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Małecka A, Østlie I, Trøen G, Małecki J, Delabie J, Tierens A, Munthe LA, Berentsen S, Tjønnfjord GE. Gene expression analysis revealed downregulation of complement receptor 1 in clonal B cells in cold agglutinin disease. Clin Exp Immunol 2024; 216:45-54. [PMID: 38133636 PMCID: PMC10929701 DOI: 10.1093/cei/uxad135] [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: 08/06/2023] [Revised: 11/03/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023] Open
Abstract
Cold agglutinin disease (CAD) is a rare B-cell lymphoproliferative disorder of the bone marrow, manifested by autoimmune hemolytic anemia caused by binding of monoclonal IgM autoantibodies to the I antigen. Underlying genetic changes have previously been reported, but their impact on gene expression profile has been unknown. Here, we define differentially expressed genes in CAD B cells. To unravel downstream alteration in cellular pathways, gene expression by RNA sequencing was undertaken. Clonal B-cell samples from 12 CAD patients and IgM-expressing memory B cells from 4 healthy individuals were analyzed. Differential expression analysis and filtering resulted in 93 genes with significant differential expression. Top upregulated genes included SLC4A1, SPTA1, YBX3, TESC, HBD, AHSP, TRAF1, HBA2, RHAG, CA1, SPTB, IL10, UBASH3B, ALAS2, HBA1, CRYM, RGCC, KANK2, and IGHV4-34. They were upregulated at least 8-fold, while complement receptor 1 (CR1/CD35) was downregulated 11-fold in clonal CAD B cells compared to control B cells. Flow cytometry analyses further confirmed reduced CR1 (CD35) protein expression by clonal CAD IgM+ B cells compared to IgM+ memory B cells in controls. CR1 (CD35) is an important negative regulator of B-cell activation and differentiation. Therefore, reduced CR1 (CD35) expression may increase activation, proliferation, and antibody production in CAD-associated clonal B cells.
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Affiliation(s)
- Agnieszka Małecka
- Department of Haematology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B-cell malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Ingunn Østlie
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Gunhild Trøen
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | | | - Jan Delabie
- Laboratory Medicine Program, University Health Network and University of Toronto, Toronto, ON, Canada
| | - Anne Tierens
- Laboratory Medicine Program, University Health Network and University of Toronto, Toronto, ON, Canada
| | - Ludvig A Munthe
- KG Jebsen Centre for B-cell malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Sigbjørn Berentsen
- Department of Research and Innovation, Haugesund Hospital, Helse Fonna Trust, Haugesund, Norway
| | - Geir E Tjønnfjord
- Department of Haematology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B-cell malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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2
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Wu Y, Leyk S, Torabi H, Höhn K, Honecker B, Tauler MDPM, Cadar D, Jacobs T, Bruchhaus I, Metwally NG. Plasmodium falciparum infection reshapes the human microRNA profiles of red blood cells and their extracellular vesicles. iScience 2023; 26:107119. [PMID: 37534175 PMCID: PMC10391920 DOI: 10.1016/j.isci.2023.107119] [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: 11/21/2022] [Revised: 03/08/2023] [Accepted: 06/09/2023] [Indexed: 08/04/2023] Open
Abstract
Plasmodium falciparum, a human malaria parasite, develops in red blood cells (RBCs), which represent approximately 70% of all human blood cells. Additionally, RBC-derived extracellular vesicles (RBC-EVs) represent 7.3% of the total EV population. The roles of microRNAs (miRNAs) in the consequences of P. falciparum infection are unclear. Here, we analyzed the miRNA profiles of non-infected human RBCs (niRBCs), ring-infected RBCs (riRBCs), and trophozoite-infected RBCs (trRBCs), as well as those of EVs secreted from these cells. Hsa-miR-451a was the most abundant miRNA in all RBC and RBC-EV populations, but its expression level was not affected by P. falciparum infection. Overall, the miRNA profiles of RBCs and their EVs were altered significantly after infection. Most of the differentially expressed miRNAs were shared between RBCs and their EVs. A target prediction analysis of the miRNAs revealed the possible identity of the genes targeted by these miRNAs (CXCL10, OAS1, IL7, and CCL5) involved in immunomodulation.
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Affiliation(s)
- Yifan Wu
- Research Group Host Parasite Interaction, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Stephanie Leyk
- Research Group Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Hanifeh Torabi
- Research Group Host Parasite Interaction, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Katharina Höhn
- Cellular Parasitology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Barbara Honecker
- Research Group Host Parasite Interaction, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | - Dániel Cadar
- Arbovirology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Thomas Jacobs
- Research Group Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Iris Bruchhaus
- Research Group Host Parasite Interaction, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Biology Department University of Hamburg, Hamburg, Germany
| | - Nahla Galal Metwally
- Research Group Host Parasite Interaction, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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Mukherjee P, Kumar K, Babu B, Purkayastha J, Chandna S. Alterations in the expression pattern of RBC membrane associated proteins (RMAPs) in whole body γ-irradiated Sprague Dawley rats. Int J Radiat Biol 2023; 99:1724-1737. [PMID: 37315317 DOI: 10.1080/09553002.2023.2219726] [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: 06/17/2022] [Revised: 05/24/2023] [Accepted: 05/24/2023] [Indexed: 06/16/2023]
Abstract
PURPOSE Peripheral blood serum/plasma proteins are frequently studied for their potential use as radiation exposure biomarkers. Here we report RBC membrane associated proteins (RMAPs), which show alterations in expression level following whole-body γ-irradiation of rats at sub-lethal/lethal doses. MATERIALS AND METHODS RBCs from peripheral blood of Sprague Dawley rats were segregated using the Ficoll-Hypaque method, and membrane fractions were hypotonically isolated at various time points (6 h, 24 h, 48 h) after γ-irradiation at 2 Gy, 5 Gy, and 7.5 Gy doses. Following purification of proteins from these fractions, two-dimensional electrophoresis (2-DE) was carried out. Treatment induced differentially expressed protein spots (≥2 fold increase/decrease) were picked up, trypsinized, and identified using LC-MS/MS analysis. Western immunoblots using protein specific antibodies were used to confirm the results. Gene ontology and interactions of these proteins were also studied. RESULTS From a number of differentially expressed radiation-responsive 2-DE protein spots detected, eight were identified unequivocally using LC-MS/MS. Out of these, actin, cytoplasmic 1 (ACTB) showed detectable yet insignificant variation (<50%) in expression. In contrast, peroxiredoxin-2 (PRDX2) and 26S proteasome regulatory subunit RPN11 (PSMD14) were the two most prominently over-expressed proteins. Five more proteins, namely tropomyosin alpha-3 chain (TPM3), exosome component 6 (EXOSC6), isoform 4 of tropomyosin alpha-1 chain (TPM1), serum albumin (ALB), and the 55 kDa erythrocyte membrane protein (P55) showed distinct alteration in their expression at different time-points and doses. ALB, EXOSC6, and PSMD14 were the most responsive at 2 Gy, albeit at different time-points. While EXOSC6 and PSMD14 showed maximum over-expression (5-12 fold) at 6 h post-irradiation, ALB expression increased progressively (4 up to 7 fold) from 6 h to 48 h. TPM1 showed over-expression (2-3 fold) at all doses and time-points tested. TPM3 showed a dose-dependent response at all time-points studied; with no variation at 2 Gy, ∼2 fold increase at 5 Gy, and 3-6 fold at the highest dose used (7.5 Gy). The p55 protein was over-expressed (∼2.5 fold) only transiently at 24 h following the lethal (7.5 Gy) dose. CONCLUSION This is the first study to report γ-radiation induced alterations in the RBC membrane associated proteins. We are further evaluating the potential of these proteins as radiation biomarkers. Due to the abundance and easy use of RBCs, this approach can prove very useful for detecting ionizing radiation exposure.
