19. Accurate diagnosis and targeted therapies for Long-COVID are lacking. We investigated vascular transformation biomarkers in Long-COVID patients. METHODS A case-control study utilizing Long-COVID patients, one to six months (median 98.5 days) post-infection, with multiplex immunoassay measurement of sixteen blood biomarkers of vascular transformation, including ANG-1, P-SEL, MMP-1, VE-Cad, Syn-1, Endoglin, PECAM-1, VEGF-A, ICAM-1, VLA-4, E-SEL, thrombomodulin, VEGF-R2, VEGF-R3, VCAM-1 and VEGF-D. RESULTS Fourteen vasculature transformation blood biomarkers were significantly elevated in Long-COVID outpatients, versus acutely ill COVID-19 inpatients and healthy controls subjects (P < 0.05). A unique two biomarker profile consisting of ANG-1/P-SEL was developed with machine learning, providing a classification accuracy for Long-COVID status of 96%. Individually, ANG-1 and P-SEL had excellent sensitivity and specificity for Long-COVID status (AUC = 1.00, P < 0.0001; validated in a secondary cohort). Specific to Long-COVID, ANG-1 levels were associated with female sex and a lack of disease interventions at follow-up (P < 0.05). CONCLUSIONS Long-COVID patients suffer prolonged, diffuse symptoms and poorer health. Vascular transformation blood biomarkers were significantly elevated in Long-COVID, with angiogenesis markers (ANG-1/P-SEL) providing classification accuracy of 96%. Vascular transformation blood biomarkers hold potential for diagnostics, and modulators of angiogenesis may have therapeutic efficacy.
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Affiliation(s)
- Maitray A Patel
- Epidemiology and Biostatistics, Western University, London, ON, N6A 3K7, Canada
| | - Michael J Knauer
- Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | | | - Mark Daley
- Epidemiology and Biostatistics, Western University, London, ON, N6A 3K7, Canada.,Computer Science, Western University, London, ON, N6A 3K7, Canada
| | | | - Claudio Martin
- Medicine, Western University, London, ON, N6A 3K7, Canada.,Lawson Health Research Institute, London, ON, N6C 2R5, Canada
| | | | - Gediminas Cepinskas
- Lawson Health Research Institute, London, ON, N6C 2R5, Canada.,Medical Biophysics, Western University, London, ON, N6A 3K7, Canada
| | - Shannon L Seney
- Lawson Health Research Institute, London, ON, N6C 2R5, Canada
| | | | | | - Brian Webb
- Thermo Fisher Scientific, Rockford, IL, USA
| | - Douglas D Fraser
- Lawson Health Research Institute, London, ON, N6C 2R5, Canada. .,Pediatrics, Western University, London, ON, N6A 3K7, Canada. .,Clinical Neurological Sciences, Western University, London, ON, N6A 3K7, Canada. .,Physiology and Pharmacology, Western University, London, ON, N6A 3K7, Canada. .,London Health Sciences Centre, Room C2-C82, 800 Commissioners Road East, London, ON, N6A 5W9, Canada.
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13
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Bojescu ED, Prim D, Pfeifer ME, Segura JM. Fluorescence-polarization immunoassays within glass fiber micro-chambers enable tobramycin quantification in whole blood for therapeutic drug monitoring at the point of care. Anal Chim Acta 2022; 1225:340240. [PMID: 36038239 DOI: 10.1016/j.aca.2022.340240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/13/2022] [Accepted: 08/02/2022] [Indexed: 11/18/2022]
Abstract
Many therapeutic drugs require monitoring of their concentration in blood followed by dose adjustments in order to ensure efficacy while minimizing adverse effects. It would be highly desirable to perform such measurements rapidly and with reduced sample volumes to support point-of-care testing. Here, we demonstrate that the concentration of small therapeutics can be determined in whole blood within paper-like membranes using Fluorescence Polarization Immunoassay (FPIA). Different types of paper-like materials such as glass microfibers, cellulose and filter paper were investigated for artefacts such as scattering or autofluorescence. Accurate determination of the fluorescence polarization of red-emitting fluorophores at sub-nanomolar concentrations was feasible within glass fiber membranes. This enabled the development of a competitive immunoassay for the quantification of the antibiotic tobramycin using only 1 μL of plasma in glass fiber micro-chambers. Furthermore, the same membrane was used for transversal separation of blood cells followed by accurate FPIA read-out at the bottom part of the micro-chamber. For quantification of tobramycin, 1 μL of whole blood was incubated with the immunoassay reagents during only 3 min before deposition in the micro-chamber and analysis. Within the therapeutic window, coefficients of variation were around 20% and recoveries between 80 and 105%. Owing to the simplified procedure requiring no centrifugation, the reduced blood sample volume and the rapid analysis time, we envision that this novel method supports the performance of therapeutic drug monitoring directly at the point of care.
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Affiliation(s)
- E-Diana Bojescu
- Institute of Life Technologies - School of Engineering, HES-SO // University of Applied Sciences Western Switzerland, Sion, Switzerland.
| | - Denis Prim
- Institute of Life Technologies - School of Engineering, HES-SO // University of Applied Sciences Western Switzerland, Sion, Switzerland.
| | - Marc E Pfeifer
- Institute of Life Technologies - School of Engineering, HES-SO // University of Applied Sciences Western Switzerland, Sion, Switzerland.
| | - Jean-Manuel Segura
- Institute of Life Technologies - School of Engineering, HES-SO // University of Applied Sciences Western Switzerland, Sion, Switzerland.
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14
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Deng Y, Lv Z, Cheng Y, Liu A, Huang Z. Clinical Application of a Safe Blood Sampling Device with an Indwelling Needle. Appl Bionics Biomech 2022; 2022:6362905. [PMID: 36091628 PMCID: PMC9458410 DOI: 10.1155/2022/6362905] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/27/2022] [Accepted: 08/02/2022] [Indexed: 11/17/2022] Open
Abstract
Background The traditional indwelling needle catheter is hard and can only complete one puncture at a time. The safety and indwelling needle catheter is soft, with a large lumen, with high success rate of blood collection, and one puncture completes two operations, so it is of important value and significance to study the new safety and indwelling needle. To explore the clinical utility of a novel blood collection device with indwelling needle for blood collection among pediatric patients. Methods A total of 300 children who were admitted to the children's hospital from March to June 2020 were selected and randomly divided into the control group (148) and the observation group (152). The control group received venipuncture using regular needles for infusion and blood collection. For the observation group, a modified indwelling needle device was used for the procedures. Comparisons were made between the two devices in five aspects: blood sample quality, operation time, needlestick incidence, related complications, and patient satisfaction. Results There was no significant difference in coagulation rate between the two groups, but slightly lower overall hemolysis incidence in the observation group. The unqualified rate of blood specimens collected in the observation group was 10.0% lower than that in the control group (P < 0.05). Shorter operation time, lower incidence of needlestick injuries, and improved satisfaction were observed in the group using the novel blood collection device. Conclusions This modified blood collection device is superior to the regular venipuncture needle, in terms of safety, efficiency, and patient satisfaction; thus, it has potential for broad clinical applications for infusion and blood collection.
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Affiliation(s)
- Yeqin Deng
- Anhui Maternal and Child Health Hospital, Anhui Medical University, Hefei, Anhui, China
| | - Zhengbing Lv
- Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
| | - Yue Cheng
- Anhui Maternal and Child Health Hospital, Anhui Medical University, Hefei, Anhui, China
| | - Annuo Liu
- School of Nursing, Anhui Medical University, Hefei, Anhui, China
| | - Zhengling Huang
- Anhui Maternal and Child Health Hospital, Anhui Medical University, Hefei, Anhui, China
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15
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Factors influencing degradation kinetics of mRNAs and half-lives of microRNAs, circRNAs, lncRNAs in blood in vitro using quantitative PCR. Sci Rep 2022; 12:7259. [PMID: 35508612 PMCID: PMC9068688 DOI: 10.1038/s41598-022-11339-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 04/21/2022] [Indexed: 12/18/2022] Open
Abstract
RNAs are rapidly degraded in samples and during collection, processing and testing. In this study, we used the same method to explore the half-lives of different RNAs and the influencing factors, and compared the degradation kinetics and characteristics of different RNAs in whole blood and experimental samples. Fresh anticoagulant blood samples were incubated at room temperature for different durations, RNAs were extracted, and genes, including internal references, were amplified by real-time quantitative PCR. A linear half-life model was established according to cycle threshold (Ct) values. The effects of experimental operations on RNA degradation before and after RNA extraction were explored. Quantitative analysis of mRNA degradation in samples and during experimental processes were explored using an orthogonal experimental design. The storage duration of blood samples at room temperature had the greatest influence on RNA degradation. The half-lives of messenger RNAs (mRNAs) was 16.4 h. The half-lives of circular RNAs (circRNAs), long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) were 24.56 ± 5.2 h, 17.46 ± 3.0 h and 16.42 ± 4.2 h, respectively. RNA degradation occurred mainly in blood samples. The half-life of mRNAs was the shortest among the four kinds of RNAs. Quantitative experiments related to mRNAs should be completed within 2 h. The half-lives of circRNAs and lncRNAs were longer than those of the former two.
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16
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Miller MR, Robinson M, Fischer L, DiBattista A, Patel MA, Daley M, Bartha R, Dekaban GA, Menon RS, Shoemaker JK, Diamandis EP, Prassas I, Fraser DD. Putative Concussion Biomarkers Identified in Adolescent Male Athletes Using Targeted Plasma Proteomics. Front Neurol 2022; 12:787480. [PMID: 34987469 PMCID: PMC8721148 DOI: 10.3389/fneur.2021.787480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/17/2021] [Indexed: 11/13/2022] Open
Abstract
Sport concussions can be difficult to diagnose and if missed, they can expose athletes to greater injury risk and long-lasting neurological disabilities. Discovery of objective biomarkers to aid concussion diagnosis is critical to protecting athlete brain health. To this end, we performed targeted proteomics on plasma obtained from adolescent athletes suffering a sports concussion. A total of 11 concussed male athletes were enrolled at our academic Sport Medicine Concussion Clinic, as well as 24 sex-, age- and activity-matched healthy control subjects. Clinical evaluation was performed and blood was drawn within 72 h of injury. Proximity extension assays were performed for 1,472 plasma proteins; a total of six proteins were considered significantly different between cohorts (P < 0.01; five proteins decreased and one protein increased). Receiver operating characteristic curves on the six individual protein biomarkers identified had areas-under-the-curves (AUCs) for concussion diagnosis ≥0.78; antioxidant 1 copper chaperone (ATOX1; AUC 0.81, P = 0.003), secreted protein acidic and rich in cysteine (SPARC; AUC 0.81, P = 0.004), cluster of differentiation 34 (CD34; AUC 0.79, P = 0.006), polyglutamine binding protein 1 (PQBP1; AUC 0.78, P = 0.008), insulin-like growth factor-binding protein-like 1 (IGFBPL1; AUC 0.78, P = 0.008) and cytosolic 5'-nucleotidase 3A (NT5C3A; AUC 0.78, P = 0.009). Combining three of the protein biomarkers (ATOX1, SPARC and NT5C3A), produced an AUC of 0.98 for concussion diagnoses (P < 0.001; 95% CI: 0.95, 1.00). Despite a paucity of studies on these three identified proteins, the available evidence points to their roles in modulating tissue inflammation and regulating integrity of the cerebral microvasculature. Taken together, our exploratory data suggest that three or less novel proteins, which are amenable to a point-of-care immunoassay, may be future candidate biomarkers for screening adolescent sport concussion. Validation with protein assays is required in larger cohorts.
