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Nguyen LT, Pollock CA, Saad S. Extraction of high quality and high yield RNA from frozen EDTA blood. Sci Rep 2024; 14:8628. [PMID: 38622175 PMCID: PMC11018810 DOI: 10.1038/s41598-024-58576-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
Peripheral blood RNA profiling, which can reveal systemic changes in gene expression and immune responses to disease onset and progression, is a powerful tool for diagnosis and biomarker discovery. This technique usually requires high quality RNA, which is only obtainable from fresh blood, or frozen blood that has been collected in special RNA-stabilisation systems. The current study aimed to develop a novel protocol to extract high quality RNA from frozen blood that had been collected in the conventional EDTA tubes. We determined that thawing EDTA blood in the presence of cell lysis/RNA stabilisation buffers (Paxgene or Nucleospin) significantly improved RNA quality (RIN) from below 5 to above 7, which to date has not been shown possible. The EDTA-Nucleospin protocol resulted in 5 times higher yield than the EDTA-Paxgene-PreAnalytix method. The average RIN and mRNA expression levels of five different genes including 18 s, ACTB, MCP1, TNFa and TXNIP using this protocol were also indifferent to those from Paxgene blood, suggesting similar RNA quality and blood transcriptome. Moreover, the protocol allows DNA to be extracted simultaneously. In conclusion, we have developed a practical and efficient protocol to extract high quality, high yield RNA from frozen EDTA blood.
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Affiliation(s)
- Long T Nguyen
- Renal Medicine, Kolling Institute, University of Sydney, Camperdown, Australia.
| | - Carol A Pollock
- Renal Medicine, Kolling Institute, University of Sydney, Camperdown, Australia
| | - Sonia Saad
- Renal Medicine, Kolling Institute, University of Sydney, Camperdown, Australia
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Vergés C, Giménez-Capitán A, Ribas V, Salgado-Borges J, March de Ribot F, Mayo-de-Las-Casas C, Armiger-Borras N, Pedraz C, Molina-Vila MÁ. Gene expression signatures in conjunctival fornix aspirates of patients with dry eye disease associated with Meibomian gland dysfunction. A proof-of-concept study. Ocul Surf 2023; 30:42-50. [PMID: 37524297 DOI: 10.1016/j.jtos.2023.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/02/2023]
Abstract
BACKGROUND Meibomian gland dysfunction (MGD) is one of the most common conditions in ophthalmic practice and the most frequent cause of evaporative dry eye disease (DED). However, the immune mechanisms leading to this pathology are not fully understood and the diagnostic tests available are limited. Here, we used the nCounter technology to analyze immune gene expression in DED-MGD that can be used for developing diagnostic signatures for DED. METHODS Conjunctival cell samples were obtained by aspiration from patients with DED-MGD (n = 27) and asymptomatic controls (n = 22). RNA was purified, converted to cDNA, preamplified and analyzed using the Gene Expression Human Immune V2 panel (NanoString), which includes 579 target and 15 housekeeping genes. A machine learning (ML) algorithm was applied to design a signature associated with DED-MGD. RESULTS Forty-five immune genes were found upregulated in DED-MGD vs. controls, involved in eight signaling pathways, IFN I/II, MHC class I/II, immunometabolism, B cell receptor, T Cell receptor, and T helper-17 (Th-17) differentiation. Additionally, statistically significant correlations were found between 31 genes and clinical characteristics of the disease such as lid margin or tear osmolarity (Pearson's r < 0.05). ML analysis using a recursive feature elimination (RFE) algorithm selected a 4-gene mRNA signature that discriminated DED-MGD from control samples with an area under the ROC curve (AUC ROC) of 0.86 and an accuracy of 77.5%. CONCLUSIONS Multiplexed mRNA analysis of conjunctival cells can be used to analyze immune gene expression patterns in patients with DED-MGD and to generate diagnostic signatures.