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Affiliation(s)
- Prabuddho Mukherjee
- Division of Molecular & Radiation Biosciences, Institute of Nuclear Medicine and Allied Sciences, DRDO, Brig. S K Majumdar Marg, Timarpur, Delhi, India
| | - Kamendra Kumar
- Division of Molecular & Radiation Biosciences, Institute of Nuclear Medicine and Allied Sciences, DRDO, Brig. S K Majumdar Marg, Timarpur, Delhi, India
| | - Bincy Babu
- Division of Molecular & Radiation Biosciences, Institute of Nuclear Medicine and Allied Sciences, DRDO, Brig. S K Majumdar Marg, Timarpur, Delhi, India
| | - Jubilee Purkayastha
- Division of Molecular & Radiation Biosciences, Institute of Nuclear Medicine and Allied Sciences, DRDO, Brig. S K Majumdar Marg, Timarpur, Delhi, India
| | - Sudhir Chandna
- Division of Molecular & Radiation Biosciences, Institute of Nuclear Medicine and Allied Sciences, DRDO, Brig. S K Majumdar Marg, Timarpur, Delhi, India
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Blackwell AD, Garcia AR. Ecoimmunology in the field: Measuring multiple dimensions of immune function with minimally invasive, field-adapted techniques. Am J Hum Biol 2022; 34:e23784. [PMID: 35861267 PMCID: PMC9786696 DOI: 10.1002/ajhb.23784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 06/29/2022] [Accepted: 07/08/2022] [Indexed: 01/25/2023] Open
Abstract
OBJECTIVE Immune function is multifaceted and characterizations based on single biomarkers may be uninformative or misleading, particularly when considered across ecological contexts. However, measuring the many facets of immunity in the field can be challenging, since many measures cannot be obtained on-site, necessitating sample preservation and transport. Here we assess state-of-the-art methods for measuring immunity, focusing on measures that require a minimal blood sample obtained from a finger prick, which can be: (1) dried on filter paper, (2) frozen in liquid nitrogen, or (3) stabilized with chemical reagents. RESULTS We review immune measures that can be obtained from point-of-care devices or from immunoassays of dried blood spots (DBSs), field methods for flow cytometry, the use of RNA or DNA sequencing and quantification, and the application of immune activation assays under field conditions. CONCLUSIONS Stable protein products, such as immunoglobulins and C-reactive protein are reliably measured in DBSs. Because less stable proteins, such as cytokines, may be problematic to measure even in fresh blood, mRNA from stabilized blood may provide a cleaner measure of cytokine and broader immune-related gene expression. Gene methylation assays or mRNA sequencing also allow for the quantification of many other parameters, including the inference of leukocyte subsets, though with less accuracy than with flow cytometry. Combining these techniques provides an improvement over single-marker studies, allowing for a more nuanced understanding of how social and ecological variables are linked to immune measures and disease risk in diverse populations and settings.
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Affiliation(s)
- Aaron D. Blackwell
- Department of AnthropologyWashington State UniversityPullmanWashingtonUSA
| | - Angela R. Garcia
- Research DepartmentPhoenix Children's HospitalPhoenixArizonaUSA,Department of Child HealthUniversity of Arizona College of MedicinePhoenixArizonaUSA
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Kumar SD, Kar D, Akhtar MN, Willard B, Roy D, Hussain T, Rajyaguru PI, Eswarappa SM. Evidence for low-level translation in human erythrocytes. Mol Biol Cell 2022; 33:br21. [PMID: 35976696 DOI: 10.1091/mbc.e21-09-0437] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
It is generally believed that human mature erythrocytes do not possess functional ribosomes, and therefore cannot synthesize proteins. However, the absence of translation is not consistent with the long lifespan of mature erythrocytes. They stay viable and functional for about 115 days in the circulatory system. Here, using highly pure preparation of human mature erythrocytes, we demonstrate the presence of translation by polysome profiling, [35S]methionine labelling and RiboPuromycylation. [35S]methionine labelling revealed that the translation in mature erythrocytes is about 10% of that observed in reticulocytes. We could observe polysomes by transmission electron microscopy in these cells. RNA-seq and quantitative RT-PCR performed on polysome fraction of these cells revealed that HBA (alpha globin) and HBB (beta globin) transcripts are translated. Using luciferase-based reporter assay and mutational studies, we show that the sequence of the 5' untranslated region is crucial for the translation of these transcripts. Furthermore, mature erythrocytes showed reduced expression of globin proteins (alpha and beta) when treated with translation inhibitors. Overall, we provide multiple lines of evidence for translation of globin mRNAs in human mature erythrocytes.
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Affiliation(s)
- Sangeetha Devi Kumar
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Debaleena Kar
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Md Noor Akhtar
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Belinda Willard
- Proteomics and Metabolomics Core, The Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Debadrita Roy
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Tanweer Hussain
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Purusharth I Rajyaguru
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Sandeep M Eswarappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, Karnataka, India
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Sae-Lee W, McCafferty CL, Verbeke EJ, Havugimana PC, Papoulas O, McWhite CD, Houser JR, Vanuytsel K, Murphy GJ, Drew K, Emili A, Taylor DW, Marcotte EM. The protein organization of a red blood cell. Cell Rep 2022; 40:111103. [PMID: 35858567 PMCID: PMC9764456 DOI: 10.1016/j.celrep.2022.111103] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/18/2022] [Accepted: 06/24/2022] [Indexed: 11/28/2022] Open
Abstract
Red blood cells (RBCs) (erythrocytes) are the simplest primary human cells, lacking nuclei and major organelles and instead employing about a thousand proteins to dynamically control cellular function and morphology in response to physiological cues. In this study, we define a canonical RBC proteome and interactome using quantitative mass spectrometry and machine learning. Our data reveal an RBC interactome dominated by protein homeostasis, redox biology, cytoskeletal dynamics, and carbon metabolism. We validate protein complexes through electron microscopy and chemical crosslinking and, with these data, build 3D structural models of the ankyrin/Band 3/Band 4.2 complex that bridges the spectrin cytoskeleton to the RBC membrane. The model suggests spring-like compression of ankyrin may contribute to the characteristic RBC cell shape and flexibility. Taken together, our study provides an in-depth view of the global protein organization of human RBCs and serves as a comprehensive resource for future research.
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Affiliation(s)
- Wisath Sae-Lee
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Caitlyn L McCafferty
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Eric J Verbeke
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Pierre C Havugimana
- Center for Network Systems Biology, Boston University, Boston, MA 02118, USA
| | - Ophelia Papoulas
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Claire D McWhite
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - John R Houser
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Kim Vanuytsel
- Center for Regenerative Medicine, Boston University School of Medicine, 670 Albany Street, Boston, MA 02118, USA
| | - George J Murphy
- Center for Regenerative Medicine, Boston University School of Medicine, 670 Albany Street, Boston, MA 02118, USA
| | - Kevin Drew
- Department of Biological Sciences, University of Illinois at Chicago, 900 S. Ashland Avenue, Chicago, IL 60607, USA
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, MA 02118, USA
| | - David W Taylor
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Edward M Marcotte
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA.
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7
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Sugasawa T, Kanki Y, Komine R, Watanabe K, Takekoshi K. Identification of RNA Markers in Red Blood Cells for Doping Control in Autologous Blood Transfusion. Genes (Basel) 2022; 13:genes13071255. [PMID: 35886040 PMCID: PMC9317427 DOI: 10.3390/genes13071255] [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: 06/14/2022] [Revised: 07/08/2022] [Accepted: 07/13/2022] [Indexed: 12/04/2022] Open
Abstract
The World Anti-Doping Agency (WADA) has prohibited the use of autologous blood transfusion (ABT) as a doping method by athletes. It is difficult to detect this doping method in laboratory tests, and a robust testing method has not yet been established. We conducted an animal experiment and used total RNA sequencing (RNA-Seq) to identify novel RNA markers to detect ABT doping within red blood cells (RBCs) as a pilot study before human trials. This study used whole blood samples from Wistar rats. The whole blood samples were mixed with a citrate–phosphate–dextrose solution with adenine (CPDA) and then stored in a refrigerator at 4 °C for 0 (control), 10, or 20 days. After each storage period, total RNA-Seq and bioinformatics were performed following RNA extraction and the purification of the RBCs. In the results, clear patterns of expression fluctuations were observed depending on the storage period, and it was found that there were large numbers of genes whose expression decreased in the 10- and 20-day periods compared to the control. Moreover, additional bioinformatic analysis identified three significant genes whose expression levels were drastically decreased according to the storage period. These results provide novel insights that may allow future studies to develop a testing method for ABT doping.
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Affiliation(s)
- Takehito Sugasawa
- Laboratory of Clinical Examination and Sports Medicine, Department of Clinical Medicine, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan; (T.S.); (Y.K.)
- Department of Sports Medicine Analysis, Open Facility Network Office, Organization for Open Facility Initiatives, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan;
| | - Yasuharu Kanki
- Laboratory of Clinical Examination and Sports Medicine, Department of Clinical Medicine, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan; (T.S.); (Y.K.)
- Department of Sports Medicine Analysis, Open Facility Network Office, Organization for Open Facility Initiatives, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan;
| | - Ritsuko Komine
- Department of Sports Medicine Analysis, Open Facility Network Office, Organization for Open Facility Initiatives, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan;
- Doctoral Program in Sports Medicine, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan
| | - Koichi Watanabe
- Faculty of Health and Sport Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8574, Japan;
| | - Kazuhiro Takekoshi
- Laboratory of Clinical Examination and Sports Medicine, Department of Clinical Medicine, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan; (T.S.); (Y.K.)