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Affiliation(s)
- Michael R Miller
- Department of Pediatrics, Western University, London, ON, Canada.,Children's Health Research Institute, London, ON, Canada
| | - Michael Robinson
- School of Health Studies, Western University, London, ON, Canada.,School of Kinesiology, Western University, London, ON, Canada.,Department of Family Medicine, Western University, London, ON, Canada
| | - Lisa Fischer
- Department of Family Medicine, Western University, London, ON, Canada
| | - Alicia DiBattista
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada.,Neurolytixs Inc., Toronto, ON, Canada
| | - Maitray A Patel
- Department of Epidemiology, Western University, London, ON, Canada
| | - Mark Daley
- Department of Epidemiology, Western University, London, ON, Canada.,Department of Computer Science, Western University, London, ON, Canada
| | - Robert Bartha
- Department of Medical Biophysics, Western University, London, ON, Canada.,Robarts Research Institute, London, ON, Canada
| | - Gregory A Dekaban
- Robarts Research Institute, London, ON, Canada.,Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Ravi S Menon
- Department of Medical Biophysics, Western University, London, ON, Canada.,Robarts Research Institute, London, ON, Canada
| | | | | | - Ioannis Prassas
- Department of Pathology and Laboratory Medicine, University of Toronto, Toronto, ON, Canada
| | - Douglas D Fraser
- Department of Pediatrics, Western University, London, ON, Canada.,Children's Health Research Institute, London, ON, Canada.,Neurolytixs Inc., Toronto, ON, Canada.,Department of Physiology and Pharmacology, Western University, London, ON, Canada.,Depatment of Clinical Neurological Sciences, Western University, London, ON, Canada
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17
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Kerachian MA, Azghandi M, Mozaffari-Jovin S, Thierry AR. Guidelines for pre-analytical conditions for assessing the methylation of circulating cell-free DNA. Clin Epigenetics 2021; 13:193. [PMID: 34663458 PMCID: PMC8525023 DOI: 10.1186/s13148-021-01182-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/04/2021] [Indexed: 02/06/2023] Open
Abstract
Methylation analysis of circulating cell-free DNA (cirDNA), as a liquid biopsy, has a significant potential to advance the detection, prognosis, and treatment of cancer, as well as many genetic disorders. The role of epigenetics in disease development has been reported in several hereditary disorders, and epigenetic modifications are regarded as one of the earliest and most significant genomic aberrations that arise during carcinogenesis. Liquid biopsy can be employed for the detection of these epigenetic biomarkers. It consists of isolation (pre-analytical) and detection (analytical) phases. The choice of pre-analytical variables comprising cirDNA extraction and bisulfite conversion methods can affect the identification of cirDNA methylation. Indeed, different techniques give a different return of cirDNA, which confirms the importance of pre-analytical procedures in clinical diagnostics. Although novel techniques have been developed for the simplification of methylation analysis, the process remains complex, as the steps of DNA extraction, bisulfite treatment, and methylation detection are each carried out separately. Recent studies have noted the absence of any standard method for the pre-analytical processing of methylated cirDNA. We have therefore conducted a comprehensive and systematic review of the important pre-analytical and analytical variables and the patient-related factors which form the basis of our guidelines for analyzing methylated cirDNA in liquid biopsy.
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Affiliation(s)
- Mohammad Amin Kerachian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran.
| | - Marjan Azghandi
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Sina Mozaffari-Jovin
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alain R Thierry
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier, France.
- INSERM, U1194, Montpellier, France.
- University of Montpellier, Montpellier, France.
- ICM, Regional Institute of Cancer of Montpellier, Montpellier, France.
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18
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Heiling S, Knutti N, Scherr F, Geiger J, Weikert J, Rose M, Jahns R, Ceglarek U, Scherag A, Kiehntopf M. Metabolite Ratios as Quality Indicators for Pre-Analytical Variation in Serum and EDTA Plasma. Metabolites 2021; 11:638. [PMID: 34564454 PMCID: PMC8465943 DOI: 10.3390/metabo11090638] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 12/18/2022] Open
Abstract
In clinical diagnostics and research, blood samples are one of the most frequently used materials. Nevertheless, exploring the chemical composition of human plasma and serum is challenging due to the highly dynamic influence of pre-analytical variation. A prominent example is the variability in pre-centrifugation delay (time-to-centrifugation; TTC). Quality indicators (QI) reflecting sample TTC are of utmost importance in assessing sample history and resulting sample quality, which is essential for accurate diagnostics and conclusive, reproducible research. In the present study, we subjected human blood to varying TTCs at room temperature prior to processing for plasma or serum preparation. Potential sample QIs were identified by Ultra high pressure liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) based metabolite profiling in samples from healthy volunteers (n = 10). Selected QIs were validated by a targeted MS/MS approach in two independent sets of samples from patients (n = 40 and n = 70). In serum, the hypoxanthine/guanosine (HG) and hypoxanthine/inosine (HI) ratios demonstrated high diagnostic performance (Sensitivity/Specificity > 80%) for the discrimination of samples with a TTC > 1 h. We identified several eicosanoids, such as 12-HETE, 15-(S)-HETE, 8-(S)-HETE, 12-oxo-HETE, (±)13-HODE and 12-(S)-HEPE as QIs for a pre-centrifugation delay > 2 h. 12-HETE, 12-oxo-HETE, 8-(S)-HETE, and 12-(S)-HEPE, and the HI- and HG-ratios could be validated in patient samples.
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Affiliation(s)
- Sven Heiling
- Institute of Clinical Chemistry and Laboratory Diagnostics and Integrated Biobank Jena (IBBJ), University Hospital Jena, Am Klinikum 1, 07747 Jena, Germany; (N.K.); (F.S.); (M.R.)
| | - Nadine Knutti
- Institute of Clinical Chemistry and Laboratory Diagnostics and Integrated Biobank Jena (IBBJ), University Hospital Jena, Am Klinikum 1, 07747 Jena, Germany; (N.K.); (F.S.); (M.R.)
| | - Franziska Scherr
- Institute of Clinical Chemistry and Laboratory Diagnostics and Integrated Biobank Jena (IBBJ), University Hospital Jena, Am Klinikum 1, 07747 Jena, Germany; (N.K.); (F.S.); (M.R.)
| | - Jörg Geiger
- Interdisciplinary Bank of Biological Material and Data Würzburg (IBDW), Straubmühlweg 2a, Haus A9, 97078 Würzburg, Germany; (J.G.); (R.J.)
| | - Juliane Weikert
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, 04103 Leipzig, Germany; (J.W.); (U.C.)
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, 04103 Leipzig, Germany
| | - Michael Rose
- Institute of Clinical Chemistry and Laboratory Diagnostics and Integrated Biobank Jena (IBBJ), University Hospital Jena, Am Klinikum 1, 07747 Jena, Germany; (N.K.); (F.S.); (M.R.)
| | - Roland Jahns
- Interdisciplinary Bank of Biological Material and Data Würzburg (IBDW), Straubmühlweg 2a, Haus A9, 97078 Würzburg, Germany; (J.G.); (R.J.)
| | - Uta Ceglarek
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, 04103 Leipzig, Germany; (J.W.); (U.C.)
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, 04103 Leipzig, Germany
| | - André Scherag
- Institute of Medical Statistics, Computer and Data Sciences, Jena University Hospital, Bachstrasse 18, 07743 Jena, Germany;
| | - Michael Kiehntopf
- Institute of Clinical Chemistry and Laboratory Diagnostics and Integrated Biobank Jena (IBBJ), University Hospital Jena, Am Klinikum 1, 07747 Jena, Germany; (N.K.); (F.S.); (M.R.)
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19
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Rimmer MP, Gregory CD, Mitchell RT. Extracellular vesicles in urological malignancies. Biochim Biophys Acta Rev Cancer 2021; 1876:188570. [PMID: 34019971 PMCID: PMC8351753 DOI: 10.1016/j.bbcan.2021.188570] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/10/2021] [Accepted: 05/13/2021] [Indexed: 12/11/2022]
Abstract
Extracellular vesicles (EVs) are small lipid bound structures released from cells containing bioactive cargoes. Both the type of cargo and amount loaded varies compared to that of the parent cell. The characterisation of EVs in cancers of the male urogenital tract has identified several cargoes with promising diagnostic and disease monitoring potential. EVs released by cancers of the male urogenital tract promote cell-to-cell communication, migration, cancer progression and manipulate the immune system promoting metastasis by evading the immune response. Their use as diagnostic biomarkers represents a new area of screening and disease detection, potentially reducing the need for invasive biopsies. Many validated EV cargoes have been found to have superior sensitivity and specificity than current diagnostic tools currently in use. The use of EVs to improve disease monitoring and develop novel therapeutics will enable clinicians to individualise patient management in the exciting era of personalised medicine.
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Affiliation(s)
- Michael P Rimmer
- MRC Centre for Reproductive Health, Queens Medical Research Institute, University of Edinburgh, UK.
| | - Christopher D Gregory
- Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, UK
| | - Rod T Mitchell
- MRC Centre for Reproductive Health, Queens Medical Research Institute, University of Edinburgh, UK.
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20
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Fraser DD, Chen M, Ren A, Miller MR, Martin C, Daley M, Diamandis EP, Prassas I. Novel severe traumatic brain injury blood outcome biomarkers identified with proximity extension assay. Clin Chem Lab Med 2021; 59:1662-1669. [PMID: 34144643 DOI: 10.1515/cclm-2021-0103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/28/2021] [Indexed: 01/04/2023]
Abstract
OBJECTIVES Severe traumatic brain injury (sTBI) patients suffer high mortality. Accurate prognostic biomarkers have not been identified. In this exploratory study, we performed targeted proteomics on plasma obtained from sTBI patients to identify potential outcome biomarkers. METHODS Blood sample was collected from patients admitted to the ICU suffering a sTBI, using standardized clinical and computerized tomography (CT) imaging criteria. Age- and sex-matched healthy control subjects and sTBI patients were enrolled. Targeted proteomics was performed on plasma with proximity extension assays (1,161 proteins). RESULTS Cohorts were well-balanced for age and sex. The majority of sTBI patients were injured in motor vehicle collisions and the most frequent head CT finding was subarachnoid hemorrhage. Mortality rate for sTBI patients was 40%. Feature selection identified the top performing 15 proteins for identifying sTBI patients from healthy control subjects with a classification accuracy of 100%. The sTBI proteome was dominated by markers of vascular pathology, immunity/inflammation, cell survival and macrophage/microglia activation. Receiver operating characteristic (ROC) curve analyses demonstrated areas-under-the-curves (AUC) for identifying sTBI that ranged from 0.870-1.000 (p≤0.005). When mortality was used as outcome, ROC curve analyses identified the top 3 proteins as Willebrand factor (vWF), Wnt inhibitory factor-1 (WIF-1), and colony stimulating factor-1 (CSF-1). Combining vWF with either WIF-1 or CSF-1 resulted in excellent mortality prediction with AUC of 1.000 for both combinations (p=0.011). CONCLUSIONS Targeted proteomics with feature classification and selection distinguished sTBI patients from matched healthy control subjects. Two protein combinations were identified that accurately predicted sTBI patient mortality. Our exploratory findings require confirmation in larger sTBI patient populations.
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Affiliation(s)
- Douglas D Fraser
- Lawson Health Research Institute, London, ON, Canada.,Pediatrics, Western University, London, ON, Canada.,Clinical Neurological Sciences, Western University, London, ON, Canada.,Physiology and Pharmacology, Western University, London, ON, Canada.,NeuroLytixs Inc., Toronto, ON, Canada
| | - Michelle Chen
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Annie Ren
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Michael R Miller
- Lawson Health Research Institute, London, ON, Canada.,Pediatrics, Western University, London, ON, Canada
| | | | - Mark Daley
- Lawson Health Research Institute, London, ON, Canada
| | - Eleftherios P Diamandis
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada.,Clinical Biochemistry, University Health Network, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Ioannis Prassas
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
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21
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Juneja GK, Castelo M, Yeh CH, Cerroni SE, Hansen BE, Chessum JE, Abraham J, Cani E, Dwivedi DJ, Fraser DD, Slessarev M, Martin C, McGilvray S, Gross PL, Liaw PC, Weitz JI, Kim PY. Biomarkers of coagulation, endothelial function, and fibrinolysis in critically ill patients with COVID-19: A single-center prospective longitudinal study. J Thromb Haemost 2021; 19:1546-1557. [PMID: 33826233 PMCID: PMC8250276 DOI: 10.1111/jth.15327] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 03/26/2021] [Accepted: 03/30/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND Immunothrombosis and coagulopathy in the lung microvasculature may lead to lung injury and disease progression in coronavirus disease 2019 (COVID-19). We aim to identify biomarkers of coagulation, endothelial function, and fibrinolysis that are associated with disease severity and may have prognostic potential. METHODS We performed a single-center prospective study of 14 adult COVID-19(+) intensive care unit patients who were age- and sex-matched to 14 COVID-19(-) intensive care unit patients, and healthy controls. Daily blood draws, clinical data, and patient characteristics were collected. Baseline values for 10 biomarkers of interest were compared between the three groups, and visualized using Fisher's linear discriminant function. Linear repeated-measures mixed models were used to screen biomarkers for associations with mortality. Selected biomarkers were further explored and entered into an unsupervised longitudinal clustering machine learning algorithm to identify trends and targets that may be used for future predictive modelling efforts. RESULTS Elevated D-dimer was the strongest contributor in distinguishing COVID-19 status; however, D-dimer was not associated with survival. Variable selection identified clot lysis time, and antigen levels of soluble thrombomodulin (sTM), plasminogen activator inhibitor-1 (PAI-1), and plasminogen as biomarkers associated with death. Longitudinal multivariate k-means clustering on these biomarkers alone identified two clusters of COVID-19(+) patients: low (30%) and high (100%) mortality groups. Biomarker trajectories that characterized the high mortality cluster were higher clot lysis times (inhibited fibrinolysis), higher sTM and PAI-1 levels, and lower plasminogen levels. CONCLUSIONS Longitudinal trajectories of clot lysis time, sTM, PAI-1, and plasminogen may have predictive ability for mortality in COVID-19.