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Affiliation(s)
- Carlos Vergés
- Department of Ophthalmology, Hospital Universitari Dexeus, Area Oftalmológica Avanzada, Universitat Politécnica de Catalunya, Barcelona, Spain.
| | - Ana Giménez-Capitán
- Pangaea Oncology, Laboratory of Oncology, Dexeus University Hospital, Barcelona, Spain
| | - Verónica Ribas
- Department of Ophthalmology, Hospital Universitari Dexeus, Area Oftalmológica Avanzada, Universitat Politécnica de Catalunya, Barcelona, Spain
| | - José Salgado-Borges
- Department of Ophthalmology, Hospital Universitari Dexeus, Area Oftalmológica Avanzada, Universitat Politécnica de Catalunya, Barcelona, Spain
| | - Francesc March de Ribot
- Department of Ophthalmology, Hospital Universitari Dexeus, Area Oftalmológica Avanzada, Universitat Politécnica de Catalunya, Barcelona, Spain
| | | | - Noelia Armiger-Borras
- Pangaea Oncology, Laboratory of Oncology, Dexeus University Hospital, Barcelona, Spain
| | - Carlos Pedraz
- Pangaea Oncology, Laboratory of Oncology, Dexeus University Hospital, Barcelona, Spain
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de Koning W, van Eijck CWF, van der Sijde F, Strijk GJ, Oostvogels AAM, Debets R, van Eijck CHJ, Mustafa DAM. Analyzing Flow Cytometry or Targeted Gene Expression Data Influences Clinical Discoveries-Profiling Blood Samples of Pancreatic Ductal Adenocarcinoma Patients. Cancers (Basel) 2023; 15:4349. [PMID: 37686626 PMCID: PMC10486875 DOI: 10.3390/cancers15174349] [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: 06/28/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
INTRODUCTION Monitoring the therapeutic response of pancreatic ductal adenocarcinoma (PDAC) patients is crucial to determine treatment strategies. Several studies have examined the effectiveness of FOLFIRINOX as a first-line treatment in patients with locally advanced pancreatic cancer, but little attention has been paid to the immunologic alterations in peripheral blood caused by this chemotherapy regimen. Furthermore, the influence of the measurement type (e.g., flow cytometry and targeted gene expression) on the clinical discoveries is unknown. Therefore, we aimed to scrutinize the influence of using flow cytometry or targeted immune gene expression to study the immunological changes in blood samples of PDAC patients who were treated with a single-cycle FOLFIRINOX combined with lipegfilgrastim (FFX-Lipeg). MATERIAL AND METHODS Whole-blood samples from 44 PDAC patients were collected at two time points: before the first FOLFIRINOX cycle and 14 days after the first cycle. EDTA blood tubes were used for multiplex flow cytometry analyses to quantify 18 immune cell populations and for complete blood count tests as the standard clinical routine. The flow cytometry data were analyzed with FlowJo software. In addition, Tempus blood tubes were used to isolate RNA and measure 1230 immune-related genes using NanoString Technology®. Data quality control, normalization, and analysis were performed using nSolver™ software and the Advanced Analysis module. RESULTS FFX-Lipeg treatment increased the number of neutrophils and monocytes, as shown by flow cytometry and complete blood count in concordance with elevated gene expression measured via targeted gene expression profiling analysis. Interestingly, flow cytometry analysis showed an increase in the number of B and T cells after treatment, while targeted gene expression analysis showed a decrease in B and T cell-specific gene expression. CONCLUSIONS Targeted gene expression complements flow cytometry analysis to provide a comprehensive understanding of the effects of FFX-Lipeg. Flow cytometry and targeted gene expression showed increases in neutrophils and monocytes after FFX-Lipeg. The number of lymphocytes is increased after treatment; nevertheless, their cell-specific gene expression levels are downregulated. This highlights that different techniques influence clinical discoveries. Therefore, it is important to carefully select the measurement technique used to study the effect of a treatment.
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Affiliation(s)
- Willem de Koning
- The Tumor Immuno-Pathology Laboratory, Department of Pathology & Clinical Bioinformatics, Erasmus University Medical Centre, 3015 GD Rotterdam, The Netherlands; (W.d.K.)
- Clinical Bioinformatics Unit, Department of Pathology & Clinical Bioinformatics, Erasmus University Medical Centre, 3015 GD Rotterdam, The Netherlands
| | - Casper W. F. van Eijck
- The Tumor Immuno-Pathology Laboratory, Department of Pathology & Clinical Bioinformatics, Erasmus University Medical Centre, 3015 GD Rotterdam, The Netherlands; (W.d.K.)