- Correspondence: ; Tel.: +81-29-853-3209
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Gajecki D, Gawryś J, Szahidewicz-Krupska E, Doroszko A. Role of Erythrocytes in Nitric Oxide Metabolism and Paracrine Regulation of Endothelial Function. Antioxidants (Basel) 2022; 11:antiox11050943. [PMID: 35624807 PMCID: PMC9137828 DOI: 10.3390/antiox11050943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/05/2022] [Accepted: 05/08/2022] [Indexed: 01/27/2023] Open
Abstract
Emerging studies provide new data shedding some light on the complex and pivotal role of red blood cells (RBCs) in nitric oxide (NO) metabolism and paracrine regulation of endothelial function. NO is involved in the regulation of vasodilatation, platelet aggregation, inflammation, hypoxic adaptation, and oxidative stress. Even though tremendous knowledge about NO metabolism has been collected, the exact RBCs’ status still requires evaluation. This paper summarizes the actual knowledge regarding the role of erythrocytes as a mobile depot of amino acids necessary for NO biotransformation. Moreover, the complex regulation of RBCs’ translocases is presented with a particular focus on cationic amino acid transporters (CATs) responsible for the NO substrates and derivatives transport. The main part demonstrates the intraerythrocytic metabolism of L-arginine with its regulation by reactive oxygen species and arginase activity. Additionally, the process of nitrite and nitrate turnover was demonstrated to be another stable source of NO, with its reduction by xanthine oxidoreductase or hemoglobin. Additional function of hemoglobin in NO synthesis and its subsequent stabilization in steady intermediates is also discussed. Furthermore, RBCs regulate the vascular tone by releasing ATP, inducing smooth muscle cell relaxation, and decreasing platelet aggregation. Erythrocytes and intraerythrocytic NO metabolism are also responsible for the maintenance of normotension. Hence, RBCs became a promising new therapeutic target in restoring NO homeostasis in cardiovascular disorders.
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Grätz C, Bui MLU, Thaqi G, Kirchner B, Loewe RP, Pfaffl MW. Obtaining Reliable RT-qPCR Results in Molecular Diagnostics—MIQE Goals and Pitfalls for Transcriptional Biomarker Discovery. Life (Basel) 2022; 12:life12030386. [PMID: 35330136 PMCID: PMC8953338 DOI: 10.3390/life12030386] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/15/2022] [Accepted: 03/02/2022] [Indexed: 11/16/2022] Open
Abstract
In this review, we discuss the development pipeline for transcriptional biomarkers in molecular diagnostics and stress the importance of a reliable gene transcript quantification strategy. Hence, a further focus is put on the MIQE guidelines and how to adapt them for biomarker discovery, from signature validation up to routine diagnostic applications. First, the advantages and pitfalls of the holistic RNA sequencing for biomarker development will be described to establish a candidate biomarker signature. Sequentially, the RT-qPCR confirmation process will be discussed to validate the discovered biomarker signature. Examples for the successful application of RT-qPCR as a fast and reproducible quantification method in routinemolecular diagnostics are provided. Based on the MIQE guidelines, the importance of “key steps” in RT-qPCR is accurately described, e.g., reverse transcription, proper reference gene selection and, finally, the application of automated RT-qPCR data analysis software. In conclusion, RT-qPCR proves to be a valuable tool in the establishment of a disease-specific transcriptional biomarker signature and will have a great future in molecular diagnostics or personalized medicine.
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Affiliation(s)
- Christian Grätz
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany; (C.G.); (M.L.U.B.); (G.T.); (B.K.)
- GeneSurge GmbH, Ottostr. 3, 80333 München, Germany;
| | - Maria L. U. Bui
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany; (C.G.); (M.L.U.B.); (G.T.); (B.K.)
- GeneSurge GmbH, Ottostr. 3, 80333 München, Germany;
| | - Granit Thaqi
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany; (C.G.); (M.L.U.B.); (G.T.); (B.K.)
| | - Benedikt Kirchner
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany; (C.G.); (M.L.U.B.); (G.T.); (B.K.)
- GeneSurge GmbH, Ottostr. 3, 80333 München, Germany;
| | | | - Michael W. Pfaffl
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany; (C.G.); (M.L.U.B.); (G.T.); (B.K.)
- Correspondence: or
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Aydin E, Dhar P, Gokhale M, Chong L, Azizoglu S, Suphioglu C. A Review of Emerging Tear Proteomics Research on the Ocular Surface in Ocular Allergy. BIOLOGY 2022; 11:biology11020312. [PMID: 35205178 PMCID: PMC8869539 DOI: 10.3390/biology11020312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/07/2022] [Accepted: 02/12/2022] [Indexed: 11/16/2022]
Abstract
Ocular allergy is an immunoglobulin E-mediated Type I hypersensitivity reaction localised to the ocular surface and surrounding tissues. Primary signs and symptoms of ocular allergy include itching, redness, irritation and inflammation. Eye-rubbing caused by itching has been shown to alter ocular surface protein concentrations in conditions linked to ocular allergy such as keratoconus. In keratoconus, the cornea begins to thin and sag over time, leading to progressive vision loss and blindness in severe conditions. Due to the high incidence of ocular allergy sufferers rubbing their eyes in response to symptoms of itching, the protein landscape of the ocular surface may be significantly altered. Differential protein expression caused by long-term inflammation and eye-rubbing may lead to subsequent changes in ocular surface structure and function over time. This review aims to summarise and explore the findings of current ocular allergy proteome research conducted using techniques such as gel electrophoresis, mass spectrometry and lab-on-a-chip proteomics. Proteins of interest for this review include differentially expressed immunoglobulins, mucins, functional proteins, enzymes and proteins with previously uncharacterised roles in ocular allergy. Additionally, potential applications of this research are addressed in terms of diagnostics, drug development and future research prospects.
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Affiliation(s)
- Esrin Aydin
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 3216, Australia;
- Deakin Optometry, Deakin University, Waurn Ponds, VIC 3216, Australia; (M.G.); (L.C.); (S.A.)
| | - Poshmaal Dhar
- School of Medicine, Deakin University, Waurn Ponds, VIC 3216, Australia;
| | - Moneisha Gokhale
- Deakin Optometry, Deakin University, Waurn Ponds, VIC 3216, Australia; (M.G.); (L.C.); (S.A.)
| | - Luke Chong
- Deakin Optometry, Deakin University, Waurn Ponds, VIC 3216, Australia; (M.G.); (L.C.); (S.A.)
| | - Serap Azizoglu
- Deakin Optometry, Deakin University, Waurn Ponds, VIC 3216, Australia; (M.G.); (L.C.); (S.A.)
| | - Cenk Suphioglu
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 3216, Australia;
- Correspondence: ; Tel.: +61-3-522-72886
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11
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Zhao Z, Shen Y, Zhao J, Chen X. microRNA expression profile of fish erythrocytes. AQUACULTURE AND FISHERIES 2021. [DOI: 10.1016/j.aaf.2020.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Prabhu SR, Ware AP, Saadi AV. Erythrocyte miRNA regulators and malarial pathophysiology. INFECTION GENETICS AND EVOLUTION 2021; 93:105000. [PMID: 34252617 DOI: 10.1016/j.meegid.2021.105000] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/18/2021] [Accepted: 07/08/2021] [Indexed: 11/24/2022]
Abstract
Pathophysiology of Plasmodium falciparum and Plasmodium vivax in malaria vis a vis host and the parasite genome interactions has been deciphered recently to present the biology of cerebral malaria, severe anaemia and placental malaria. Small non-coding RNAs have exhibited their potential to be considered as indicators and regulators of diseases. The malarial pathologies and their associated mechanisms mediated by miRNAs and their role in haematopoiesis and red cell-related disorders are elucidated. Evidence of miRNA carrying exosome-like vesicles released during infection, delivering signals to endothelial cells enhancing gene expression, resulting in parasite sequestration and complications leading to pathologies of cerebral malaria are important breakthroughs. Pregnancy malaria showed Plasmodium surface antigen promoted erythrocyte sequestration in the placental intervillous space, provoking disease development and assorted complications. Syncytiotrophoblast-derived microparticles during pregnancy and fetus development may predict pathophysiological progression on account of their altered miRNA cargoes in malaria.