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Affiliation(s)
- Ganeem K Juneja
- Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, Canada
- Department of Medical Sciences, McMaster University, Hamilton, ON, Canada
| | - Matthew Castelo
- Department of Surgery, University of Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Calvin H Yeh
- Department of Medicine, Division of Emergency Medicine, University of Toronto, Toronto, ON, Canada
| | - Samantha E Cerroni
- Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Bettina E Hansen
- Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - James E Chessum
- Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, Canada
- Department of Medical Sciences, McMaster University, Hamilton, ON, Canada
| | - Joel Abraham
- Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, Canada
- Department of Medical Sciences, McMaster University, Hamilton, ON, Canada
| | - Erblin Cani
- Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, Canada
- Department of Medical Sciences, McMaster University, Hamilton, ON, Canada
| | - Dhruva J Dwivedi
- Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Douglas D Fraser
- Lawson Health Research Institute, London, ON, Canada
- Pediatrics, Western University, London, ON, Canada
- Clinical Neurological Sciences, Western University, London, ON, Canada
- Physiology & Pharmacology, Western University, London, ON, Canada
| | - Marat Slessarev
- Lawson Health Research Institute, London, ON, Canada
- Medicine, Western University, London, ON, Canada
| | - Claudio Martin
- Lawson Health Research Institute, London, ON, Canada
- Medicine, Western University, London, ON, Canada
| | - Scott McGilvray
- Department of Medicine, Division of Emergency Medicine, University of Toronto, Toronto, ON, Canada
| | - Peter L Gross
- Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Patricia C Liaw
- Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Jeffrey I Weitz
- Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Paul Y Kim
- Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
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22
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Fraser DD, Cepinskas G, Slessarev M, Martin CM, Daley M, Patel MA, Miller MR, Patterson EK, O’Gorman DB, Gill SE, Higgins I, John JPP, Melo C, Nini L, Wang X, Zeidler J, Cruz-Aguado JA. Critically Ill COVID-19 Patients Exhibit Anti-SARS-CoV-2 Serological Responses. PATHOPHYSIOLOGY 2021; 28:212-223. [PMID: 35366258 PMCID: PMC8830473 DOI: 10.3390/pathophysiology28020014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 12/16/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, is a global health care emergency. Anti-SARS-CoV-2 serological profiling of critically ill COVID-19 patients was performed to determine their humoral response. Blood was collected from critically ill ICU patients, either COVID-19 positive (+) or COVID-19 negative (-), to measure anti-SARS-CoV-2 immunoglobulins: IgM; IgA; IgG; and Total Ig (combined IgM/IgA/IgG). Cohorts were similar, with the exception that COVID-19+ patients had a greater body mass indexes, developed bilateral pneumonias more frequently and suffered increased hypoxia when compared to COVID-19- patients (p < 0.05). The mortality rate for COVID-19+ patients was 50%. COVID-19 status could be determined by anti-SARS-CoV-2 serological responses with excellent classification accuracies on ICU day 1 (89%); ICU day 3 (96%); and ICU days 7 and 10 (100%). The importance of each Ig isotype for determining COVID-19 status on combined ICU days 1 and 3 was: Total Ig, 43%; IgM, 27%; IgA, 24% and IgG, 6%. Peak serological responses for each Ig isotype occurred on different ICU days (IgM day 13 > IgA day 17 > IgG persistently increased), with the Total Ig peaking at approximately ICU day 18. Those COVID-19+ patients who died had earlier or similar peaks in IgA and Total Ig in their ICU stay when compared to patients who survived (p < 0.005). Critically ill COVID-19 patients exhibit anti-SARS-CoV-2 serological responses, including those COVID-19 patients who ultimately died, suggesting that blunted serological responses did not contribute to mortality. Serological profiling of critically ill COVID-19 patients may aid disease surveillance, patient cohorting and help guide antibody therapies such as convalescent plasma.
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Affiliation(s)
- Douglas D. Fraser
- Lawson Health Research Institute, London, ON N6C 2R5, Canada; (G.C.); (M.S.); (C.M.M.); (M.D.); (M.R.M.); (E.K.P.); (D.B.O.); (S.E.G.)
- Department of Pediatrics, Western University, London, ON N6A 3K7, Canada
- Department of Clinical Neurological Sciences, Western University, London, ON N6A 3K7, Canada
- Department of Physiology & Pharmacology, Western University, London, ON N6A 3K7, Canada
| | - Gediminas Cepinskas
- Lawson Health Research Institute, London, ON N6C 2R5, Canada; (G.C.); (M.S.); (C.M.M.); (M.D.); (M.R.M.); (E.K.P.); (D.B.O.); (S.E.G.)
- Department of Medical Biophysics, Western University, London, ON N6A 3K7, Canada
| | - Marat Slessarev
- Lawson Health Research Institute, London, ON N6C 2R5, Canada; (G.C.); (M.S.); (C.M.M.); (M.D.); (M.R.M.); (E.K.P.); (D.B.O.); (S.E.G.)
- Department of Medicine, Western University, London, ON N6A 3K7, Canada
| | - Claudio M. Martin
- Lawson Health Research Institute, London, ON N6C 2R5, Canada; (G.C.); (M.S.); (C.M.M.); (M.D.); (M.R.M.); (E.K.P.); (D.B.O.); (S.E.G.)
- Department of Medicine, Western University, London, ON N6A 3K7, Canada
| | - Mark Daley
- Lawson Health Research Institute, London, ON N6C 2R5, Canada; (G.C.); (M.S.); (C.M.M.); (M.D.); (M.R.M.); (E.K.P.); (D.B.O.); (S.E.G.)
- Department of Computer Science, Western University, London, ON N6A 3K7, Canada;
- The Vector Institute for Artificial Intelligence, Toronto, ON M5G 1M1, Canada
| | - Maitray A. Patel
- Department of Computer Science, Western University, London, ON N6A 3K7, Canada;
| | - Michael R. Miller
- Lawson Health Research Institute, London, ON N6C 2R5, Canada; (G.C.); (M.S.); (C.M.M.); (M.D.); (M.R.M.); (E.K.P.); (D.B.O.); (S.E.G.)
- Department of Pediatrics, Western University, London, ON N6A 3K7, Canada
| | - Eric K. Patterson
- Lawson Health Research Institute, London, ON N6C 2R5, Canada; (G.C.); (M.S.); (C.M.M.); (M.D.); (M.R.M.); (E.K.P.); (D.B.O.); (S.E.G.)
| | - David B. O’Gorman
- Lawson Health Research Institute, London, ON N6C 2R5, Canada; (G.C.); (M.S.); (C.M.M.); (M.D.); (M.R.M.); (E.K.P.); (D.B.O.); (S.E.G.)
- Department of Surgery, Western University, London, ON N6A 3K7, Canada
- Department of Biochemistry, Western University, London, ON N6A 3K7, Canada
| | - Sean E. Gill
- Lawson Health Research Institute, London, ON N6C 2R5, Canada; (G.C.); (M.S.); (C.M.M.); (M.D.); (M.R.M.); (E.K.P.); (D.B.O.); (S.E.G.)
- Department of Physiology & Pharmacology, Western University, London, ON N6A 3K7, Canada
- Department of Medicine, Western University, London, ON N6A 3K7, Canada
| | - Ian Higgins
- Diagnostics Biochem Canada, London, ON N6M 1A1, Canada; (I.H.); (J.P.P.J.); (C.M.); (L.N.); (X.W.); (J.Z.); (J.A.C.-A.)
| | - Julius P. P. John
- Diagnostics Biochem Canada, London, ON N6M 1A1, Canada; (I.H.); (J.P.P.J.); (C.M.); (L.N.); (X.W.); (J.Z.); (J.A.C.-A.)
| | - Christopher Melo
- Diagnostics Biochem Canada, London, ON N6M 1A1, Canada; (I.H.); (J.P.P.J.); (C.M.); (L.N.); (X.W.); (J.Z.); (J.A.C.-A.)
| | - Lylia Nini
- Diagnostics Biochem Canada, London, ON N6M 1A1, Canada; (I.H.); (J.P.P.J.); (C.M.); (L.N.); (X.W.); (J.Z.); (J.A.C.-A.)
| | - Xiaoqin Wang
- Diagnostics Biochem Canada, London, ON N6M 1A1, Canada; (I.H.); (J.P.P.J.); (C.M.); (L.N.); (X.W.); (J.Z.); (J.A.C.-A.)
| | - Johannes Zeidler
- Diagnostics Biochem Canada, London, ON N6M 1A1, Canada; (I.H.); (J.P.P.J.); (C.M.); (L.N.); (X.W.); (J.Z.); (J.A.C.-A.)
| | - Jorge A. Cruz-Aguado
- Diagnostics Biochem Canada, London, ON N6M 1A1, Canada; (I.H.); (J.P.P.J.); (C.M.); (L.N.); (X.W.); (J.Z.); (J.A.C.-A.)
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23
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Chen M, Ren AH, Prassas I, Soosaipillai A, Lim B, Fraser DD, Diamandis EP. Plasma Protein Profiling by Proximity Extension Assay Technology Reveals Novel Biomarkers of Traumatic Brain Injury-A Pilot Study. J Appl Lab Med 2021; 6:1165-1178. [PMID: 33778875 DOI: 10.1093/jalm/jfab004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 01/15/2021] [Indexed: 01/04/2023]
Abstract
BACKGROUND Traumatic brain injury (TBI) is a significant public health issue affecting nearly 69 million patients worldwide per year. Reliable diagnostic biomarkers are urgently needed to aid in disease diagnosis and prognosis and to guide patient aftercare. Blood biomarkers represent an attractive modality to quickly, cheaply, and objectively evaluate clinical status. We hypothesize that deep and quantitative plasma proteomic profiling with a novel technology, proximity extension assay, may lead to the discovery of diagnostic and/or prognostic biomarkers of TBI. METHODS We used high-throughput proximity extension assays (PEA) to quantify the relative abundance of over 1000 unique proteins in plasma. PEA is a highly sensitive multiplex immunoassay capable of detecting very low-abundance proteins (down to fg/mL) in complex biological matrices. Our patient cohort consisted of severe TBI (sTBI) patients, matched healthy controls, and another non-TBI group that was included in the analysis to validate the specificity of the candidates during the selection process. The obtained protein quantification data was then filtered to identify candidate biomarkers through statistical analysis, literature searches, and comparison to our reference control groups. RESULTS Overall, we identified 6 novel candidate TBI biomarkers. Candidates exhibit a significant increase in plasma protein abundance in sTBI when comparing between healthy controls and sTBI patients. Candidates generally had low expression in our reference groups compared with the sTBI group. CONCLUSIONS Our preliminary findings represent a starting point for future validation. These biomarkers, either alone or in combination, may have significant clinical utility in aiding in TBI diagnosis, prognosis, and/or management.