- Department of Surgery, Erasmus University Medical Centre, 3015 GD Rotterdam, The Netherlands
| | - Fleur van der Sijde
- The Tumor Immuno-Pathology Laboratory, Department of Pathology & Clinical Bioinformatics, Erasmus University Medical Centre, 3015 GD Rotterdam, The Netherlands; (W.d.K.)
- Department of Surgery, Erasmus University Medical Centre, 3015 GD Rotterdam, The Netherlands
| | - Gaby J. Strijk
- The Tumor Immuno-Pathology Laboratory, Department of Pathology & Clinical Bioinformatics, Erasmus University Medical Centre, 3015 GD Rotterdam, The Netherlands; (W.d.K.)
- Department of Surgery, Erasmus University Medical Centre, 3015 GD Rotterdam, The Netherlands
| | - Astrid A. M. Oostvogels
- Laboratory of Tumor Immunology, Department of Medical Oncology, Erasmus University Medical Centre, 3015 GD Rotterdam, The Netherlands
| | - Reno Debets
- Laboratory of Tumor Immunology, Department of Medical Oncology, Erasmus University Medical Centre, 3015 GD Rotterdam, The Netherlands
| | - Casper H. J. van Eijck
- Department of Surgery, Erasmus University Medical Centre, 3015 GD Rotterdam, The Netherlands
| | - Dana A. M. Mustafa
- The Tumor Immuno-Pathology Laboratory, Department of Pathology & Clinical Bioinformatics, Erasmus University Medical Centre, 3015 GD Rotterdam, The Netherlands; (W.d.K.)
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van Eijck CWF, de Koning W, van der Sijde F, Moskie M, Groot Koerkamp B, Homs MYV, van der Burg SH, van Eijck CHJ, Mustafa DAM. A multigene circulating biomarker to predict the lack of FOLFIRINOX response after a single cycle in patients with pancreatic ductal adenocarcinoma. Eur J Cancer 2023; 181:119-134. [PMID: 36652890 DOI: 10.1016/j.ejca.2022.12.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/30/2022]
Abstract
INTRODUCTION 5-fluorouracil, folinic acid, irinotecan and oxaliplatin (FOLFIRINOX) is promising in treating patients with pancreatic ductal adenocarcinoma. However, many patients and physicians are reluctant to start FOLFIRINOX due to its high toxicity and limited clinical response rates. In this study, we investigated the effect of a single FOLFIRINOX cycle, in combination with a granulocyte colony-stimulating factor, on the blood immune transcriptome of patients with pancreatic ductal adenocarcinoma. We aimed to identify an early circulating biomarker to predict the lack of FOLFIRINOX response. METHODS Blood samples of 68 patients from all disease stages, who received at least four FOLFIRINOX cycles, were collected at baseline and after the first cycle. The response to treatment was radiologically evaluated following the Response Evaluation Criteria in Solid Tumours criteria 1.1. Targeted immune-gene expression profiling (GEP) was performed using NanoString technologies. To predict the lack of FOLFIRINOX response, we developed a FOLFIRINOX delta GEP (FFX-ΔGEP) score. RESULTS A single FOLFIRINOX cycle significantly altered 395 genes, correlating to 30 significant alterations in relative immune cell abundances and pathway activities. The eight-gene (BID, FOXP3, KIR3DL1, MAF, PDGFRB, RRAD, SIGLEC1 and TGFB2) FFX-ΔGEP score predicted the lack of FOLFIRINOX response with a leave-one-out cross-validated area under the curve (95% confidence interval) of 0.87 (0.60-0.98), thereby outperforming the predictiveness of absolute and proportional Δcarbohydrate antigen19-9 values. CONCLUSIONS A single FOLFIRINOX cycle, combined with granulocyte colony-stimulating factor, alters the peripheral immune transcriptome indisputably. Our novel FFX-ΔGEP is, to our knowledge, the first multigene early circulating biomarker that predicts the lack of FOLFIRINOX response after one cycle. Validation in a larger independent patient cohort is crucial before clinical implementation.