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Affiliation(s)
- Sowmya R Prabhu
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Akshay P Ware
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Abdul Vahab Saadi
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
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13
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Goodswen SJ, Kennedy PJ, Ellis JT. Applying Machine Learning to Predict the Exportome of Bovine and Canine Babesia Species That Cause Babesiosis. Pathogens 2021; 10:660. [PMID: 34071992 PMCID: PMC8226867 DOI: 10.3390/pathogens10060660] [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: 04/07/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 01/08/2023] Open
Abstract
Babesia infection of red blood cells can cause a severe disease called babesiosis in susceptible hosts. Bovine babesiosis causes global economic loss to the beef and dairy cattle industries, and canine babesiosis is considered a clinically significant disease. Potential therapeutic targets against bovine and canine babesiosis include members of the exportome, i.e., those proteins exported from the parasite into the host red blood cell. We developed three machine learning-derived methods (two novel and one adapted) to predict for every known Babesia bovis, Babesia bigemina, and Babesia canis protein the probability of being an exportome member. Two well-studied apicomplexan-related species, Plasmodium falciparum and Toxoplasma gondii, with extensive experimental evidence on their exportome or excreted/secreted proteins were used as important benchmarks for the three methods. Based on 10-fold cross validation and multiple train-validation-test splits of training data, we expect that over 90% of the predicted probabilities accurately provide a secretory or non-secretory indicator. Only laboratory testing can verify that predicted high exportome membership probabilities are creditable exportome indicators. However, the presented methods at least provide those proteins most worthy of laboratory validation and will ultimately save time and money.
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Affiliation(s)
- Stephen J. Goodswen
- School of Life Sciences, University of Technology Sydney, 15 Broadway, Ultimo, NSW 2007, Australia;
| | - Paul J. Kennedy
- School of Computer Science, Faculty of Engineering and Information Technology, Australian Artificial Intelligence Institute, University of Technology Sydney, 15 Broadway, Ultimo, NSW 2007, Australia;
| | - John T. Ellis
- School of Life Sciences, University of Technology Sydney, 15 Broadway, Ultimo, NSW 2007, Australia;
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14
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Khan A, Jahejo AR, Qiao ML, Han XY, Cheng QQ, Mangi RA, Qadir MF, Zhang D, Bi YH, Wang Y, Gao GF, Tian WX. NF-кB pathway genes expression in chicken erythrocytes infected with avian influenza virus subtype H9N2. Br Poult Sci 2021; 62:666-671. [PMID: 33843365 DOI: 10.1080/00071668.2021.1902478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
1. Chicken erythrocytes in blood vessels are the most abundant circulating cells, which participate in the host's immune responses. The transcription factor nuclear factor-kappa B (NF-κB) plays a vital role in the inflammatory response following viral infections. However, the expression of the NF-κB pathway, and other immune-related genes in chicken erythrocytes infected with low pathogenic avian influenza virus (LPAIV H9N2), has not been extensively studied.2. The following study determined the interaction of LPAIV H9N2 with chicken erythrocytes using indirect immunofluorescence microscopy. This was followed by investigating myeloid differentiation primary response 88 (MyD88), C-C motif chemokine ligand 5 (CCL5), melanoma differentiation-associated protein 5 (MDA5), the inhibitor of nuclear factor-kappa B kinase subunit epsilon (IKBKE), NF-κB inhibitor alpha (NFKBIA), NF-κB inhibitor epsilon (NFKBIE), interferon-alpha (IFN-α), colony-stimulating factor 3 (CSF3) and tumour necrosis factor receptor-associated factor 6 (TRAF6) by mRNA expression using quantitative real-time PCR (qRT-PCR) at four different time intervals (0, 2, 6 and 10 h).3. There was a significant interaction between erythrocytes and LPAIV H9N2 virus. Furthermore, the mRNA expression of the NF-κB pathway and other immune-related genes were significantly up-regulated at 2 h post-infection in infected chicken erythrocytes, except for TRAF6, which were significantly downregulated. While at 0 h post-infection, IFN-α and CSF3 were significantly upregulated, whereas NFKBIA was significantly downregulated. Further expression of MDA5, CCL5 and NFKBIA was upregulated, while TRAF6 was downregulated at 6 h post-infection. In infected erythrocytes, expression of MyD88, CCL5 and IKBKE was upregulated. However, IFN-α and TRAF6 were downregulated at 10 h post-infection.4. These results give initial evidence that the NF-κB pathway, and other genes related to immunity, in chicken erythrocytes may contribute to LPAIV subtype H9N2 and induce host immune responses.
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Affiliation(s)
- A Khan
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - A R Jahejo
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - M L Qiao
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - X Y Han
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Q Q Cheng
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - R A Mangi
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - M F Qadir
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - D Zhang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Y H Bi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Collaborative Innovation Center of Infectious Diseases, Institute of Microbiology, Center for Influenza Research and Early-Warning (CASCIRE), Chinese Academy of Science, Beijing, China
| | - Y Wang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - G F Gao
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - W X Tian
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
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15
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Della Pelle G, Kostevšek N. Nucleic Acid Delivery with Red-Blood-Cell-Based Carriers. Int J Mol Sci 2021; 22:5264. [PMID: 34067699 PMCID: PMC8156122 DOI: 10.3390/ijms22105264] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 12/27/2022] Open
Abstract
Gene therapy has the potential to become a staple of 21st-century medicine. However, to overcome the limitations of existing gene-delivery therapies, that is, poor stability and inefficient and delivery and accumulation of nucleic acids (NAs), safe drug-delivery systems (DDSs) allowing the prolonged circulation and expression of the administered genes in vivo are needed. In this review article, the development of DDSs over the past 70 years is briefly described. Since synthetic DDSs can be recognized and eliminated as foreign substances by the immune system, new approaches must be found. Using the body's own cells as DDSs is a unique and exciting strategy and can be used in a completely new way to overcome the critical limitations of existing drug-delivery approaches. Among the different circulatory cells, red blood cells (RBCs) are the most abundant and thus can be isolated in sufficiently large quantities to decrease the complexity and cost of the treatment compared to other cell-based carriers. Therefore, in the second part, this article describes 70 years of research on the development of RBCs as DDSs, covering the most important RBC properties and loading methods. In the third part, it focuses on RBCs as the NA delivery system with advantages and drawbacks discussed to decide whether they are suitable for NA delivery in vivo.
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Affiliation(s)
- Giulia Della Pelle
- Department for Nanostructured Materials, Jožef Stefan Institute, Jamova Cesta 39, 1000 Ljubljana, Slovenia;
- Jožef Stefan International Postgraduate School, Jamova Cesta 39, 1000 Ljubljana, Slovenia
| | - Nina Kostevšek
- Department for Nanostructured Materials, Jožef Stefan Institute, Jamova Cesta 39, 1000 Ljubljana, Slovenia;
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16
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Sun C, Sun Y, Wu P, Ding W, Wang S, Li J, Liang L, Chai C, Fu Y, Li Z, Zhu L, Ju J, Liao X, Huang X, Feng L, Ma D, He L, Chen D, Chen G, Jin X, Wu P. Longitudinal multi-omics transition associated with fatality in critically ill COVID-19 patients. Intensive Care Med Exp 2021; 9:13. [PMID: 33721144 PMCID: PMC7957447 DOI: 10.1186/s40635-021-00373-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 02/03/2021] [Indexed: 12/11/2022] Open
Abstract
Purpose Critically ill COVID-19 patients have significantly increased risk of death. Although several circulating biomarkers are thought to be related to COVID-19 severity, few studies have focused on the characteristics of critically ill patients with different outcomes. The objective of this study was to perform a longitudinal investigation of the potential mechanisms affecting the prognosis of critically ill COVID-19 patients. Methods In addition to clinical data, 113 whole blood samples and 85 serum samples were collected from 33 severe and critical COVID-19 patients without selected comorbidities. Multi-omics analysis was then performed using longitudinal samples. Results Obvious transcriptional transitions were more frequent in critical survivors than in critical non-survivors, indicating that phase transition may be related to survival. Based on analysis of differentially expressed genes during transition, the erythrocyte differentiation pathway was significantly enriched. Furthermore, clinical data indicated that red blood cell counts showed greater fluctuation in survivors than in non-survivors. Moreover, declining red blood cell counts and hemoglobin levels were validated as prognostic markers of poor outcome in an independent cohort of 114 critical COVID-19 patients. Protein–metabolite–lipid network analysis indicated that tryptophan metabolism and melatonin may contribute to molecular transitions in critical COVID-19 patients with different outcomes. Conclusions This study systematically and comprehensively depicted the longitudinal hallmarks of critical COVID-19 patients and indicated that multi-omics transition may impact the prognosis. Take home message Frequent transcriptional phase transitions may contribute to outcome in critically ill COVID-19 patients. Furthermore, fluctuation in red blood cell and hemoglobin levels may relate to poor prognosis. The biological function of melatonin was suppressed in COVID-19 non-survivors, which may provide a potential theoretical basis for clinical administration.