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Affiliation(s)
- Michelle Chen
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Annie H Ren
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Ioannis Prassas
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Antoninus Soosaipillai
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Bryant Lim
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Douglas D Fraser
- Department of Pediatrics, Western University, London, ON, Canada
| | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada.,Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
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24
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Fraser DD, Cepinskas G, Slessarev M, Martin CM, Daley M, Patel MA, Miller MR, Patterson EK, O'Gorman DB, Gill SE, Oehler S, Miholits M, Webb B. Detection and Profiling of Human Coronavirus Immunoglobulins in Critically Ill Coronavirus Disease 2019 Patients. Crit Care Explor 2021; 3:e0369. [PMID: 33786445 PMCID: PMC7994038 DOI: 10.1097/cce.0000000000000369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVES Coronavirus disease 2019 continues to spread worldwide with high levels of morbidity and mortality. We performed anticoronavirus immunoglobulin G profiling of critically ill coronavirus disease 2019 patients to better define their underlying humoral response. DESIGN Blood was collected at predetermined ICU days to measure immunoglobulin G with a research multiplex assay against four severe acute respiratory syndrome coronavirus 2 proteins/subunits and against all six additionally known human coronaviruses. SETTING Tertiary care ICU and academic laboratory. SUBJECTS ICU patients suspected of being infected with severe acute respiratory syndrome coronavirus 2 had blood collected until either polymerase chain reaction testing was confirmed negative on ICU day 3 (coronavirus disease 2019 negative) or until death or discharge if the patient tested polymerase chain reaction positive (coronavirus disease 2019 positive). INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS Age- and sex-matched healthy controls and ICU patients who were either coronavirus disease 2019 positive or coronavirus disease 2019 negative were enrolled. Cohorts were well-balanced with the exception that coronavirus disease 2019 positive patients had greater body mass indexes, presented with bilateral pneumonias more frequently, and suffered lower Pao2:Fio2 ratios, when compared with coronavirus disease 2019 negative patients (p < 0.05). Mortality rate for coronavirus disease 2019 positive patients was 50%. On ICU days 1-3, anti-severe acute respiratory syndrome coronavirus 2 immunoglobulin G was significantly elevated in coronavirus disease 2019 positive patients, as compared to both healthy control subjects and coronavirus disease 2019 negative patients (p < 0.001). Weak severe acute respiratory syndrome coronavirus immunoglobulin G serologic responses were also detected, but not other coronavirus subtypes. The four anti-severe acute respiratory syndrome coronavirus 2 immunoglobulin G were maximal by ICU day 3, with all four anti-severe acute respiratory syndrome coronavirus 2 immunoglobulin G providing excellent diagnostic potential (severe acute respiratory syndrome coronavirus 2 Spike 1 protein immunoglobulin G, area under the curve 1.0, p < 0.0005; severe acute respiratory syndrome coronavirus receptor binding domain immunoglobulin G, area under the curve, 0.93-1.0; p ≤ 0.0001; severe acute respiratory syndrome coronavirus 2 Spike proteins immunoglobulin G, area under the curve, 1.0; p < 0.0001; severe acute respiratory syndrome coronavirus 2 Nucleocapsid protein immunoglobulin G area under the curve, 0.90-0.95; p ≤ 0.0003). Anti-severe acute respiratory syndrome coronavirus 2 immunoglobulin G increased and/or plateaued over 10 ICU days. CONCLUSIONS Critically ill coronavirus disease 2019 patients exhibited anti-severe acute respiratory syndrome coronavirus 2 immunoglobulin G, whereas serologic responses to non-severe acute respiratory syndrome coronavirus 2 antigens were weak or absent. Detection of human coronavirus immunoglobulin G against the different immunogenic structural proteins/subunits with multiplex assays may be useful for pathogen identification, patient cohorting, and guiding convalescent plasma therapy.
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Affiliation(s)
- Douglas D Fraser
- Lawson Health Research Institute, London, ON, Canada
- Pediatrics, Western University, London, ON, Canada
- Clinical Neurological Sciences, Western University, London, ON, Canada
- Physiology & Pharmacology, Western University, London, ON, Canada
| | - Gediminas Cepinskas
- Lawson Health Research Institute, London, ON, Canada
- Medical Biophysics, Western University, London, ON, Canada
| | - Marat Slessarev
- Lawson Health Research Institute, London, ON, Canada
- Medicine, Western University, London, ON, Canada
| | - Claudio M Martin
- Lawson Health Research Institute, London, ON, Canada
- Medicine, Western University, London, ON, Canada
| | - Mark Daley
- Lawson Health Research Institute, London, ON, Canada
- Computer Science, Western University, London, ON, Canada
- The Vector Institute for Artificial Intelligence, Toronto, ON, Canada
| | | | - Michael R Miller
- Lawson Health Research Institute, London, ON, Canada
- Pediatrics, Western University, London, ON, Canada
| | | | - David B O'Gorman
- Lawson Health Research Institute, London, ON, Canada
- Surgery, Western University, London, ON, Canada
- Biochemistry, Western University, London, ON, Canada
| | - Sean E Gill
- Lawson Health Research Institute, London, ON, Canada
- Physiology & Pharmacology, Western University, London, ON, Canada
- Medicine, Western University, London, ON, Canada
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25
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Gill SE, Dos Santos CC, O'Gorman DB, Carter DE, Patterson EK, Slessarev M, Martin C, Daley M, Miller MR, Cepinskas G, Fraser DD. Transcriptional profiling of leukocytes in critically ill COVID19 patients: implications for interferon response and coagulation. Intensive Care Med Exp 2020; 8:75. [PMID: 33306162 PMCID: PMC7729690 DOI: 10.1186/s40635-020-00361-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/19/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND COVID19 is caused by the SARS-CoV-2 virus and has been associated with severe inflammation leading to organ dysfunction and mortality. Our aim was to profile the transcriptome in leukocytes from critically ill patients positive for COVID19 compared to those negative for COVID19 to better understand the COVID19-associated host response. For these studies, all patients admitted to our tertiary care intensive care unit (ICU) suspected of being infected with SARS-CoV-2, using standardized hospital screening methodologies, had blood samples collected at the time of admission to the ICU. Transcriptome profiling of leukocytes via ribonucleic acid sequencing (RNAseq) was then performed and differentially expressed genes as well as significantly enriched gene sets were identified. RESULTS We enrolled seven COVID19 + (PCR positive, 2 SARS-CoV-2 genes) and seven age- and sex-matched COVID19- (PCR negative) control ICU patients. Cohorts were well-balanced with the exception that COVID19- patients had significantly higher total white blood cell counts and circulating neutrophils and COVID19 + patients were more likely to suffer bilateral pneumonia. The mortality rate for this cohort of COVID19 + ICU patients was 29%. As indicated by both single-gene based and gene set (GSEA) approaches, the major disease-specific transcriptional responses of leukocytes in critically ill COVID19 + ICU patients were: (i) a robust overrepresentation of interferon-related gene expression; (ii) a marked decrease in the transcriptional level of genes contributing to general protein synthesis and bioenergy metabolism; and (iii) the dysregulated expression of genes associated with coagulation, platelet function, complement activation, and tumour necrosis factor/interleukin 6 signalling. CONCLUSIONS Our findings demonstrate that critically ill COVID19 + patients on day 1 of admission to the ICU display a unique leukocyte transcriptional profile that distinguishes them from COVID19- patients, providing guidance for future targeted studies exploring novel prognostic and therapeutic aspects of COVID19.
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Affiliation(s)
- Sean E Gill
- Lawson Health Research Institute, London, ON, Canada. .,Physiology and Pharmacology, Western University, London, ON, Canada. .,Medicine, Western University, London, ON, Canada. .,Victoria Research Labs, Room A6-134, 800 Commissioners Road East, London, ON, N6A 5W9, Canada.
| | - Claudia C Dos Santos
- Interdepartmental Division of Critical Care Medicine and Keenan Center for Biomedical Research of St. Michael's Hospital, University of Toronto, Toronto, ON, Canada
| | - David B O'Gorman
- Lawson Health Research Institute, London, ON, Canada.,Biochemistry, Western University, London, ON, Canada
| | - David E Carter
- London Regional Genomics Centre, Western University, London, ON, Canada
| | | | - Marat Slessarev
- Lawson Health Research Institute, London, ON, Canada.,Medicine, Western University, London, ON, Canada
| | - Claudio Martin
- Lawson Health Research Institute, London, ON, Canada.,Medicine, Western University, London, ON, Canada
| | - Mark Daley
- Lawson Health Research Institute, London, ON, Canada.,Computer Science, Western University, London, ON, Canada
| | - Michael R Miller
- Lawson Health Research Institute, London, ON, Canada.,Pediatrics, Western University, London, ON, Canada
| | - Gediminas Cepinskas
- Lawson Health Research Institute, London, ON, Canada.,Medical Biophysics, Western University, London, ON, Canada
| | - Douglas D Fraser
- Lawson Health Research Institute, London, ON, Canada. .,Physiology and Pharmacology, Western University, London, ON, Canada. .,Pediatrics, Western University, London, ON, Canada. .,London Health Sciences Centre, Room C2-C82, 800 Commissioners Road East, London, ON, N6A 5W9, Canada.
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Fraser DD, Slessarev M, Martin CM, Daley M, Patel MA, Miller MR, Patterson EK, O'Gorman DB, Gill SE, Wishart DS, Mandal R, Cepinskas G. Metabolomics Profiling of Critically Ill Coronavirus Disease 2019 Patients: Identification of Diagnostic and Prognostic Biomarkers. Crit Care Explor 2020; 2:e0272. [PMID: 33134953 PMCID: PMC7587450 DOI: 10.1097/cce.0000000000000272] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES Coronavirus disease 2019 continues to spread rapidly with high mortality. We performed metabolomics profiling of critically ill coronavirus disease 2019 patients to understand better the underlying pathologic processes and pathways, and to identify potential diagnostic/prognostic biomarkers. DESIGN Blood was collected at predetermined ICU days to measure the plasma concentrations of 162 metabolites using both direct injection-liquid chromatography-tandem mass spectrometry and proton nuclear magnetic resonance. SETTING Tertiary-care ICU and academic laboratory. SUBJECTS Patients admitted to the ICU suspected of being infected with severe acute respiratory syndrome coronavirus 2, using standardized hospital screening methodologies, had blood samples collected until either testing was confirmed negative on ICU day 3 (coronavirus disease 2019 negative) or until ICU day 10 if the patient tested positive (coronavirus disease 2019 positive). INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS Age- and sex-matched healthy controls and ICU patients that were either coronavirus disease 2019 positive or coronavirus disease 2019 negative were enrolled. Cohorts were well balanced with the exception that coronavirus disease 2019 positive patients suffered bilateral pneumonia more frequently than coronavirus disease 2019 negative patients. Mortality rate for coronavirus disease 2019 positive ICU patients was 40%. Feature selection identified the top-performing metabolites for identifying coronavirus disease 2019 positive patients from healthy control subjects and was dominated by increased kynurenine and decreased arginine, sarcosine, and lysophosphatidylcholines. Arginine/kynurenine ratio alone provided 100% classification accuracy between coronavirus disease 2019 positive patients and healthy control subjects (p = 0.0002). When comparing the metabolomes between coronavirus disease 2019 positive and coronavirus disease 2019 negative patients, kynurenine was the dominant metabolite and the arginine/kynurenine ratio provided 98% classification accuracy (p = 0.005). Feature selection identified creatinine as the top metabolite for predicting coronavirus disease 2019-associated mortality on both ICU days 1 and 3, and both creatinine and creatinine/arginine ratio accurately predicted coronavirus disease 2019-associated death with 100% accuracy (p = 0.01). CONCLUSIONS Metabolomics profiling with feature classification easily distinguished both healthy control subjects and coronavirus disease 2019 negative patients from coronavirus disease 2019 positive patients. Arginine/kynurenine ratio accurately identified coronavirus disease 2019 status, whereas creatinine/arginine ratio accurately predicted coronavirus disease 2019-associated death. Administration of tryptophan (kynurenine precursor), arginine, sarcosine, and/or lysophosphatidylcholines may be considered as potential adjunctive therapies.
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Affiliation(s)
- Douglas D Fraser
- Lawson Health Research Institute, London, ON, Canada
- Department of Pediatrics, Western University, London, ON, Canada
- Department of Clinical Neurological Sciences, Western University, London, ON, Canada
- Department of Physiology and Pharmacology, Western University, London, ON, Canada
| | - Marat Slessarev
- Lawson Health Research Institute, London, ON, Canada
- Department of Medicine, Western University, London, ON, Canada
| | - Claudio M Martin
- Lawson Health Research Institute, London, ON, Canada
- Department of Medicine, Western University, London, ON, Canada
| | - Mark Daley
- Lawson Health Research Institute, London, ON, Canada
- Department of Computer Science, Western University, London, ON, Canada
- Vector Institute for Artificial Intelligence, Toronto, ON, Canada
| | - Maitray A Patel
- Department of Computer Science, Western University, London, ON, Canada
| | - Michael R Miller
- Lawson Health Research Institute, London, ON, Canada
- Department of Pediatrics, Western University, London, ON, Canada
| | | | - David B O'Gorman
- Lawson Health Research Institute, London, ON, Canada
- Department of Surgery, Western University, London, ON, Canada
- Department of Biochemistry, Western University, London, ON, Canada
| | - Sean E Gill
- Lawson Health Research Institute, London, ON, Canada
- Department of Physiology and Pharmacology, Western University, London, ON, Canada
- Department of Medicine, Western University, London, ON, Canada
| | - David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- The Metabolomics Innovation Centre, Edmonton, AB, Canada
| | - Rupasri Mandal
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- The Metabolomics Innovation Centre, Edmonton, AB, Canada
| | - Gediminas Cepinskas
- Lawson Health Research Institute, London, ON, Canada
- Department of Medical Biophysics, Western University, London, ON, Canada
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Novel Outcome Biomarkers Identified With Targeted Proteomic Analyses of Plasma From Critically Ill Coronavirus Disease 2019 Patients. Crit Care Explor 2020; 2:e0189. [PMID: 32904064 PMCID: PMC7449255 DOI: 10.1097/cce.0000000000000189] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Supplemental Digital Content is available in the text. Coronavirus disease 2019 patients admitted to the ICU have high mortality. The host response to coronavirus disease 2019 has only been partially elucidated, and prognostic biomarkers have not been identified. We performed targeted proteomics on critically ill coronavirus disease 2019 patients to better understand their pathophysiologic mediators and to identify potential outcome markers.