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Affiliation(s)
- Casper W F van Eijck
- Department of Surgery, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, the Netherlands; Department of Pathology Unit of Tumour Immuno-Pathology, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, the Netherlands.
| | - Willem de Koning
- Department of Pathology Unit of Tumour Immuno-Pathology, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, the Netherlands; Department of Pathology Unit of Clinical Bioinformatics, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, the Netherlands.
| | - Fleur van der Sijde
- Department of Surgery, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, the Netherlands; Department of Pathology Unit of Tumour Immuno-Pathology, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, the Netherlands.
| | - Miranda Moskie
- Department of Surgery, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, the Netherlands.
| | - Bas Groot Koerkamp
- Department of Surgery, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, the Netherlands.
| | - Marjolein Y V Homs
- Department of Medical Oncology, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, the Netherlands.
| | - Sjoerd H van der Burg
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, 2300 RC Leiden, the Netherlands.
| | - Casper H J van Eijck
- Department of Surgery, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, the Netherlands; Department of Pathology Unit of Tumour Immuno-Pathology, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, the Netherlands.
| | - Dana A M Mustafa
- Department of Pathology Unit of Tumour Immuno-Pathology, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, the Netherlands.
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Justin Margret J, Jain SK. Overview of gene expression techniques with an emphasis on vitamin D related studies. Curr Med Res Opin 2023; 39:205-217. [PMID: 36537177 DOI: 10.1080/03007995.2022.2159148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Each cell controls when and how its genes must be expressed for proper function. Every function in a cell is driven by signaling molecules through various regulatory cascades. Different cells in a multicellular organism may express very different sets of genes, even though they contain the same DNA. The set of genes expressed in a cell determines the set of proteins and functional RNAs it contains, giving it its unique properties. Malfunction in gene expression harms the cell and can lead to the development of various disease conditions. The use of rapid high-throughput gene expression profiling unravels the complexity of human disease at various levels. Peripheral blood mononuclear cells (PBMC) have been used frequently to understand gene expression homeostasis in various disease conditions. However, more studies are required to validate whether PBMC gene expression patterns accurately reflect the expression of other cells or tissues. Vitamin D, which is responsible for a multitude of health consequences, is also an immune modulatory hormone with major biological activities in the innate and adaptive immune systems. Vitamin D exerts its diverse biological effects in target tissues by regulating gene expression and its deficiency, is recognized as a public health problem worldwide. Understanding the genetic factors that affect vitamin D has the potential benefit that it will make it easier to identify individuals who require supplementation. Different technological advances in gene expression can be used to identify and assess the severity of disease and aid in the development of novel therapeutic interventions. This review focuses on different gene expression approaches and various clinical studies of vitamin D to investigate the role of gene expression in identifying the molecular signature of the disease.
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Affiliation(s)
- Jeffrey Justin Margret
- Department of Pediatrics, Louisiana State University Health Sciences Center-Shreveport, Shreveport, LA, USA
| | - Sushil K Jain
- Department of Pediatrics, Louisiana State University Health Sciences Center-Shreveport, Shreveport, LA, USA
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The Value of SIRT1/FOXO1 Signaling Pathway in Early Detection of Cardiovascular Risk in Children with β-Thalassemia Major. Biomedicines 2022; 10:biomedicines10102601. [PMID: 36289866 PMCID: PMC9599077 DOI: 10.3390/biomedicines10102601] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/25/2022] Open
Abstract
Background: Atherosclerosis represents one of the major causes of morbidity in children with β-thalassemia major (β-TM). Aim: This study was designed to investigate SIRT1-FOXO1 signaling in β-TM children and their role in early detection of premature atherosclerosis. Methods: We equally subdivided 100 Egyptian children aged 6−14 years with β-TM according to carotid intima media thickness (CIMT) into 50 with CIMT < 0.5 mm and 50 with CIMT ≥ 0.5 mm, and 50 healthy children of matched age were included. They were subjected to evaluation of SIRT1, heat shock protein 72 (HSP72), and hepcidin levels via ELISA and forkhead box protein 1 (FOXO1) mRNA expression using real-time PCR in PBMCs; meanwhile, malondialdehyde (MDA), superoxide dismutase (SOD), and catalase activities were evaluated spectrophotometrically. Results: Our results show significantly high values for CIMT, β-stiffness, atherogenic index of plasma (AIP), MDA, HSP72 and FOXO1, ferritin with significantly low hepcidin, SOD, catalase, and SIRT1 in β-TM as compared to controls with a more significant difference in β-TM with CIMT ≥ 0.5 mm than those with CIMT < 0.5 mm. A significant positive correlation between CIMT and MDA, HSP72, and FOXO1 gene expression was found, while a significant negative correlation with hepcidin, SOD, catalase, and SIRT1 was found. FOXO1 gene expression and HSP72 levels were the strongest independent determinants of CIMT. Conclusion: In β-TM, FOXO1 signaling is activated with low levels of SIRT1, and this is attributed to accelerated atherosclerosis in β-TM, which would be crucial in prediction of atherosclerosis.