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Affiliation(s)
- Chaoyang Sun
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China.,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuzhe Sun
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Ping Wu
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Wencheng Ding
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China.,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shiyou Wang
- BGI-Shenzhen, Shenzhen, 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Jiafeng Li
- BGI-Shenzhen, Shenzhen, 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Langchao Liang
- BGI-Shenzhen, Shenzhen, 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Chaochao Chai
- BGI-Shenzhen, Shenzhen, 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Yu Fu
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China.,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | | | - Linnan Zhu
- Shenzhen Bay Laboratory, Shenzhen, 518107, China
| | - Jia Ju
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xin Liao
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Xiaoyuan Huang
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China.,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ling Feng
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Ding Ma
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China.,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liang He
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China.
| | | | - Gang Chen
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China. .,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, 518083, China. .,School of Medicine, South China University of Technology, Guangzhou, 510006, Guangdong, China. .,Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Peng Wu
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China. .,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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17
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Ostheim P, Don Mallawaratchy A, Müller T, Schüle S, Hermann C, Popp T, Eder S, Combs SE, Port M, Abend M. Acute radiation syndrome-related gene expression in irradiated peripheral blood cell populations. Int J Radiat Biol 2021; 97:474-484. [PMID: 33476246 DOI: 10.1080/09553002.2021.1876953] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/22/2020] [Accepted: 01/05/2021] [Indexed: 10/22/2022]
Abstract
PURPOSE In a nuclear or radiological event, an early diagnostic tool is needed to distinguish the worried well from those individuals who may later develop life-threatenFing hematologic acute radiation syndrome. We examined the contribution of the peripheral blood's cell populations on radiation-induced gene expression (GE) changes. MATERIALS AND METHODS EDTA-whole-blood from six healthy donors was X-irradiated with 0 and 4Gy and T-lymphocytes, B-lymphocytes, NK-cells and granulocytes were separated using immunomagnetic methods. GE were examined in cell populations and whole blood. RESULTS The cell populations contributed to the total RNA amount with a ratio of 11.6 for T-lymphocytes, 1.2 for B-cells, 1.2 for NK-cells, 1.0 for granulocytes. To estimate the contribution of GE per cell population, the baseline (0Gy) and the radiation-induced fold-change in GE relative to unexposed was considered for each gene. The T-lymphocytes (74.8%/80.5%) contributed predominantly to the radiation-induced up-regulation observed for FDXR/DDB2 and the B-lymphocytes (97.1%/83.8%) for down-regulated POU2AF1/WNT3 with a similar effect on whole blood gene expression measurements reflecting a corresponding order of magnitude. CONCLUSIONS T- and B-lymphocytes contributed predominantly to the radiation-induced up-regulation of FDXR/DDB2 and down-regulation of POU2AF1/WNT3. This study underlines the use of FDXR/DDB2 for biodosimetry purposes and POU2AF1/WNT3 for effect prediction of acute health effects.
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Affiliation(s)
- Patrick Ostheim
- Bundeswehr Institute of Radiobiology affiliated to the University Ulm, Munich, Germany
| | | | - Thomas Müller
- Bundeswehr Institute of Radiobiology affiliated to the University Ulm, Munich, Germany
| | - Simone Schüle
- Bundeswehr Institute of Radiobiology affiliated to the University Ulm, Munich, Germany
| | - Cornelius Hermann
- Bundeswehr Institute of Radiobiology affiliated to the University Ulm, Munich, Germany
| | - Tanja Popp
- Bundeswehr Institute of Radiobiology affiliated to the University Ulm, Munich, Germany
| | - Stefan Eder
- Bundeswehr Institute of Radiobiology affiliated to the University Ulm, Munich, Germany
| | - Stephanie E Combs
- Department of Radiation Oncology, Technical University of Munich (TUM), Munich, Germany
- Institute of Radiation Medicine (IRM), Department of Radiation Sciences (DRS), Helmholtz Zentrum München (HMGU), Oberschleißheim, Germany
- Deutsches Konsortium für Translationale Krebsforschung (DKTK), Munich, Germany
| | - Matthias Port
- Bundeswehr Institute of Radiobiology affiliated to the University Ulm, Munich, Germany
| | - Michael Abend
- Bundeswehr Institute of Radiobiology affiliated to the University Ulm, Munich, Germany
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18
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Variation in Expression of Reference Genes across Life Stages of a Bee, Megachile rotundata. INSECTS 2021; 12:insects12010036. [PMID: 33418888 PMCID: PMC7825039 DOI: 10.3390/insects12010036] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/22/2020] [Accepted: 12/31/2020] [Indexed: 01/19/2023]
Abstract
Simple Summary Reference genes are key to normalizing expression data across samples of organisms collected after different treatments are applied, but often, reference genes are not properly validated for this purpose. In this report, we screened several genes for a solitary bee, Megachile rotundata, and identified two (RPS18, and RPL8) with very stable expression levels across all life stages of the bee, and under a variety of environmental conditions, including during and after diapause. These genes should make good reference genes. We also identified other genes with stable expression, even if used only for a limited number of developmental stages. This information is important for future gene expression studies on these bees, but it also demonstrates the importance of validating reference genes in general. Abstract The alfalfa leafcutting bee, Megachile rotundata is widely used in the western United States as a pollinator for alfalfa seed production. Unfortunately, immatures experience high mortality in agriculturally managed populations. Quantified gene expression could be used to identify how this bee responds during different life stages to pathogens, environmental toxins, and other stresses, but stably expressed reference genes are needed to normalize transcription data. We evaluated twelve candidate genes for their transcription stability across different life stages, including during and after diapause. RPS18 and RPL8 were the two most stably expressed genes, followed by RPS5 and RPL27A. These genes were also very stable even during and after diapause, while the most variable genes being APN, PMIIM, NPC2, and Cr-PII had increased expression levels during larval growth and were also variable during and after diapause. The four reference genes we identified in M. rotundata may prove useful for transcriptomic studies in other bees as well, such as honey bees.
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Ohkawa R, Low H, Mukhamedova N, Fu Y, Lai SJ, Sasaoka M, Hara A, Yamazaki A, Kameda T, Horiuchi Y, Meikle PJ, Pernes G, Lancaster G, Ditiatkovski M, Nestel P, Vaisman B, Sviridov D, Murphy A, Remaley AT, Sviridov D, Tozuka M. Cholesterol transport between red blood cells and lipoproteins contributes to cholesterol metabolism in blood. J Lipid Res 2020; 61:1577-1588. [PMID: 32907987 PMCID: PMC7707172 DOI: 10.1194/jlr.ra120000635] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Lipoproteins play a key role in transport of cholesterol to and from tissues. Recent studies have also demonstrated that red blood cells (RBCs), which carry large quantities of free cholesterol in their membrane, play an important role in reverse cholesterol transport. However, the exact role of RBCs in systemic cholesterol metabolism is poorly understood. RBCs were incubated with autologous plasma or isolated lipoproteins resulting in a significant net amount of cholesterol moved from RBCs to HDL, while cholesterol from LDL moved in the opposite direction. Furthermore, the bi-directional cholesterol transport between RBCs and plasma lipoproteins was saturable and temperature-, energy-, and time-dependent, consistent with an active process. We did not find LDLR, ABCG1, or scavenger receptor class B type 1 in RBCs but found a substantial amount of ABCA1 mRNA and protein. However, specific cholesterol efflux from RBCs to isolated apoA-I was negligible, and ABCA1 silencing with siRNA or inhibition with vanadate and Probucol did not inhibit the efflux to apoA-I, HDL, or plasma. Cholesterol efflux from and cholesterol uptake by RBCs from Abca1+/+ and Abca1-/- mice were similar, arguing against the role of ABCA1 in cholesterol flux between RBCs and lipoproteins. Bioinformatics analysis identified ABCA7, ABCG5, lipoprotein lipase, and mitochondrial translocator protein as possible candidates that may mediate the cholesterol flux. Together, these results suggest that RBCs actively participate in cholesterol transport in the blood, but the role of cholesterol transporters in RBCs remains uncertain.