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Endothelial Injury and Glycocalyx Degradation in Critically Ill Coronavirus Disease 2019 Patients: Implications for Microvascular Platelet Aggregation. Crit Care Explor 2020; 2:e0194. [PMID: 32904031 PMCID: PMC7449254 DOI: 10.1097/cce.0000000000000194] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Objectives Coronavirus disease 2019 is caused by the novel severe acute respiratory syndrome coronavirus 2 virus. Patients admitted to the ICU suffer from microvascular thrombosis, which may contribute to mortality. Our aim was to profile plasma thrombotic factors and endothelial injury markers in critically ill coronavirus disease 2019 ICU patients to help understand their thrombotic mechanisms. Design Daily blood coagulation and thrombotic factor profiling with immunoassays and in vitro experiments on human pulmonary microvascular endothelial cells. Setting Tertiary care ICU and academic laboratory. Subjects All patients admitted to the ICU suspected of being infected with severe acute respiratory syndrome coronavirus 2, using standardized hospital screening methodologies, had daily blood samples collected until testing was confirmed coronavirus disease 2019 negative on either ICU day 3 or ICU day 7 if the patient was coronavirus disease 2019 positive. Interventions None. Measurement and Main Results Age- and sex-matched healthy control subjects and ICU patients that were either coronavirus disease 2019 positive or coronavirus disease 2019 negative were enrolled. Cohorts were well balanced with the exception that coronavirus disease 2019 positive patients were more likely than coronavirus disease 2019 negative patients to suffer bilateral pneumonia. Mortality rate for coronavirus disease 2019 positive ICU patients was 40%. Compared with healthy control subjects, coronavirus disease 2019 positive patients had higher plasma von Willebrand factor (p < 0.001) and glycocalyx-degradation products (chondroitin sulfate and syndecan-1; p < 0.01). When compared with coronavirus disease 2019 negative patients, coronavirus disease 2019 positive patients had persistently higher soluble P-selectin, hyaluronic acid, and syndecan-1 (p < 0.05), particularly on ICU day 3 and thereafter. Thrombosis profiling on ICU days 1-3 predicted coronavirus disease 2019 status with 85% accuracy and patient mortality with 86% accuracy. Surface hyaluronic acid removal from human pulmonary microvascular endothelial cells with hyaluronidase treatment resulted in depressed nitric oxide, an instigating mechanism for platelet adhesion to the microvascular endothelium. Conclusions Thrombosis profiling identified endothelial activation and glycocalyx degradation in coronavirus disease 2019 positive patients. Our data suggest that medications to protect and/or restore the endothelial glycocalyx, as well as platelet inhibitors, should be considered for further study.
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Fraser DD, Cepinskas G, Slessarev M, Martin C, Daley M, Miller MR, O'Gorman DB, Gill SE, Patterson EK, Dos Santos CC. Inflammation Profiling of Critically Ill Coronavirus Disease 2019 Patients. Crit Care Explor 2020; 2:e0144. [PMID: 32696007 PMCID: PMC7314329 DOI: 10.1097/cce.0000000000000144] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES Coronavirus disease 2019 is caused by severe acute respiratory syndrome-coronavirus-2 infection to which there is no community immunity. Patients admitted to ICUs have high mortality, with only supportive therapies available. Our aim was to profile plasma inflammatory analytes to help understand the host response to coronavirus disease 2019. DESIGN Daily blood inflammation profiling with immunoassays. SETTING Tertiary care ICU and academic laboratory. SUBJECTS All patients admitted to the ICU suspected of being infected with severe acute respiratory syndrome-coronavirus-2, using standardized hospital screening methodologies, had daily blood samples collected until either testing was confirmed negative on ICU day 3 (coronavirus disease 2019 negative), or until ICU day 7 if the patient was positive (coronavirus disease 2019 positive). INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS Age- and sex-matched healthy controls and ICU patients that were either coronavirus disease 2019 positive or coronavirus disease 2019 negative were enrolled. Cohorts were well-balanced with the exception that coronavirus disease 2019 positive patients were more likely than coronavirus disease 2019 negative patients to suffer bilateral pneumonia. Mortality rate for coronavirus disease 2019 positive ICU patients was 40%. We measured 57 inflammatory analytes and then analyzed with both conventional statistics and machine learning. Twenty inflammatory analytes were different between coronavirus disease 2019 positive patients and healthy controls (p < 0.01). Compared with coronavirus disease 2019 negative patients, coronavirus disease 2019 positive patients had 17 elevated inflammatory analytes on one or more of their ICU days 1-3 (p < 0.01), with feature classification identifying the top six analytes between cohorts as tumor necrosis factor, granzyme B, heat shock protein 70, interleukin-18, interferon-gamma-inducible protein 10, and elastase 2. While tumor necrosis factor, granzyme B, heat shock protein 70, and interleukin-18 were elevated for all seven ICU days, interferon-gamma-inducible protein 10 transiently elevated on ICU days 2 and 3 and elastase 2 increased over ICU days 2-7. Inflammation profiling predicted coronavirus disease 2019 status with 98% accuracy, whereas elevated heat shock protein 70 was strongly associated with mortality. CONCLUSIONS While many inflammatory analytes were elevated in coronavirus disease 2019 positive ICU patients, relative to healthy controls, the top six analytes distinguishing coronavirus disease 2019 positive ICU patients from coronavirus disease 2019 negative ICU patients were tumor necrosis factor, granzyme B, heat shock protein 70, interleukin-18, interferon-gamma-inducible protein 10, and elastase 2.
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Affiliation(s)
- Douglas D Fraser
- Lawson Health Research Institute, London, ON, Canada
- Departments of Pediatrics, Clinical Neurological Sciences and Physiology and Pharmacology, Western University, London, ON, Canada
| | - Gediminas Cepinskas
- Lawson Health Research Institute, London, ON, Canada
- Department of Medical Biophysics, Western University, London, ON, Canada
| | - Marat Slessarev
- Lawson Health Research Institute, London, ON, Canada
- Department of Medicine, Western University, London, ON, Canada
| | - Claudio Martin
- Lawson Health Research Institute, London, ON, Canada
- Department of Medicine, Western University, London, ON, Canada
| | - Mark Daley
- Lawson Health Research Institute, London, ON, Canada
- Department of Computer Science, Western University, London, ON, Canada
- The Vector Institute for Artificial Intelligence, Toronto, ON, Canada
| | - Michael R Miller
- Lawson Health Research Institute, London, ON, Canada
- Departments of Pediatrics, Clinical Neurological Sciences and Physiology and Pharmacology, Western University, London, ON, Canada
| | - David B O'Gorman
- Lawson Health Research Institute, London, ON, Canada
- Department of Surgery, Western University, London, ON, Canada
| | - Sean E Gill
- Lawson Health Research Institute, London, ON, Canada
- Department of Medicine, Western University, London, ON, Canada
- Department of Physiology and Pharmacology, Western University, London, ON, Canada
| | | | - Claudia C Dos Santos
- Keenan Research Center for Biomedical Research, Unity Health Toronto, Toronto, ON, Canada
- Interdepartmental Division of Critical Care and Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
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Hu J, Zhang QX, Xiao TT, Pan MC, Cai YM. Residual Negative Pressure in Vacuum Blood-Collection Tube and Hemolysis in Pediatric Blood Specimens. Lab Med 2020; 51:41-46. [PMID: 31185079 DOI: 10.1093/labmed/lmz026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVE To determine a method to reduce specimen hemolysis rates in pediatric blood specimens. METHODS A total of 290 blood specimens from pediatric patients were classified into the capped group or uncapped group. The hemolysis index and levels of lactate dehydrogenase (LDH) were measured using an automated biochemical analyzer. Also, we performed a paired test to measure the concentration of free hemoglobin in specimens from 25 randomly selected healthy adult volunteers, using a direct spectrophotometric technique. RESULTS The hemolytic rate of capped specimens was 2-fold higher than that of uncapped specimens. We found significant differences for LDH. Also, there was a significant difference in the concentration of free hemoglobin in the random-volunteers test. CONCLUSIONS Eliminating the residual negative pressure of vacuum blood-collection tubes was effective at reducing the macrohemolysis and/or microhemolysis rate.
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Affiliation(s)
- Jing Hu
- Department of Clinical Laboratory, The First Affiliated Hospital of Shantou University Medical College, China
| | - Qiao-Xin Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Shantou University Medical College, China
| | - Tong-Tong Xiao
- Department of Clinical Laboratory, The First Affiliated Hospital of Shantou University Medical College, China
| | - Mei-Chen Pan
- Department of Clinical Laboratory, The First Affiliated Hospital of Shantou University Medical College, China
| | - Ying-Mu Cai
- Department of Clinical Laboratory, The First Affiliated Hospital of Shantou University Medical College, China
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Chen M, Soosaipillai A, Fraser DD, Diamandis EP. Discovery of novel plasma biomarker ratios to discriminate traumatic brain injury. F1000Res 2019; 8:1695. [PMID: 32047603 PMCID: PMC6979479 DOI: 10.12688/f1000research.20445.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/12/2019] [Indexed: 01/17/2023] Open
Abstract
Background: Traumatic brain injury (TBI) is a major cause of death and disability. Despite increased awareness, reliable biomarkers are urgently needed to aid in all forms of traumatic brain injury diagnosis and prognosis. Methods: Here, we aim to assess the diagnostic utility of known and novel TBI biomarkers in a pilot patient cohort of severe TBI (sTBI) patients and healthy controls. We analyzed concentrations of S100 calcium binding protein B (S100B), neuron specific enolase (NSE), human kallikrein 6 (hK6) and prostaglandin D2 synthase (PGDS) using ELISA immunoassays. Results: Plasma levels of hK6 and PGDS were significantly lower in sTBI compared with controls, while S100B and NSE were significantly higher. Furthermore, we show that ratios of NSE and S100B with hK6 and PGDS may be able to determine the presence of sTBI better than single markers alone. Conclusions: The findings presented here represent a starting point for future validation, where biomarker ratios can be tested in independent TBI cohorts.
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Affiliation(s)
- Michelle Chen
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Antoninus Soosaipillai
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Douglas D. Fraser
- Department of Pediatrics, Western University, London, Ontario, Canada
| | - Eleftherios P. Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Clinical Biochemistry, University Health Network, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
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Cameron S, Gillio-Meina C, Ranger A, Choong K, Fraser DD. Collection and Analyses of Cerebrospinal Fluid for Pediatric Translational Research. Pediatr Neurol 2019; 98:3-17. [PMID: 31280949 DOI: 10.1016/j.pediatrneurol.2019.05.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 05/23/2019] [Accepted: 05/27/2019] [Indexed: 12/18/2022]
Abstract
Cerebrospinal fluid sample collection and analysis is imperative to better elucidate central nervous system injury and disease in children. Sample collection methods are varied and carry with them certain ethical and biologic considerations, complications, and contraindications. Establishing best practices for sample collection, processing, storage, and transport will ensure optimal sample quality. Cerebrospinal fluid samples can be affected by a number of factors including subject age, sampling method, sampling location, volume extracted, fraction, blood contamination, storage methods, and freeze-thaw cycles. Indicators of sample quality can be assessed by matrix-associated laser desorption/ionization time-of-flight mass spectrometry and include cystatin C fragments, oxidized proteins, prostaglandin D synthase, and evidence of blood contamination. Precise documentation of sample collection processes and the establishment of meticulous handling procedures are essential for the creation of clinically relevant biospecimen repositories. In this review we discuss the ethical considerations and best practices for cerebrospinal fluid collection, as well as the influence of preanalytical factors on cerebrospinal fluid analyses. Cerebrospinal fluid biomarkers in highly researched pediatric diseases or disorders are discussed.
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Affiliation(s)
| | | | - Adrianna Ranger
- Pediatrics, Western University, London, Ontario, Canada; Clinical Neurological Sciences, Western University, London, Ontario, Canada
| | - Karen Choong
- Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Douglas D Fraser
- Pediatrics, Western University, London, Ontario, Canada; Children's Health Research Institute, London, Ontario, Canada; Clinical Neurological Sciences, Western University, London, Ontario, Canada; Physiology and Pharmacology, Western University, London, Ontario, Canada; Translational Research Centre, London, Ontario, Canada.