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Distinct CholinomiR Blood Cell Signature as a Potential Modulator of the Cholinergic System in Women with Fibromyalgia Syndrome. Cells 2022; 11:cells11081276. [PMID: 35455956 PMCID: PMC9031252 DOI: 10.3390/cells11081276] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/04/2022] [Accepted: 04/06/2022] [Indexed: 11/25/2022] Open
Abstract
Fibromyalgia syndrome (FMS) is a heterogeneous chronic pain syndrome characterized by musculoskeletal pain and other key co-morbidities including fatigue and a depressed mood. FMS involves altered functioning of the central and peripheral nervous system (CNS, PNS) and immune system, but the specific molecular pathophysiology remains unclear. Anti-cholinergic treatment is effective in FMS patient subgroups, and cholinergic signaling is a strong modulator of CNS and PNS immune processes. Therefore, we used whole blood small RNA-sequencing of female FMS patients and healthy controls to profile microRNA regulators of cholinergic transcripts (CholinomiRs). We compared microRNA profiles with those from Parkinson’s disease (PD) patients with pain as disease controls. We validated the sequencing results with quantitative real-time PCR (qRT-PCR) and identified cholinergic targets. Further, we measured serum cholinesterase activity in FMS patients and healthy controls. Small RNA-sequencing revealed FMS-specific changes in 19 CholinomiRs compared to healthy controls and PD patients. qRT-PCR validated miR-182-5p upregulation, distinguishing FMS patients from healthy controls. mRNA targets of CholinomiRs bone morphogenic protein receptor 2 and interleukin 6 signal transducer were downregulated. Serum acetylcholinesterase levels and cholinesterase activity in FMS patients were unchanged. Our findings identified an FMS-specific CholinomiR signature in whole blood, modulating immune-related gene expression.
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Rozowsky JS, Meesters-Ensing JI, Lammers JAS, Belle ML, Nierkens S, Kranendonk MEG, Kester LA, Calkoen FG, van der Lugt J. A Toolkit for Profiling the Immune Landscape of Pediatric Central Nervous System Malignancies. Front Immunol 2022; 13:864423. [PMID: 35464481 PMCID: PMC9022116 DOI: 10.3389/fimmu.2022.864423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
The prognosis of pediatric central nervous system (CNS) malignancies remains dismal due to limited treatment options, resulting in high mortality rates and long-term morbidities. Immunotherapies, including checkpoint inhibition, cancer vaccines, engineered T cell therapies, and oncolytic viruses, have promising results in some hematological and solid malignancies, and are being investigated in clinical trials for various high-grade CNS malignancies. However, the role of the tumor immune microenvironment (TIME) in CNS malignancies is mostly unknown for pediatric cases. In order to successfully implement immunotherapies and to eventually predict which patients would benefit from such treatments, in-depth characterization of the TIME at diagnosis and throughout treatment is essential. In this review, we provide an overview of techniques for immune profiling of CNS malignancies, and detail how they can be utilized for different tissue types and studies. These techniques include immunohistochemistry and flow cytometry for quantifying and phenotyping the infiltrating immune cells, bulk and single-cell transcriptomics for describing the implicated immunological pathways, as well as functional assays. Finally, we aim to describe the potential benefits of evaluating other compartments of the immune system implicated by cancer therapies, such as cerebrospinal fluid and blood, and how such liquid biopsies are informative when designing immune monitoring studies. Understanding and uniformly evaluating the TIME and immune landscape of pediatric CNS malignancies will be essential to eventually integrate immunotherapy into clinical practice.