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Affiliation(s)
- Ryunosuke Ohkawa
- Department of Analytical Laboratory Chemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan; Baker Heart and Diabetes Institute, Melbourne, Australia.
| | - Hann Low
- Baker Heart and Diabetes Institute, Melbourne, Australia
| | | | - Ying Fu
- Baker Heart and Diabetes Institute, Melbourne, Australia
| | - Shao-Jui Lai
- Department of Analytical Laboratory Chemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Mai Sasaoka
- Department of Analytical Laboratory Chemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ayuko Hara
- Department of Analytical Laboratory Chemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Azusa Yamazaki
- Department of Analytical Laboratory Chemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takahiro Kameda
- Department of Analytical Laboratory Chemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yuna Horiuchi
- Department of Analytical Laboratory Chemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Peter J Meikle
- Baker Heart and Diabetes Institute, Melbourne, Australia
| | - Gerard Pernes
- Baker Heart and Diabetes Institute, Melbourne, Australia
| | | | | | - Paul Nestel
- Baker Heart and Diabetes Institute, Melbourne, Australia
| | - Boris Vaisman
- Lipoprotein Section, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Denis Sviridov
- Lipoprotein Section, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andrew Murphy
- Baker Heart and Diabetes Institute, Melbourne, Australia
| | - Alan T Remaley
- Lipoprotein Section, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dmitri Sviridov
- Baker Heart and Diabetes Institute, Melbourne, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia.
| | - Minoru Tozuka
- Department of Analytical Laboratory Chemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan; Life Science Research Center, Nagano Children's Hospital, Azumino, Japan
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20
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Yu WB, Ye ZH, Chen X, Shi JJ, Lu JJ. The development of small-molecule inhibitors targeting CD47. Drug Discov Today 2020; 26:561-568. [PMID: 33197622 DOI: 10.1016/j.drudis.2020.11.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 10/12/2020] [Accepted: 11/05/2020] [Indexed: 12/12/2022]
Abstract
Immunotherapy has become an indispensable part of cancer treatment. A pivotal phagocytosis checkpoint, named cluster of differentiation 47 (CD47), which functions as 'don't eat me' signal to protect cells from phagocytosis upon interaction with signal regulatory protein alpha (SIRPα) on macrophages, has recently attracted much attention. Numerous antibodies targeting the CD47/SIRPα axis have shown encouraging efficacy in clinical trials. Meanwhile, studies on small-molecule inhibitors that interfere with CD47/SIRPα interaction or regulate CD47 expression are also in full swing. In this review, we summarize the small-molecule inhibitors interrupting the binding of CD47/SIRPα and regulating CD47 at the transcriptional, translational, and post-translational modification (PTM) levels. We provide perspectives and strategies for targeting the CD47/SIRPα phagocytosis checkpoint.
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Affiliation(s)
- Wei-Bang Yu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Zi-Han Ye
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Xiuping Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Jia-Jie Shi
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China.
| | - Jin-Jian Lu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China.
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21
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Oosterom N, Fiocco M, Kloos RQH, van der Sluis IM, Pieters R, van Zelst BD, Smith DEC, van den Heuvel-Eibrink MM, de Jonge R, Heil SG. The evaluation of red blood cell folate and methotrexate levels during protocol M in childhood acute lymphoblastic leukemia. BMC Cancer 2020; 20:940. [PMID: 32998716 PMCID: PMC7526241 DOI: 10.1186/s12885-020-07422-y] [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] [Received: 06/25/2020] [Accepted: 09/16/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND After High-Dose Methotrexate (HD-MTX), folinic acid rescue therapy (Leucovorin) is administered to reduce side effects in pediatric acute lymphoblastic leukemia (ALL) patients. Leucovorin and MTX are structural analogues, possibly competing for cellular transport and intracellular metabolism. We hypothesize that Leucovorin accumulates during consecutive courses, which might result in a lower MTX uptake. METHODS We prospectively measured red blood cell (RBC) folate and MTX levels during four HD-MTX and Leucovorin courses in 43 patients treated according the DCOG ALL-11 protocol with 2-weekly HD-MTX (5 g/m2/dose) and Leucovorin (15 mg/m2/dose) using LC-MS/MS. We estimated a linear mixed model to assess the relationship between these variables over time. RESULTS Both RBC MTX-PG and folate levels increased significantly during protocol M. MTX-PG2-5 levels increased most substantially after the first two HD-MTX courses (until median 113.0 nmol/L, IQR 76.8-165.2) after which levels plateaued during the 3d and 4th course (until median 141.3 nmol/L, IQR 100.2-190.2). In parallel, folate levels increased most substantially after the first two HD-MTX courses (until median 401.6 nmol/L, IQR 163.3-594.2) after which levels plateaued during the 3d and 4th course (until median 411.5 nmol/L, IQR 240.3-665.6). The ratio folate/MTX-PG decreased significantly over time, which was mostly due to the relatively higher increase (delta) of MTX-PG. CONCLUSION These results suggest that the increase in RBC folate levels does not seem to have a large effect on RBC MTX levels. Future studies, assessing competition of Leucovorin and MTX on other cellular mechanisms which might negatively affect treatment efficacy, are necessary.
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Affiliation(s)
- N Oosterom
- Princess Máxima Center for Pediatric Oncology, Postbus 113, 3720 AC Bilthoven, Utrecht, The Netherlands. .,Department of Clinical Chemistry, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
| | - M Fiocco
- Princess Máxima Center for Pediatric Oncology, Postbus 113, 3720 AC Bilthoven, Utrecht, The Netherlands.,Mathematical Institute, Leiden University, Leiden, The Netherlands.,Department of Biomedical Data Sciences, Leiden University Medical Center, Medical Statistics, Leiden, The Netherlands
| | - R Q H Kloos
- Department of Pediatric Oncology/Hematology, Erasmus Medical Center-Sophia's Children's Hospital, Rotterdam, The Netherlands
| | - I M van der Sluis
- Princess Máxima Center for Pediatric Oncology, Postbus 113, 3720 AC Bilthoven, Utrecht, The Netherlands
| | - R Pieters
- Princess Máxima Center for Pediatric Oncology, Postbus 113, 3720 AC Bilthoven, Utrecht, The Netherlands
| | - B D van Zelst
- Department of Clinical Chemistry, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - D E C Smith
- Department of Clinical Chemistry, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | - R de Jonge
- Department of Clinical Chemistry, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - S G Heil
- Department of Clinical Chemistry, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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22
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Masselli E, Pozzi G, Gobbi G, Merighi S, Gessi S, Vitale M, Carubbi C. Cytokine Profiling in Myeloproliferative Neoplasms: Overview on Phenotype Correlation, Outcome Prediction, and Role of Genetic Variants. Cells 2020. [PMID: 32967342 DOI: 10.3390/cells9092136.pmid:32967342;pmcid:pmc7564952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023] Open
Abstract
Among hematologic malignancies, the classic Philadelphia-negative chronic myeloproliferative neoplasms (MPNs) are considered a model of inflammation-related cancer development. In this context, the use of immune-modulating agents has recently expanded the MPN therapeutic scenario. Cytokines are key mediators of an auto-amplifying, detrimental cross-talk between the MPN clone and the tumor microenvironment represented by immune, stromal, and endothelial cells. This review focuses on recent advances in cytokine-profiling of MPN patients, analyzing different expression patterns among the three main Philadelphia-negative (Ph-negative) MPNs, as well as correlations with disease molecular profile, phenotype, progression, and outcome. The role of the megakaryocytic clone as the main source of cytokines, particularly in myelofibrosis, is also reviewed. Finally, we report emerging intriguing evidence on the contribution of host genetic variants to the chronic pro-inflammatory state that typifies MPNs.
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Affiliation(s)
- Elena Masselli
- Department of Medicine and Surgery, Anatomy Unit, University of Parma, Via Gramsci 14, 43126 Parma, Italy
- University Hospital of Parma, AOU-PR, Via Gramsci 14, 43126 Parma, Italy
| | - Giulia Pozzi
- Department of Medicine and Surgery, Anatomy Unit, University of Parma, Via Gramsci 14, 43126 Parma, Italy
| | - Giuliana Gobbi
- Department of Medicine and Surgery, Anatomy Unit, University of Parma, Via Gramsci 14, 43126 Parma, Italy
| | - Stefania Merighi
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Stefania Gessi
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Marco Vitale
- Department of Medicine and Surgery, Anatomy Unit, University of Parma, Via Gramsci 14, 43126 Parma, Italy
- University Hospital of Parma, AOU-PR, Via Gramsci 14, 43126 Parma, Italy
| | - Cecilia Carubbi
- Department of Medicine and Surgery, Anatomy Unit, University of Parma, Via Gramsci 14, 43126 Parma, Italy
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23
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Masselli E, Pozzi G, Gobbi G, Merighi S, Gessi S, Vitale M, Carubbi C. Cytokine Profiling in Myeloproliferative Neoplasms: Overview on Phenotype Correlation, Outcome Prediction, and Role of Genetic Variants. Cells 2020; 9:cells9092136. [PMID: 32967342 PMCID: PMC7564952 DOI: 10.3390/cells9092136] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/18/2020] [Accepted: 09/19/2020] [Indexed: 12/16/2022] Open
Abstract
Among hematologic malignancies, the classic Philadelphia-negative chronic myeloproliferative neoplasms (MPNs) are considered a model of inflammation-related cancer development. In this context, the use of immune-modulating agents has recently expanded the MPN therapeutic scenario. Cytokines are key mediators of an auto-amplifying, detrimental cross-talk between the MPN clone and the tumor microenvironment represented by immune, stromal, and endothelial cells. This review focuses on recent advances in cytokine-profiling of MPN patients, analyzing different expression patterns among the three main Philadelphia-negative (Ph-negative) MPNs, as well as correlations with disease molecular profile, phenotype, progression, and outcome. The role of the megakaryocytic clone as the main source of cytokines, particularly in myelofibrosis, is also reviewed. Finally, we report emerging intriguing evidence on the contribution of host genetic variants to the chronic pro-inflammatory state that typifies MPNs.