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Gohar F, McArdle A, Jones M, Callan N, Hernandez B, Kessel C, Miranda-Garcia M, Lavric M, Holzinger D, Pretzer C, Lainka E, Vastert SJ, de Roock S, FitzGerald O, Pennington SR, Foell D. Molecular signature characterisation of different inflammatory phenotypes of systemic juvenile idiopathic arthritis. Ann Rheum Dis 2019; 78:1107-1113. [DOI: 10.1136/annrheumdis-2019-215051] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/14/2019] [Accepted: 04/02/2019] [Indexed: 12/13/2022]
Abstract
ObjectivesThe International League of Associations for Rheumatology classification criteria define systemic juvenile idiopathic arthritis (SJIA) by the presence of fever, rash and chronic arthritis. Recent initiatives to revise current criteria recognise that a lack of arthritis complicates making the diagnosis early, while later a subgroup of patients develops aggressive joint disease. The proposed biphasic model of SJIA also implies a ‘window of opportunity’ to abrogate the development of chronic arthritis. We aimed to identify novel SJIA biomarkers during different disease phases.MethodsChildren with active SJIA were subgrouped clinically as systemic autoinflammatory disease with fever (SJIAsyst) or polyarticular disease (SJIApoly). A discovery cohort of n=10 patients per SJIA group, plus n=10 with infection, was subjected to unbiased label-free liquid chromatography mass spectrometry (LC-MS/MS) and immunoassay screens. In a separate verification cohort (SJIAsyst, n=45; SJIApoly, n=29; infection, n=32), candidate biomarkers were measured by multiple reaction monitoring MS (MRM-MS) and targeted immunoassays.ResultsSignatures differentiating the two phenotypes of SJIA could be identified. LC-MS/MS in the discovery cohort differentiated SJIAsyst from SJIApoly well, but less effectively from infection. Targeted MRM verified the discovery data and, combined with targeted immunoassays, correctly identified 91% (SJIAsyst vs SJIApoly) and 77% (SJIAsyst vs infection) of all cases.ConclusionsMolecular signatures differentiating two phenotypes of SJIA were identified suggesting shifts in underlying immunological processes in this biphasic disease. Biomarker signatures separating SJIA in its initial autoinflammatory phase from the main differential diagnosis (ie, infection) could aid early-stage diagnostic decisions, while markers of a phenotype switch could inform treat-to-target strategies.
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Kumar A, Singh M, Bhatia P, Singh A. Audit of Quality and Quantity of Nucleic Acid Yield from Pediatric Acute Leukemia Cases Following a Bio-banking Initiative. Indian J Hematol Blood Transfus 2019; 35:77-82. [PMID: 30828152 DOI: 10.1007/s12288-018-0975-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 06/15/2018] [Indexed: 10/28/2022] Open
Abstract
Information which can be harvested from a biological sample has greatly improved with advancements in diagnostic technologies. However, in developing countries, the awareness about usefulness of bio-banking concept is lacking and centres which do offer it, depend mainly on - 20 or - 80 °C for sample storage due to lack of sophisticated infrastructure like vapour phase nitrogen storage preservation. Hence in these resource constraint settings, timely audit of quality of nucleic acids extractable from samples stored is of utmost importance. In this study, we explore the effect of - 20 °C storage over nucleic acids (DNA/RNA) isolated from blood samples of 180 patients with various leukaemia's following a bio-banking initiative. We observed that the integrity and quality of both DNA and RNA were maintained in 70 and 80% samples respectively over time as reflected by their concentration measurements and inherent uniform expression of housekeeping gene GAPDH. Only 3.7% of the RNA samples and 4.2% of the DNA samples yielded very low concentrations despite minimizing processing and technical loss. In nutshell, audit of our biobank sample yield highlights that storage of blood samples at - 20 °C does not compromise the fidelity of nucleic acids for future diagnostic and research work in a resource constraint setting.
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Affiliation(s)
- A Kumar
- 1University of Pittsburgh School of Medicine, Pittsburgh, USA.,2Pediatric Hematology - Oncology Unit, Department of Pediatrics, APC, PGIMER, Chandigarh, India
| | - M Singh
- 2Pediatric Hematology - Oncology Unit, Department of Pediatrics, APC, PGIMER, Chandigarh, India
| | - P Bhatia
- 2Pediatric Hematology - Oncology Unit, Department of Pediatrics, APC, PGIMER, Chandigarh, India
| | - A Singh
- 1University of Pittsburgh School of Medicine, Pittsburgh, USA
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CECHIM GIOVANA, CHIES JOSÉA. In vitro generation of human monocyte-derived dendritic cells methodological aspects in a comprehensive review. ACTA ACUST UNITED AC 2019. [DOI: 10.1590/0001-3765201920190310] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Li Q, Wang X, Li X, He X, Wan Q, Yin J, Sun J, Yang X, Chen Q, Miao X. Obtaining High-Quality Blood Specimens for Downstream Applications: A Review of Current Knowledge and Best Practices. Biopreserv Biobank 2018; 16:411-418. [PMID: 30383403 DOI: 10.1089/bio.2018.0052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Blood is a biological fluid that contains multiple blood fraction and cellular components. High-quality blood specimens are essential prerequisites for various downstream applications such as molecular epidemiology studies, genomics, and proteomics studies. Currently, protocols and research publications concerning the collection, handling, preservation, and stability of blood or blood fractions are constantly emerging. Moreover, standardized guidelines are a requirement for biorepositories to tightly control preanalytical variables originating from these procedures and obtain high-quality blood specimen for downstream analyses. In this review article, we summarize the best practices and fit-for-purpose protocols regarding blood collection, processing, storage, and stability. In addition, we present some typical quality biomarkers, which could be used to evaluate the integrity of blood specimens.
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Affiliation(s)
- Qiyuan Li
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Xian Wang
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Xue Li
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Xuheng He
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Qian Wan
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Jiefang Yin
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Jianbo Sun
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Xiaoping Yang
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Qiaohong Chen
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Xinyuan Miao
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
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Kumar M, Choudhury Y, Ghosh SK, Mondal R. Application and optimization of minimally invasive cell-free DNA techniques in oncogenomics. Tumour Biol 2018; 40:1010428318760342. [PMID: 29484962 DOI: 10.1177/1010428318760342] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The conventional method of measuring biomarkers in malignant tissue samples has already given subversive growth in cancer diagnosis, prognosis, and therapy selection. However, the regression and heterogeneity associated with tumor tissue biopsy have urged for the development of an alternative approach. Considering the limitations, cell-free DNA has emerged as a surrogate alternative, facilitating preoperative chemoradiotherapy (p < 0.0001) treatment response in rectal cancer and detection of biomarker in lung cancer. This potential of cell-free DNA in several other cancers has yet to be explored based on clinical relevance by optimizing the preanalytical factors. This review has highlighted the crucial parameters from blood collection to cell-free DNA analysis that has a significant impact on the accuracy and reliability of clinical data. The quantity of cell-free DNA is also a limiting factor. Therefore, a proper preanalytical factor for blood collection, its stability, centrifugation speed, and plasma storage condition are to be optimized for developing cancer-specific biomarkers useful for clinical purpose. Liquid biopsy-based origin of cell-free DNA has revolutionized the area of cancer research. Lack of preanalytical and analytical procedures may be considered for identification of novel biomarkers through next-generation sequencing of tumor-originated cell-free DNA in contradiction to tissue biopsy for cancer-specific biomarkers.
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Affiliation(s)
- Manish Kumar
- 1 Department of Biotechnology, Assam University, Silchar, India
| | | | - Sankar Kumar Ghosh
- 1 Department of Biotechnology, Assam University, Silchar, India.,2 University of Kalyani, Kalyani, India
| | - Rosy Mondal
- 3 Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, India
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Elevated Leukocyte Azurophilic Enzymes in Human Diabetic Ketoacidosis Plasma Degrade Cerebrovascular Endothelial Junctional Proteins. Crit Care Med 2017; 44:e846-53. [PMID: 27071071 DOI: 10.1097/ccm.0000000000001720] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
OBJECTIVE Diabetic ketoacidosis in children is associated with vasogenic cerebral edema, possibly due to the release of destructive polymorphonuclear neutrophil azurophilic enzymes. Our objectives were to measure plasma azurophilic enzyme levels in children with diabetic ketoacidosis, to correlate plasma azurophilic enzyme levels with diabetic ketoacidosis severity, and to determine whether azurophilic enzymes disrupt the blood-brain barrier in vitro. DESIGN Prospective clinical and laboratory study. SETTING The Children's Hospital, London Health Sciences Centre. SUBJECTS Pediatric type 1 diabetes patients; acute diabetic ketoacidosis or age-/sex-matched insulin-controlled. MEASUREMENTS AND MAIN RESULTS Acute diabetic ketoacidosis in children was associated with elevated polymorphonuclear neutrophils. Plasma azurophilic enzymes were elevated in diabetic ketoacidosis patients, including human leukocyte elastase (p < 0.001), proteinase-3 (p < 0.01), and myeloperoxidase (p < 0.001). A leukocyte origin of human leukocyte elastase and proteinase-3 in diabetic ketoacidosis was confirmed with buffy coat quantitative real-time polymerase chain reaction (p < 0.01). Of the three azurophilic enzymes elevated, only proteinase-3 levels correlated with diabetic ketoacidosis severity (p = 0.002). Recombinant proteinase-3 applied to human brain microvascular endothelial cells degraded both the tight junction protein occludin (p < 0.05) and the adherens junction protein VE-cadherin (p < 0.05). Permeability of human brain microvascular endothelial cell monolayers was increased by recombinant proteinase-3 application (p = 0.010). CONCLUSIONS Our results indicate that diabetic ketoacidosis is associated with systemic polymorphonuclear neutrophil activation and degranulation. Of all the polymorphonuclear neutrophil azurophilic enzymes examined, only proteinase-3 correlated with diabetic ketoacidosis severity and potently degraded the blood-brain barrier in vitro. Proteinase-3 might mediate vasogenic edema during diabetic ketoacidosis, and selective proteinase-3 antagonists may offer future vascular- and neuroprotection.
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Yeung RSM, Albani S, Feldman BM, Mellins E, Prakken B, Wedderburn LR. Enhancing translational research in paediatric rheumatology through standardization. Nat Rev Rheumatol 2016; 12:684-690. [PMID: 27652504 DOI: 10.1038/nrrheum.2016.156] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The past decade has seen many successes in translational rheumatology, from dramatic improvements in outcomes brought about by novel biologic therapies, to the discovery of new monogenic inflammatory disorders. Advances in molecular medicine, combined with progress towards precision care, provide an excellent opportunity to accelerate the translation of biological understanding to the bedside. However, although the field of rheumatology is a leader in the standardization of data collection and measures of disease activity, it lags behind in standardization of biological sample collection and assay performance. Uniform approaches are necessary for robust collaborative research, particularly in rare diseases. Standardization is also critical to increase reproducibility between centres, a prerequisite for clinical implementation of translational research. This Perspectives article emphasizes the need for standardization and implementation of best practices, presented in the context of lessons learned from international biorepository networks.
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Affiliation(s)
- Rae S M Yeung
- Department of Paediatrics, Division of Rheumatology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada; and at the Department of Immunology and the Institute of Medical Science, University of Toronto Faculty of Medicine, Medical Sciences Building, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Salvatore Albani
- Duke-National University of Singapore Graduate Medical School, 8 College Road, 169857, Singapore
| | - Brian M Feldman
- Department of Paediatrics and Institute of Medical Science, University of Toronto Faculty of Medicine, Medical Sciences Building, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada; the Division of Rheumatology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada; and at the Institute of Health Policy Management and Evaluation, The Dalla Lana School of Public Health, University of Toronto, 155 College Street, Toronto, Ontario M5T 3M7, Canada
| | - Elizabeth Mellins
- Department of Pediatrics and the Stanford Program in Immunology, Stanford University, 300 Pasteur Drive, Stanford, California 94305, USA
| | - Berent Prakken
- Department of Immunology, University Medical Centre, Heidelberglaan 100, 3584 CX Utrecht, Netherlands
| | - Lucy R Wedderburn
- Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK
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Gohar F, Kessel C, Lavric M, Holzinger D, Foell D. Review of biomarkers in systemic juvenile idiopathic arthritis: helpful tools or just playing tricks? Arthritis Res Ther 2016; 18:163. [PMID: 27411444 PMCID: PMC4944486 DOI: 10.1186/s13075-016-1069-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 06/29/2016] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Diagnosing systemic juvenile idiopathic arthritis (SJIA) can be extremely challenging if typical arthritis is lacking. A variety of biomarkers have been described for the diagnosis and management of SJIA. However, very few markers have been well-validated. In addition, increasing numbers of biomarkers are identified by high throughput or multi-marker panels. METHOD We identified diagnostic or prognostic biomarkers by systematic literature review, evaluating each according to a predefined level of verification, validation or clinical utility. Diagnostic biomarkers were those identifying SJIA versus (1) non-SJIA conditions or healthy controls (HC) or (2) other non-systemic JIA subtypes. Prognostic biomarkers were those specifically tested for the prediction of (1) disease flare, (2) increased disease activity +/- discrimination of active versus inactive disease, or (3) macrophage activation syndrome (MAS). RESULTS Fifty-five studies fulfilled the inclusion criteria identifying 68 unique biomarkers, of which 50/68 (74 %) were investigated by only a single research group. Candidate marker verification and clinical utility was evaluated according to whether markers were readily and reliably measurable, investigated by independent study groups, discovered by more than one method (i.e. verified markers) and validated in independent cohorts. This evaluation revealed diagnostic biomarkers of high interest for further evaluation in the diagnostic approach to SJIA that included heme oxygenase-1, interleukin-6 (IL-6), IL-12, IL-18, osteoprotegerin, S100 calcium-binding protein A12 (S100A12) and S100A8/A9. CONCLUSION In summary, a number of biomarkers were identified, though most had limited evidence for their use. However, our findings combined with the identified studies could inform validation studies, whether in single or multi-marker assays, which are urgently needed.