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Affiliation(s)
| | | | | | - Muriël L. Belle
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Stefan Nierkens
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | | | | | - Friso G. Calkoen
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
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Komini C, Bounas A. Recovery of RNA from avian nucleated whole blood stored under field conditions: an evaluation of commercial methods. Br Poult Sci 2022; 63:730-734. [PMID: 35373667 DOI: 10.1080/00071668.2022.2061838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
1. Whole blood can be used to gain insights on several molecular mechanisms involved in animal physiology. However, its use to extract RNA from organisms that carry nucleated red blood cells is limited due to its high nuclease content and instability under field conditions. 2. Here, we evaluate three commercially available RNA preservation and extraction methods applied to avian whole blood samples kept in different storage conditions to identify the most suitable ones for use in field studies. 3. Whole blood starting volume was the most important factor; only samples with a starting volume of 50 µl yielded RNA whereas all 100 µl samples failed to provide any RNA regardless of the method used. RNA concentration decreased with storage time in every method employed. Samples stored at -20 °C yielded higher RNA concentration than the ones stored at 4°C although some possible effects of freeze-thaw cycles were observed. 4. For the two out of three methods it is likely that DNA contamination and/or extensive degradation of RNA could have taken place. Only whole blood stored and extracted using the Quick RNA Whole Blood kit provided high quality RNA in every condition tested.
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Affiliation(s)
- Chrysoula Komini
- Department of Biological Applications and Technology, University of Ioannina, 45110, Ioannina, Greece
| | - Anastasios Bounas
- Department of Biological Applications and Technology, University of Ioannina, 45110, Ioannina, Greece
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10
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Raven N, Klaassen M, Madsen T, Thomas F, Hamede R, Ujvari B. Transmissible cancer influences immune gene expression in an endangered marsupial, the Tasmanian devil (Sarcophilus harrisii). Mol Ecol 2022; 31:2293-2311. [PMID: 35202488 PMCID: PMC9310804 DOI: 10.1111/mec.16408] [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: 11/13/2020] [Accepted: 02/14/2022] [Indexed: 11/28/2022]
Abstract
Understanding the effects of wildlife diseases on populations requires insight into local environmental conditions, host defence mechanisms, host life‐history trade‐offs, pathogen population dynamics, and their interactions. The survival of Tasmanian devils (Sarcophilus harrisii) is challenged by a novel, fitness limiting pathogen, Tasmanian devil facial tumour disease (DFTD), a clonally transmissible, contagious cancer. In order to understand the devils’ capacity to respond to DFTD, it is crucial to gain information on factors influencing the devils’ immune system. By using RT‐qPCR, we investigated how DFTD infection in association with intrinsic (sex and age) and environmental (season) factors influences the expression of 10 immune genes in Tasmanian devil blood. Our study showed that the expression of immune genes (both innate and adaptive) differed across seasons, a pattern that was altered when infected with DFTD. The expression of immunogbulins IgE and IgM:IgG showed downregulation in colder months in DFTD infected animals. We also observed strong positive association between the expression of an innate immune gene, CD16, and DFTD infection. Our results demonstrate that sampling across seasons, age groups and environmental conditions are beneficial when deciphering the complex ecoevolutionary interactions of not only conventional host‐parasite systems, but also of host and diseases with high mortality rates, such as transmissible cancers.