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Affiliation(s)
- Elena Masselli
- Department of Medicine and Surgery, Anatomy Unit, University of Parma, Via Gramsci 14, 43126 Parma, Italy; (G.P.); (G.G.); (C.C.)
- University Hospital of Parma, AOU-PR, Via Gramsci 14, 43126 Parma, Italy
- Correspondence: (E.M.); (M.V.); Tel.: +39-052-190-6655 (E.M.); +39-052-103-3032 (M.V.)
| | - Giulia Pozzi
- Department of Medicine and Surgery, Anatomy Unit, University of Parma, Via Gramsci 14, 43126 Parma, Italy; (G.P.); (G.G.); (C.C.)
| | - Giuliana Gobbi
- Department of Medicine and Surgery, Anatomy Unit, University of Parma, Via Gramsci 14, 43126 Parma, Italy; (G.P.); (G.G.); (C.C.)
| | - Stefania Merighi
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, 44121 Ferrara, Italy; (S.M.); (S.G.)
| | - Stefania Gessi
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, 44121 Ferrara, Italy; (S.M.); (S.G.)
| | - Marco Vitale
- Department of Medicine and Surgery, Anatomy Unit, University of Parma, Via Gramsci 14, 43126 Parma, Italy; (G.P.); (G.G.); (C.C.)
- University Hospital of Parma, AOU-PR, Via Gramsci 14, 43126 Parma, Italy
- Correspondence: (E.M.); (M.V.); Tel.: +39-052-190-6655 (E.M.); +39-052-103-3032 (M.V.)
| | - Cecilia Carubbi
- Department of Medicine and Surgery, Anatomy Unit, University of Parma, Via Gramsci 14, 43126 Parma, Italy; (G.P.); (G.G.); (C.C.)
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24
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Cheng L, Yu H, Wrobel JA, Li G, Liu P, Hu Z, Xu XN, Su L. Identification of pathogenic TRAIL-expressing innate immune cells during HIV-1 infection in humanized mice by scRNA-Seq. JCI Insight 2020; 5:135344. [PMID: 32406872 DOI: 10.1172/jci.insight.135344] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 04/24/2020] [Indexed: 12/11/2022] Open
Abstract
Depletion of CD4+ T cells during HIV-1 infection is mostly mediated by inflammatory cells via indirect but not clearly defined mechanisms. In this report, we used single-cell RNA-Seq (scRNA-Seq) technology to study HIV-induced transcriptomic change in innate immune cells in lymphoid organs. We performed scRNA-Seq on hCD45+hCD3-hCD19- human leukocytes isolated from spleens of humanized NOD/Rag2-/-γc-/- (NRG) mice transplanted with human CD34+ hematopoietic stem progenitor cells (NRG-hu HSC mice). We identified major populations of innate immune cells, including plasmacytoid dendritic cells (pDCs), myeloid dendritic cells (mDCs), macrophages, NK cells, and innate lymphoid cells (ILCs). HIV-1 infection significantly upregulated genes involved in type I IFN inflammatory pathways in each of the innate immune subsets. Interestingly, we found that TRAIL was upregulated in the innate immune populations, including pDCs, mDCs, macrophages, NK cells, and ILCs. We further demonstrated that blockade of the TRAIL signaling pathway in NRG-hu HSC mice prevented HIV-1-induced CD4+ T cell depletion in vivo. In summary, we characterized HIV-induced transcriptomic changes of innate immune cells in the spleen at single-cell levels, identified the TRAIL+ innate immune cells, and defined an important role of the TRAIL signaling pathway in HIV-1-induced CD4+ T cell depletion in vivo.
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Affiliation(s)
- Liang Cheng
- Lineberger Comprehensive Cancer Center and.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Haisheng Yu
- Lineberger Comprehensive Cancer Center and.,Key Laboratory of Human Disease Comparative Medicine of Ministry of Health, Beijing Key Laboratory for Animal Models of Emerging and Re-emerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | | | | | - Peng Liu
- Lineberger Comprehensive Cancer Center and
| | - Zhiyuan Hu
- Lineberger Comprehensive Cancer Center and
| | - Xiao-Ning Xu
- Department of Medicine, Chelsea and Westminster Hospital, Imperial College London, London, United Kingdom
| | - Lishan Su
- Lineberger Comprehensive Cancer Center and.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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25
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Ding H, Yu J, Chang W, Liu F, He Z. Searching for differentially expressed proteins in spinal cord injury based on the proteomics analysis. Life Sci 2020; 242:117235. [DOI: 10.1016/j.lfs.2019.117235] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 12/21/2019] [Accepted: 12/25/2019] [Indexed: 02/07/2023]
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26
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Oosterom N, de Jonge R, Smith DEC, Pieters R, Tissing WJE, Fiocco M, van Zelst BD, van den Heuvel-Eibrink MM, Heil SG. Changes in intracellular folate metabolism during high-dose methotrexate and Leucovorin rescue therapy in children with acute lymphoblastic leukemia. PLoS One 2019; 14:e0221591. [PMID: 31527879 PMCID: PMC6748431 DOI: 10.1371/journal.pone.0221591] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/09/2019] [Indexed: 01/19/2023] Open
Abstract
Background Methotrexate (MTX) is an important anti-folate agent in pediatric acute lymphoblastic leukemia (ALL) treatment. Folinic acid rescue therapy (Leucovorin) is administered after MTX to reduce toxicity. Previous studies hypothesized that Leucovorin could ‘rescue’ both normal healthy cells and leukemic blasts from cell death. We assessed whether Leucovorin is able to restore red blood cell folate levels after MTX. Methods We prospectively determined erythrocyte folate levels (5-methyltetrahydrofolate (THF) and non-methyl THF) and serum folate levels in 67 children with ALL before start (T0) and after stop (T1) of HD-MTX and Leucovorin courses. Results Erythrocyte folate levels increased between T0 and T1 (mean ± SD: 416.7 ± 145.5 nmol/L and 641.2 ± 196.3 nmol/L respectively, p<0.001). This was due to an increase in 5-methyl THF levels (mean increase: 217.7 ± 209.5 nmol/L, p<0.001), whereas non-methyl THF levels did not change (median increase: 0.6 nmol/L [-9.9–11.1], p = 0.676). Serum folate levels increased between T0 and T1 (median increase: 29.2 nmol/L [32.9–74.0], p<0.001). Results were not significantly affected by age, sex, ALL immunophenotype and MTHFR c.677C>T genotype. Conclusion Intracellular folate levels accumulate after HD-MTX and Leucovorin therapy in children with ALL, suggesting that Leucovorin restores the intracellular folate pool. Future studies are necessary to assess concomitant lower uptake of MTX.
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Affiliation(s)
- Natanja Oosterom
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Erasmus MC, University Medical Center Rotterdam, Department of Clinical Chemistry, Rotterdam, The Netherlands
| | - Robert de Jonge
- VU Medical Center, Department of Clinical Chemistry, Amsterdam, The Netherlands.,Academic Medical Center, Department of Clinical Chemistry, Amsterdam, The Netherlands
| | - Desiree E C Smith
- VU Medical Center, Department of Clinical Chemistry, Amsterdam, The Netherlands
| | - Rob Pieters
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Wim J E Tissing
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Department of Pediatric Oncology, University of Groningen, Beatrix Children's Hospital, University Medical Center Groningen, Groningen, The Netherlands
| | - Marta Fiocco
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Mathematical Institute, Leiden University, Leiden, The Netherlands.,Leiden University Medical Center, Department of Biomedical Data Sciences, Leiden, The Netherlands
| | - Bertrand D van Zelst
- Erasmus MC, University Medical Center Rotterdam, Department of Clinical Chemistry, Rotterdam, The Netherlands
| | | | - Sandra G Heil
- Erasmus MC, University Medical Center Rotterdam, Department of Clinical Chemistry, Rotterdam, The Netherlands
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27
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Thiemeyer H, Taher L, Schille JT, Harder L, Hungerbuehler SO, Mischke R, Hewicker-Trautwein M, Kiełbowicz Z, Brenig B, Schütz E, Beck J, Murua Escobar H, Nolte I. Suitability of ultrasound-guided fine-needle aspiration biopsy for transcriptome sequencing of the canine prostate. Sci Rep 2019; 9:13216. [PMID: 31519932 PMCID: PMC6744464 DOI: 10.1038/s41598-019-49271-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 08/15/2019] [Indexed: 02/06/2023] Open
Abstract
Ultrasound-guided fine-needle aspiration (US-FNA) biopsy is a widely used minimally invasive sampling procedure for cytological diagnosis. This study investigates the feasibility of using US-FNA samples for both cytological diagnosis and whole transcriptome RNA-sequencing analysis (RNA-Seq), with the ultimate aim of improving canine prostate cancer management. The feasibility of the US-FNA procedure was evaluated intra vitam on 43 dogs. Additionally, aspirates from 31 euthanised dogs were collected for standardising the procedure. Each aspirate was separated into two subsamples: for cytology and RNA extraction. Additional prostate tissue samples served as control for RNA quantity and quality evaluation, and differential expression analysis. The US-FNA sampling procedure was feasible in 95% of dogs. RNA isolation of US-FNA samples was successfully performed using phenol-chloroform extraction. The extracted RNA of 56% of a subset of US-FNA samples met the quality requirements for RNA-Seq. Expression analysis revealed that only 153 genes were exclusively differentially expressed between non-malignant US-FNAs and tissues. Moreover, only 36 differentially expressed genes were associated with the US-FNA sampling technique and unrelated to the diagnosis. Furthermore, the gene expression profiles clearly distinguished between non-malignant and malignant samples. This proves US-FNA to be useful for molecular profiling.