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Affiliation(s)
- Faekah Gohar
- Department of Paediatric Rheumatology and Immunology, University of Münster, Domagkstraße 3, D-48149, Münster, Germany
| | - Christoph Kessel
- Department of Paediatric Rheumatology and Immunology, University of Münster, Domagkstraße 3, D-48149, Münster, Germany
| | - Miha Lavric
- Department of Paediatric Rheumatology and Immunology, University of Münster, Domagkstraße 3, D-48149, Münster, Germany
| | - Dirk Holzinger
- Department of Paediatric Rheumatology and Immunology, University of Münster, Domagkstraße 3, D-48149, Münster, Germany
| | - Dirk Foell
- Department of Paediatric Rheumatology and Immunology, University of Münster, Domagkstraße 3, D-48149, Münster, Germany.
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Mogasale V, Ramani E, Mogasale VV, Park J. What proportion of Salmonella Typhi cases are detected by blood culture? A systematic literature review. Ann Clin Microbiol Antimicrob 2016; 15:32. [PMID: 27188991 PMCID: PMC4869319 DOI: 10.1186/s12941-016-0147-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 05/09/2016] [Indexed: 12/29/2022] Open
Abstract
Blood culture is often used in definitive diagnosis of typhoid fever while, bone marrow culture has a greater sensitivity and considered reference standard. The sensitivity of blood culture measured against bone marrow culture results in measurement bias because both tests are not fully sensitive. Here we propose a combination of the two cultures as a reference to define true positive S. Typhi cases. Based on a systematic literature review, we identified ten papers that had performed blood and bone marrow culture for S. Typhi in same subjects. We estimated the weighted mean of proportion of cases detected by culture measured against true S. Typhi positive cases using a random effects model. Of 529 true positive S. Typhi cases, 61 % (95 % CI 52–70 %) and 96 % (95 % CI 93–99 %) were detected by blood and bone marrow cultures respectively. Blood culture sensitivity was 66 % (95 % CI 56–75 %) when compared with bone marrow culture results. The use of blood culture sensitivity as a proxy measure to estimate the proportion of typhoid fever cases detected by blood culture is likely to be an underestimate. As blood culture sensitivity is used as a correction factor in estimating typhoid disease burden, epidemiologists and policy makers should account for the underestimation.
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Affiliation(s)
- Vittal Mogasale
- Policy and Economic Research Department, Development and Delivery Unit, International Vaccine Institute, Seoul, Republic of Korea.
| | - Enusa Ramani
- Policy and Economic Research Department, Development and Delivery Unit, International Vaccine Institute, Seoul, Republic of Korea
| | - Vijayalaxmi V Mogasale
- Epidemiology Department, Development and Delivery Unit, International Vaccine Institute, Seoul, Republic of Korea
| | - JuYeon Park
- Biostatistics and Data Management Department, Development and Delivery Unit, International Vaccine Institute, Seoul, Republic of Korea
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Woo M, Patterson EK, Cepinskas G, Clarson C, Omatsu T, Fraser DD. Dynamic regulation of plasma matrix metalloproteinases in human diabetic ketoacidosis. Pediatr Res 2016; 79:295-300. [PMID: 26492282 DOI: 10.1038/pr.2015.215] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 07/31/2015] [Indexed: 01/15/2023]
Abstract
BACKGROUND Diabetic ketoacidosis (DKA) in children is associated with cerebrovascular-related complications. We recently reported that DKA facilitates leukocyte adherence to the brain microvascular endothelium. Adhered leukocytes can release enzymes that instigate vascular dysfunction. Our aims were to measure plasma levels of leukocyte-derived matrix metalloproteinases (MMPs) from DKA patients and to correlate plasma MMP concentrations with DKA severity. METHODS Plasma was obtained from children with type 1 diabetes, either in DKA (n = 16) or insulin controlled (CON; n = 16). Antibody microarray and gelatin zymography were used to quantify plasma MMPs and their endogenous tissue inhibitors (TIMPs). MMP concentrations were correlated with DKA severity (blood pH). Quantitative PCR of leukocyte mRNA was used to help determine the origin of plasma MMPs. RESULTS DKA was associated with altered plasma levels of ↓MMP-2 (P < 0.001), ↑MMP-8 (P < 0.001), ↑MMP-9 (P < 0.05), and ↑TIMP-4 (P < 0.001), as compared with CON. Elevated MMP-8 and MMP-9 were both positively correlated with DKA severity (P < 0.05). DKA was associated with increased leukocyte mRNA for MMP-8, MMP-9, and TIMP-4 (P < 0.005). CONCLUSION MMPs are dynamically regulated during DKA. Plasma MMP-8 and MMP-9 concentrations correlate with DKA severity and are known to degrade brain microvascular endothelial cell tight junctions. Thus, leukocyte-derived MMPs might contribute to DKA-associated cerebrovascular complications.
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Affiliation(s)
- Martin Woo
- Department of Physiology and Pharmacology, Western University, London, Ontario, Canada
- Children's Health Research Institute, London, Ontario, Canada
- Centre for Critical Illness Research, London, Ontario, Canada
| | | | - Gediminas Cepinskas
- Centre for Critical Illness Research, London, Ontario, Canada
- Medical Biophysics, Western University, London, Ontario, Canada
| | - Cheril Clarson
- Children's Health Research Institute, London, Ontario, Canada
- Pediatrics, Western University, London, Ontario, Canada
| | - Tatsushi Omatsu
- Centre for Critical Illness Research, London, Ontario, Canada
- Pediatrics, Western University, London, Ontario, Canada
| | - Douglas D Fraser
- Department of Physiology and Pharmacology, Western University, London, Ontario, Canada
- Children's Health Research Institute, London, Ontario, Canada
- Centre for Critical Illness Research, London, Ontario, Canada
- Pediatrics, Western University, London, Ontario, Canada
- Clinical Neurological Sciences, Western University, London, Ontario, Canada
- Translational Research Centre, London, Ontario, Canada
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Wallace MAG, Kormos TM, Pleil JD. Blood-borne biomarkers and bioindicators for linking exposure to health effects in environmental health science. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART B, CRITICAL REVIEWS 2016; 19:380-409. [PMID: 27759495 PMCID: PMC6147038 DOI: 10.1080/10937404.2016.1215772] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Environmental health science aims to link environmental pollution sources to adverse health outcomes to develop effective exposure intervention strategies that reduce long-term disease risks. Over the past few decades, the public health community recognized that health risk is driven by interaction between the human genome and external environment. Now that the human genetic code has been sequenced, establishing this "G × E" (gene-environment) interaction requires a similar effort to decode the human exposome, which is the accumulation of an individual's environmental exposures and metabolic responses throughout the person's lifetime. The exposome is composed of endogenous and exogenous chemicals, many of which are measurable as biomarkers in blood, breath, and urine. Exposure to pollutants is assessed by analyzing biofluids for the pollutant itself or its metabolic products. New methods are being developed to use a subset of biomarkers, termed bioindicators, to demonstrate biological changes indicative of future adverse health effects. Typically, environmental biomarkers are assessed using noninvasive (excreted) media, such as breath and urine. Blood is often avoided for biomonitoring due to practical reasons such as medical personnel, infectious waste, or clinical setting, despite the fact that blood represents the central compartment that interacts with every living cell and is the most relevant biofluid for certain applications and analyses. The aims of this study were to (1) review the current use of blood samples in environmental health research, (2) briefly contrast blood with other biological media, and (3) propose additional applications for blood analysis in human exposure research.
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Affiliation(s)
- M Ariel Geer Wallace
- a Exposure Methods and Measurement Division, National Exposure Research Laboratory, Office of Research and Development , U.S. Environmental Protection Agency , Research Triangle Park , North Carolina , USA
| | | | - Joachim D Pleil
- a Exposure Methods and Measurement Division, National Exposure Research Laboratory, Office of Research and Development , U.S. Environmental Protection Agency , Research Triangle Park , North Carolina , USA
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Gillio-Meina C, Zielke HR, Fraser DD. Translational Research in Pediatrics IV: Solid Tissue Collection and Processing. Pediatrics 2016; 137:peds.2015-0490. [PMID: 26659457 DOI: 10.1542/peds.2015-0490] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/05/2015] [Indexed: 11/24/2022] Open
Abstract
Solid tissues are critical for child-health research. Specimens are commonly obtained at the time of biopsy/surgery or postmortem. Research tissues can also be obtained at the time of organ retrieval for donation or from tissue that would otherwise have been discarded. Navigating the ethics of solid tissue collection from children is challenging, and optimal handling practices are imperative to maximize tissue quality. Fresh biopsy/surgical specimens can be affected by a variety of factors, including age, gender, BMI, relative humidity, freeze/thaw steps, and tissue fixation solutions. Postmortem tissues are also vulnerable to agonal factors, body storage temperature, and postmortem intervals. Nonoptimal tissue handling practices result in nucleotide degradation, decreased protein stability, artificial posttranslational protein modifications, and altered lipid concentrations. Tissue pH and tryptophan levels are 2 methods to judge the quality of solid tissue collected for research purposes; however, the RNA integrity number, together with analyses of housekeeping genes, is the new standard. A comprehensive clinical data set accompanying all tissue samples is imperative. In this review, we examined: the ethical standards relating to solid tissue procurement from children; potential sources of solid tissues; optimal practices for solid tissue processing, handling, and storage; and reliable markers of solid tissue quality.
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Affiliation(s)
- Carolina Gillio-Meina
- Translational Research Centre, London, Ontario, Canada; Children's Health Research Institute, London, Ontario, Canada
| | | | - Douglas D Fraser
- Translational Research Centre, London, Ontario, Canada; Children's Health Research Institute, London, Ontario, Canada; Centre for Critical Illness Research, Critical Care Medicine and Pediatrics, Clinical Neurologic Sciences, and Physiology and Pharmacology, Western University, London, Ontario, Canada
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Ping B, Tsuno S, Wang X, Ishihara Y, Yamashita T, Miura K, Miyoshi F, Shinohara Y, Matsuki T, Tanabe Y, Tanaka N, Ogawa T, Shiota G, Miura N. Comparative study of ¹⁸F-FDG-PET/CT imaging and serum hTERT mRNA quantification in cancer diagnosis. Cancer Med 2015; 4:1603-11. [PMID: 26275387 PMCID: PMC4618631 DOI: 10.1002/cam4.508] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/11/2015] [Accepted: 07/14/2015] [Indexed: 12/18/2022] Open
Abstract
We have reported on the clinical usefulness of human telomerase reverse transcriptase (hTERT) mRNA quantification in sera in patients with several cancers. Positron emission tomography–computed tomography (PET/CT) using 18F-fluorodeoxyglucose (FDG) has recently become an excellent modality for detecting cancer. We performed a diagnostic comparative study of FDG-PET/CT and hTERT mRNA quantification in patients with cancer. Four hundred seventy subjects, including 125 healthy individuals and 345 outpatients with cancer who had received medical treatments for cancer in their own or other hospitals, were enrolled. The subjects were diagnosed by FDG-PET/CT, and we measured their serum hTERT mRNA levels using real-time RT-PCR, correlating the quantified values with the clinical course. In this prospective study, we statistically assessed the sensitivity and specificity, and their clinical significance. hTERT mRNA and FDG-PET/CT were demonstrated to be correlated with the clinical parameters of metastasis and recurrence (P < 0.001), and of recurrence and tumor number in cancer compared with noncancer patients, respectively. A multivariate analysis showed a significant difference in the detection by FDG-PET/CT, 18F-FDG uptake, the detection by hTERT mRNA, and age. The use of both FDG-PET/CT and hTERT mRNA resulted in a positivity of 94.4% (221/234) for the detection of viable tumor cells. FDG-PET/CT is superior to hTERT mRNA quantification in the early detection of cancer and combinative use of FDG-PET/CT and hTERT mRNA may improve the diagnostic accuracy of cancer.