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Affiliation(s)
- N Raven
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic, 3216, Australia
| | - M Klaassen
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic, 3216, Australia
| | - T Madsen
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic, 3216, Australia
| | - F Thomas
- CREEC/CANECEV (CREES), Montpellier, France.,MIVEGEC, Université de Montpellier, CNRS, IRD, Montpellier, France
| | - R Hamede
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic, 3216, Australia.,School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia
| | - B Ujvari
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic, 3216, Australia
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Broekhuizen M, Hitzerd E, van den Bosch TPP, Dumas J, Verdijk RM, van Rijn BB, Danser AHJ, van Eijck CHJ, Reiss IKM, Mustafa DAM. The Placental Innate Immune System Is Altered in Early-Onset Preeclampsia, but Not in Late-Onset Preeclampsia. Front Immunol 2022; 12:780043. [PMID: 34992598 PMCID: PMC8724430 DOI: 10.3389/fimmu.2021.780043] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/29/2021] [Indexed: 12/18/2022] Open
Abstract
Preeclampsia is a severe placenta-related pregnancy disorder that is generally divided into two subtypes named early-onset preeclampsia (onset <34 weeks of gestation), and late-onset preeclampsia (onset ≥34 weeks of gestation), with distinct pathophysiological origins. Both forms of preeclampsia have been associated with maternal systemic inflammation. However, alterations in the placental immune system have been less well characterized. Here, we studied immunological alterations in early- and late-onset preeclampsia placentas using a targeted expression profile approach. RNA was extracted from snap-frozen placenta samples (healthy n=13, early-onset preeclampsia n=13, and late-onset preeclampsia n=6). The expression of 730 immune-related genes from the Pan Cancer Immune Profiling Panel was measured, and the data were analyzed in the advanced analysis module of nSolver software (NanoString Technology). The results showed that early-onset preeclampsia placentas displayed reduced expression of complement, and toll-like receptor (TLR) associated genes, specifically TLR1 and TLR4. Mast cells and M2 macrophages were also decreased in early-onset preeclampsia compared to healthy placentas. The findings were confirmed by an immunohistochemistry approach using 20 healthy, 19 early-onset preeclampsia, and 10 late-onset preeclampsia placentas. We conclude that the placental innate immune system is altered in early-onset preeclampsia compared to uncomplicated pregnancies. The absence of these alterations in late-onset preeclampsia placentas indicates dissimilar immunological profiles. The study revealed distinct pathophysiological processes in early-onset and late-onset preeclampsia placentas and imply that a tailored treatment to each subtype is desirable.
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Affiliation(s)
- Michelle Broekhuizen
- Division of Neonatology, Department of Pediatrics, Erasmus University Medical Center, Rotterdam, Netherlands.,Division of Pharmacology and Vascular Medicine, Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, Netherlands.,Division of Experimental Cardiology, Department of Cardiology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Emilie Hitzerd
- Division of Neonatology, Department of Pediatrics, Erasmus University Medical Center, Rotterdam, Netherlands.,Division of Pharmacology and Vascular Medicine, Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, Netherlands
| | | | - Jasper Dumas
- Department of Pathology, Erasmus University Medical Center, Rotterdam, Netherlands.,The Tumor Immuno-Pathology (TIP) Laboratory, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Robert M Verdijk
- Department of Pathology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Bas B van Rijn
- Department of Obstetrics and Gynecology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - A H Jan Danser
- Division of Pharmacology and Vascular Medicine, Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Casper H J van Eijck
- Department of Surgery, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Irwin K M Reiss
- Division of Neonatology, Department of Pediatrics, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Dana A M Mustafa
- Department of Pathology, Erasmus University Medical Center, Rotterdam, Netherlands.,The Tumor Immuno-Pathology (TIP) Laboratory, Erasmus University Medical Center, Rotterdam, Netherlands
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12
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Yamagata H, Kobayashi A, Tsunedomi R, Seki T, Kobayashi M, Hagiwara K, Chen C, Uchida S, Okada G, Fuchikami M, Kamishikiryo T, Iga JI, Numata S, Kinoshita M, Kato TA, Hashimoto R, Nagano H, Okamoto Y, Ueno S, Ohmori T, Nakagawa S. Optimized protocol for the extraction of RNA and DNA from frozen whole blood sample stored in a single EDTA tube. Sci Rep 2021; 11:17075. [PMID: 34426633 PMCID: PMC8382694 DOI: 10.1038/s41598-021-96567-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/11/2021] [Indexed: 01/27/2023] Open
Abstract
Cryopreservation of whole blood is useful for DNA collection, and clinical and basic research. Blood samples in ethylenediaminetetraacetic acid disodium salt (EDTA) tubes stored at − 80 °C are suitable for DNA extraction, but not for high-quality RNA extraction. Herein, a new methodology for high-quality RNA extraction from human blood samples is described. Quickly thawing frozen whole blood on aluminum blocks at room temperature could minimize RNA degradation, and improve RNA yield and quality compared with thawing the samples in a 37 °C water bath. Furthermore, the use of the NucleoSpin RNA kit increased RNA yield by fivefold compared with the PAXgene Blood RNA Kit. Thawing blood samples on aluminum blocks significantly increased the DNA yield by ~ 20% compared with thawing in a 37 °C water bath or on ice. Moreover, by thawing on aluminum blocks and using the NucleoSpin RNA and QIAamp DNA Blood kits, the extraction of RNA and DNA of sufficient quality and quantity was achieved from frozen EDTA whole blood samples that were stored for up to 8.5 years. Thus, extracting RNA from frozen whole blood in EDTA tubes after long-term storage is feasible. These findings may help advance gene expression analysis, as well as biomarker research for various diseases.
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Affiliation(s)
- Hirotaka Yamagata
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan. .,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
| | - Ayumi Kobayashi
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Ryouichi Tsunedomi
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Tomoe Seki
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Masaaki Kobayashi
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Kosuke Hagiwara
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Chong Chen
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Shusaku Uchida
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.,SK Project, Medical Innovation Center, Kyoto University Graduate School of Medicine, 53 Shogoin‑Kawahara‑cho, Sakyo‑ku, Kyoto, 606‑8507, Japan
| | - Go Okada
- Department of Psychiatry and Neurosciences, Graduate School of Biomedical Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Manabu Fuchikami
- Department of Psychiatry and Neurosciences, Graduate School of Biomedical Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Toshiharu Kamishikiryo
- Department of Psychiatry and Neurosciences, Graduate School of Biomedical Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Jun-Ichi Iga
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, 791-0295, Japan
| | - Shusuke Numata
- Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, 3-18-5 Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Makoto Kinoshita
- Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, 3-18-5 Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Takahiro A Kato
- Department of Neuropsychiatry, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Ryota Hashimoto
- Department of Pathology of Mental Diseases, National Institute of Mental Health, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo, 187-8553, Japan
| | - Hiroaki Nagano
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Yasumasa Okamoto
- Department of Psychiatry and Neurosciences, Graduate School of Biomedical Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Shuichi Ueno
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, 791-0295, Japan
| | - Tetsuro Ohmori
- Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, 3-18-5 Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Shin Nakagawa
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
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13
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Kazemi Fard T, Ahmadi R, Akbari T, Moradi N, Fadaei R, Kazemi Fard M, Fallah S. Klotho, FOXO1 and cytokines associations in patients with coronary artery disease. Cytokine 2021; 141:155443. [PMID: 33582500 DOI: 10.1016/j.cyto.2021.155443] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 01/20/2023]
Abstract
INTRODUCTION Atherosclerosis is one of the main reasons for adult mortality in advanced populations and countries with high stress levels. Klotho family are single-pass trans-membrane proteins that involve in the genesis and progression of various diseases, including acardiovascular disease, apoptosis and stress oxidative imbalance. Present study, investigates the pattern of changes in Klotho and FOXO1 gene expressions and levels in atherosclerosis. METHODS Present case control study consisted of 79 patients with atherosclerosis and 78 healthy controls. PBMC (peripheral mono-nuclear blood cells) expression levels of Klotho and FOXO1 were assayed, using qPCR method. Serum concentration of Klotho and FOXO1 were measured by ELISA method. RESULTS A significant reduction was found in PBMC genes expression levels of Klotho (P < 0.01) of patients as comparison with controls. PBMC Gene expression of FOXO1 in patients was increased significantly (P < 0.01) when compared with controls. Pearson analysis showed a positive correlation between PBMC Klotho gene expression and Klotho levels of patients (P < 0.01). The correlation between serum concentrations of Klotho and FOXO1 of patients was also positive significantly (P < 0.01). AUC of ROC for gene expression and serum concentration of Klotho in patients were 0.701 and 0.737 respectively. CONCLUSION Investigating the PBMC gene expression and serum concentration of Klotho in patients with atherosclerosis is suggested could be a convenient novel biomarker for predicting, prognosis, monitoring the disease progression and designing a suitable drug for patients with atherosclerosis.
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Affiliation(s)
- Toktam Kazemi Fard
- Department of Biochemistry, Faculty of Basic Sciences, Islamic Azad University, Tehran North Branch, Tehran, Iran; Department of Biochemistry, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Reza Ahmadi
- Department of Biochemistry, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran; Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Tooran Akbari
- Department of Biochemistry, Faculty of Basic Sciences, Islamic Azad University, Tehran North Branch, Tehran, Iran; Department of Biochemistry, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Nariman Moradi
- Cellular and Molecular Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Reza Fadaei
- Sleep Disorders Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | | | - Soudabeh Fallah
- Department of Biochemistry, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.
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