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Affiliation(s)
- Bingqiong Ping
- Division of Pharmacotherapeutics, Department of Pathophysiological and Therapeutic Science, Faculty of Medicine, Tottori University, 86 Nishicho, Yonago, Tottori, 683-8503, Japan
| | - Satoshi Tsuno
- Division of Pharmacotherapeutics, Department of Pathophysiological and Therapeutic Science, Faculty of Medicine, Tottori University, 86 Nishicho, Yonago, Tottori, 683-8503, Japan
| | - Xinhui Wang
- Division of Pharmacotherapeutics, Department of Pathophysiological and Therapeutic Science, Faculty of Medicine, Tottori University, 86 Nishicho, Yonago, Tottori, 683-8503, Japan
| | - Yoshitaka Ishihara
- Division of Pharmacotherapeutics, Department of Pathophysiological and Therapeutic Science, Faculty of Medicine, Tottori University, 86 Nishicho, Yonago, Tottori, 683-8503, Japan
| | - Taro Yamashita
- Division of Pharmacotherapeutics, Department of Pathophysiological and Therapeutic Science, Faculty of Medicine, Tottori University, 86 Nishicho, Yonago, Tottori, 683-8503, Japan
| | - Keigo Miura
- PEZY-Pharma, 86 Nishicho, Yonago, Tottori, 683-8503, Japan
| | - Fuminori Miyoshi
- Division of Radiology, Department of Pathophysiological and Therapeutic Science, Faculty of Medicine, Tottori University, 36-1 Nishicho, Yonago, Tottori, 683-8504, Japan
| | - Yuki Shinohara
- Division of Radiology, Department of Pathophysiological and Therapeutic Science, Faculty of Medicine, Tottori University, 36-1 Nishicho, Yonago, Tottori, 683-8504, Japan
| | - Tsutomu Matsuki
- Department of Radiology, Tottori Municipal Hospital, 1-1 Matoba, Tottori, Tottori, 680-8501, Japan
| | - Yoshio Tanabe
- Department of Radiology, Tottori Municipal Hospital, 1-1 Matoba, Tottori, Tottori, 680-8501, Japan
| | - Noriaki Tanaka
- Department of Radiology, Tottori Municipal Hospital, 1-1 Matoba, Tottori, Tottori, 680-8501, Japan
| | - Toshihide Ogawa
- Division of Radiology, Department of Pathophysiological and Therapeutic Science, Faculty of Medicine, Tottori University, 36-1 Nishicho, Yonago, Tottori, 683-8504, Japan
| | - Goshi Shiota
- Division of Molecular and Genetic Medicine, Department of Genetic Medicine and Regenerative Therapeutics, Tottori University School of Medicine, 86 Nishicho, Yonago, Tottori, 683-8503, Japan
| | - Norimasa Miura
- Division of Pharmacotherapeutics, Department of Pathophysiological and Therapeutic Science, Faculty of Medicine, Tottori University, 86 Nishicho, Yonago, Tottori, 683-8503, Japan
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Nett ST, Noble JA, Levin DL, Cvijanovich NZ, Vavilala MS, Jarvis JD, Flori HR. Biomarkers and genetics of brain injury risk in diabetic ketoacidosis: A pilot study. J Pediatr Intensive Care 2015; 3. [PMID: 26097769 DOI: 10.3233/pic-14091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Diabetic ketoacidosis (DKA) is the primary cause of death for children with diabetes, especially when complicated by cerebral edema. Central nervous system (CNS) involvement is common, however the mechanism of, and predictors of CNS dysfunction/injury are largely unknown. In this observational pilot study, blood was collected from pediatric DKA patients at three time points (consent, 12 hr and 24 hr after beginning treatment), to test genetic markers, ribonucleic acid expression and plasma biomarkers reflecting inflammation (tumor necrosis factor-alpha [TNF-α], interleukin-6 [IL-6]) and cerebral dysfunction and/or possible injury (S100β, glial fibrillary acidic protein [GFAP]). Thirty patients were enrolled in the study. The average age was 11.3 yr, 73% were new onset diabetes and 53% were female. Forty percent exhibited abnormal mentation (Glasgow Coma Scale <15), consistent with CNS dysfunction. IL-6 and TNF-α were elevated in plasma, suggesting systemic inflammation. GFAP was measurable in 45% of patients and correlated positively with GCS. Only two patients had detectable levels of S100β. In conclusion, children with DKA often present with evidence of acute neurologic dysfunction or injury. We have demonstrated the feasibility of exploring genetic and biochemical markers of potential importance in the pathophysiology of CNS dysfunction and/or possible injury in DKA. We have identified IL-6, TNF-α and GFAP as potentially important markers for further exploration. A larger, follow-up study will help to better understand the extent and type of CNS injury in DKA as well as the mechanism underlying this dysfunction/injury.
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Affiliation(s)
- Sholeen T Nett
- Department of Pediatric Critical Care Medicine, Dartmouth Hitchcock Medical Center, One Medical Center Drive, Lebanon, NH, USA
| | - Janelle A Noble
- Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - Daniel L Levin
- Department of Pediatric Critical Care Medicine, Dartmouth Hitchcock Medical Center, One Medical Center Drive, Lebanon, NH, USA
| | - Natalie Z Cvijanovich
- Department of Pediatric Critical Care Medicine, Children's Hospital and Research Center Oakland, Oakland, CA, USA
| | - Monica S Vavilala
- Department of Pediatric Critical Care Medicine, University of Washington Children's Hospital, Seattle, WA, USA
| | - J Dean Jarvis
- Department of Pediatric Critical Care Medicine, Dartmouth Hitchcock Medical Center, One Medical Center Drive, Lebanon, NH, USA
| | - Heidi R Flori
- Department of Pediatric Critical Care Medicine, Children's Hospital and Research Center Oakland, Oakland, CA, USA
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Yin P, Lehmann R, Xu G. Effects of pre-analytical processes on blood samples used in metabolomics studies. Anal Bioanal Chem 2015; 407:4879-92. [PMID: 25736245 PMCID: PMC4471316 DOI: 10.1007/s00216-015-8565-x] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 02/13/2015] [Accepted: 02/13/2015] [Indexed: 12/17/2022]
Abstract
Every day, analytical and bio-analytical chemists make sustained efforts to improve the sensitivity, specificity, robustness, and reproducibility of their methods. Especially in targeted and non-targeted profiling approaches, including metabolomics analysis, these objectives are not easy to achieve; however, robust and reproducible measurements and low coefficients of variation (CV) are crucial for successful metabolomics approaches. Nevertheless, all efforts from the analysts are in vain if the sample quality is poor, i.e. if preanalytical errors are made by the partner during sample collection. Preanalytical risks and errors are more common than expected, even when standard operating procedures (SOP) are used. This risk is particularly high in clinical studies, and poor sample quality may heavily bias the CV of the final analytical results, leading to disappointing outcomes of the study and consequently, although unjustified, to critical questions about the analytical performance of the approach from the partner who provided the samples. This review focuses on the preanalytical phase of liquid chromatography–mass spectrometry-driven metabolomics analysis of body fluids. Several important preanalytical factors that may seriously affect the profile of the investigated metabolome in body fluids, including factors before sample collection, blood drawing, subsequent handling of the whole blood (transportation), processing of plasma and serum, and inadequate conditions for sample storage, will be discussed. In addition, a detailed description of latent effects on the stability of the blood metabolome and a suggestion for a practical procedure to circumvent risks in the preanalytical phase will be given. The procedures and potential problems in preanalytical aspects of metabolomics studies using blood samples. Bias in the preanalytical phase may lead to unwanted results in the subsequential studies ![]()
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Affiliation(s)
- Peiyuan Yin
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
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Daoud H, Alharfi I, Alhelali I, Charyk Stewart T, Qasem H, Fraser DD. Brain injury biomarkers as outcome predictors in pediatric severe traumatic brain injury. Neurocrit Care 2015; 20:427-35. [PMID: 23943317 DOI: 10.1007/s12028-013-9879-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
BACKGROUND To systematically review the literature on brain injury biomarkers, defined as any injury biomarker detected in cerebrospinal fluid (CSF) or blood injury biomarkers primarily expressed in the brain parenchyma, to determine outcome prediction in pediatric severe traumatic brain injury (sTBI). METHODS A search of MEDLINE(®), EMBASE(®), PsycINFO(®), Pubmed(®), and the Cochrane Database, as well as grey literature sources, personal contacts, hand searches, and reference lists. The search terms used were traumatic brain injury, biomarkers, prognosis, and children. No language, publication type, or publication date restrictions were imposed. All articles were critically reviewed by two clinicians independently. RESULTS A total of 7,150 articles were identified initially with 16 studies identified for review. Eighteen different biomarkers were examined; 11 in CSF and 7 in blood. Outcomes assessed included either in-hospital mortality or functional state (hospital discharge, 3-months or 6-months; Glasgow Outcome Scale or Pediatric Cerebral Performance Category). Significant correlations were established between sTBI outcomes and various biomarkers in CSF (IL-6, IL-8, IL-1β, S100β, NGF, NSE, DCX, ET-1, HMGB-1, cytochrome C) and blood (GFAP, NF-H, UCH-L1, SBDP-145, leptin). Mixed results were obtained for blood S100β. Outcome did not correlate with several biomarkers in either CSF (BDNF, GDNF, α-Syn) or blood (NSE, MBP). The Class of Evidence was considered II in 1 study and III in the remaining 15 studies. CONCLUSIONS Based on the status of current sTBI biomarker research, we recommend that future research should be directed at both novel biomarker discovery and validation of biomarker panels in large, well-designed longitudinal studies.
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Affiliation(s)
- Hani Daoud
- Department of Paediatrics, Western University, London, ON, Canada
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Sample processing obscures cancer-specific alterations in leukemic transcriptomes. Proc Natl Acad Sci U S A 2014; 111:16802-7. [PMID: 25385641 DOI: 10.1073/pnas.1413374111] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Substantial effort is currently devoted to identifying cancer-associated alterations using genomics. Here, we show that standard blood collection procedures rapidly change the transcriptional and posttranscriptional landscapes of hematopoietic cells, resulting in biased activation of specific biological pathways; up-regulation of pseudogenes, antisense RNAs, and unannotated coding isoforms; and RNA surveillance inhibition. Affected genes include common mutational targets and thousands of other genes participating in processes such as chromatin modification, RNA splicing, T- and B-cell activation, and NF-κB signaling. The majority of published leukemic transcriptomes exhibit signals of this incubation-induced dysregulation, explaining up to 40% of differences in gene expression and alternative splicing between leukemias and reference normal transcriptomes. The effects of sample processing are particularly evident in pan-cancer analyses. We provide biomarkers that detect prolonged incubation of individual samples and show that keeping blood on ice markedly reduces changes to the transcriptome. In addition to highlighting the potentially confounding effects of technical artifacts in cancer genomics data, our study emphasizes the need to survey the diversity of normal as well as neoplastic cells when characterizing tumors.
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50
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Radhakrishnan D, Yamashita C, Gillio-Meina C, Fraser DD. Translational research in pediatrics III: bronchoalveolar lavage. Pediatrics 2014; 134:135-54. [PMID: 24982109 DOI: 10.1542/peds.2013-1911] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The role of flexible bronchoscopy and bronchoalveolar lavage (BAL) for the care of children with airway and pulmonary diseases is well established, with collected BAL fluid most often used clinically for microbiologic pathogen identification and cellular analyses. More recently, powerful analytic research methods have been used to investigate BAL samples to better understand the pathophysiological basis of pediatric respiratory disease. Investigations have focused on the cellular components contained in BAL fluid, such as macrophages, lymphocytes, neutrophils, eosinophils, and mast cells, as well as the noncellular components such as serum molecules, inflammatory proteins, and surfactant. Molecular techniques are frequently used to investigate BAL fluid for the presence of infectious pathologies and for cellular gene expression. Recent advances in proteomics allow identification of multiple protein expression patterns linked to specific respiratory diseases, whereas newer analytic techniques allow for investigations on surfactant quantification and function. These translational research studies on BAL fluid have aided our understanding of pulmonary inflammation and the injury/repair responses in children. We review the ethics and practices for the execution of BAL in children for translational research purposes, with an emphasis on the optimal handling and processing of BAL samples.
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Affiliation(s)
- Dhenuka Radhakrishnan
- Departments of Pediatrics,Children's Health Research Institute, London, Ontario, Canada
| | - Cory Yamashita
- Medicine,Centre for Critical Illness Research, Western University, London, Ontario, Canada; andPhysiology and Pharmacology, and
| | | | - Douglas D Fraser
- Departments of Pediatrics,Children's Health Research Institute, London, Ontario, Canada;Centre for Critical Illness Research, Western University, London, Ontario, Canada; andPhysiology and Pharmacology, andClinical Neurologic Sciences, Western University, London, Ontario, Canada;Translational Research Centre, London, Ontario, Canada
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