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Affiliation(s)
- H Thiemeyer
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- Department of Haematology/Oncology/Palliative Care, Rostock University Medical Centre, Rostock, Germany
| | - L Taher
- Division of Bioinformatics, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - J T Schille
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- Department of Haematology/Oncology/Palliative Care, Rostock University Medical Centre, Rostock, Germany
| | - L Harder
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - S O Hungerbuehler
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - R Mischke
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - M Hewicker-Trautwein
- Institute of Pathology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Z Kiełbowicz
- Department and Clinic of Veterinary Surgery, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - B Brenig
- University of Göttingen, Institute of Veterinary Medicine, Göttingen, Germany
| | - E Schütz
- Chronix Biomedical, Göttingen, Germany
| | - J Beck
- Chronix Biomedical, Göttingen, Germany
| | - H Murua Escobar
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- Department of Haematology/Oncology/Palliative Care, Rostock University Medical Centre, Rostock, Germany
| | - I Nolte
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany.
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28
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Paquette AG, Brockway HM, Price ND, Muglia LJ. Comparative transcriptomic analysis of human placentae at term and preterm delivery. Biol Reprod 2019; 98:89-101. [PMID: 29228154 PMCID: PMC5803773 DOI: 10.1093/biolre/iox163] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 11/30/2017] [Indexed: 12/11/2022] Open
Abstract
Preterm birth affects 1 out of every 10 infants in the United States, resulting in substantial neonatal morbidity and mortality. Currently, there are few predictive markers and few treatment options to prevent preterm birth. A healthy, functioning placenta is essential to positive pregnancy outcomes. Previous studies have suggested that placental pathology may play a role in preterm birth etiology. Therefore, we tested the hypothesis that preterm placentae may exhibit unique transcriptomic signatures compared to term samples reflective of their abnormal biology leading to this adverse outcome. We aggregated publicly available placental villous microarray data to generate a preterm and term sample dataset (n = 133, 55 preterm placentae and 78 normal term placentae). We identified differentially expressed genes using the linear regression for microarray (LIMMA) package and identified perturbations in known biological networks using Differential Rank Conservation (DIRAC). We identified 129 significantly differentially expressed genes between term and preterm placenta with 96 genes upregulated and 33 genes downregulated (P-value <0.05). Significant changes in gene expression in molecular networks related to Tumor Protein 53 and phosphatidylinositol signaling were identified using DIRAC. We have aggregated a uniformly normalized transcriptomic dataset and have identified novel and established genes and pathways associated with developmental regulation of the placenta and potential preterm birth pathology. These analyses provide a community resource to integrate with other high-dimensional datasets for additional insights in normal placental development and its disruption.
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Affiliation(s)
| | - Heather M Brockway
- Division of Human Genetics, Center for Prevention of Preterm Birth, Cincinnati Children's, Hospital Medical Center, Cincinnati, Ohio, USA
| | | | - Louis J Muglia
- Division of Human Genetics, Center for Prevention of Preterm Birth, Cincinnati Children's, Hospital Medical Center, Cincinnati, Ohio, USA
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29
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Niu S, Jahejo AR, Jia FJ, Li X, Ning GB, Zhang D, Ma HL, Hao WF, Gao WW, Zhao YJ, Gao SM, Li GL, Li JH, Yan F, Gao RK, Bi YH, Han LX, Gao GF, Tian WX. Transcripts of antibacterial peptides in chicken erythrocytes infected with Marek's disease virus. BMC Vet Res 2018; 14:363. [PMID: 30463541 PMCID: PMC6249751 DOI: 10.1186/s12917-018-1678-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 10/30/2018] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Chicken erythrocytes are involved in immunity through binding of toll-like receptors (TLRs) with their ligands to activate downstream signaling and lead to cytokine production in erythrocytes. Some avian β-defensins (AvBDs) are constitutively expressed in tissues and some others can be induced by various bacteria and viruses. However, the expression of AvBDs in erythrocytes has not yet been studied extensively. RESULTS The transcripts of eight AvBDs (AvBD1 to AvBD7, and AvBD9) and liver-expressed antimicrobial peptide-2 (LEAP-2) were found in normal chicken erythrocytes. The expression levels of AvBD2, 4 and 7 were significantly increased (P < 0.01), whereas the levels of AvBD1, 6 and 9 were significantly decreased (P < 0.01) after Marek's disease virus (MDV) infection. The mRNA expression level of LEAP-2 was not significantly changed after MDV infection. Highest viral nucleic acid (VNA) of MDV in the feather tips among the tested time points was found at 14 days post-infection (d.p.i.). In addition, 35 MD5-related gene segments were detected in the erythrocytes at 14 d.p.i. by transcriptome sequencing. CONCLUSIONS These results suggest that the AvBDs in chicken erythrocytes may participate in MDV-induced host immune responses.
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Affiliation(s)
- Sheng Niu
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China
| | - Ali Raza Jahejo
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China
| | - Fa-Jie Jia
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China
| | - Xin Li
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China
| | - Guan-Bao Ning
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China
| | - Ding Zhang
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China
| | - Hai-Li Ma
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China
| | - Wei-Fang Hao
- Taiyuan Center for Disease Control and Prevention, Taiyuan, 030024, China
| | - Wen-Wei Gao
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China
| | - Yu-Jun Zhao
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China
| | - Shi-Min Gao
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China
| | - Gui-Lan Li
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China
| | - Jian-Hui Li
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China
| | - Fang Yan
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China
| | - Rong-Kun Gao
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China
| | - Yu-Hai Bi
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing, 100101, China
| | - Ling-Xia Han
- Department of Laboratory Animal and Comparative Medicine, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China.
| | - George F Gao
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China. .,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing, 100101, China.
| | - Wen-Xia Tian
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China.
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30
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Hopp L, Loeffler-Wirth H, Nersisyan L, Arakelyan A, Binder H. Footprints of Sepsis Framed Within Community Acquired Pneumonia in the Blood Transcriptome. Front Immunol 2018; 9:1620. [PMID: 30065722 PMCID: PMC6056630 DOI: 10.3389/fimmu.2018.01620] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 06/29/2018] [Indexed: 12/14/2022] Open
Abstract
We analyzed the blood transcriptome of sepsis framed within community-acquired pneumonia (CAP) and characterized its molecular and cellular heterogeneity in terms of functional modules of co-regulated genes with impact for the underlying pathophysiological mechanisms. Our results showed that CAP severity is associated with immune suppression owing to T-cell exhaustion and HLA and chemokine receptor deactivation, endotoxin tolerance, macrophage polarization, and metabolic conversion from oxidative phosphorylation to glycolysis. We also found footprints of host's response to viruses and bacteria, altered levels of mRNA from erythrocytes and platelets indicating coagulopathy that parallel severity of sepsis and survival. Finally, our data demonstrated chromatin re-modeling associated with extensive transcriptional deregulation of chromatin modifying enzymes, which suggests the extensive changes of DNA methylation with potential impact for marker selection and functional characterization. Based on the molecular footprints identified, we propose a novel stratification of CAP cases into six groups differing in the transcriptomic scores of CAP severity, interferon response, and erythrocyte mRNA expression with impact for prognosis. Our analysis increases the resolution of transcriptomic footprints of CAP and reveals opportunities for selecting sets of transcriptomic markers with impact for translation of omics research in terms of patient stratification schemes and sets of signature genes.
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Affiliation(s)
- Lydia Hopp
- Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Leipzig, Germany
| | - Henry Loeffler-Wirth
- Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Leipzig, Germany
| | - Lilit Nersisyan
- Group of Bioinformatics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
| | - Arsen Arakelyan
- Group of Bioinformatics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
| | - Hans Binder
- Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Leipzig, Germany
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Haberberger A, Kirchner B, Riedmaier I, Henschler R, Wichmann C, Buhmann R, Pfaffl MW. Changes in the microRNA expression profile during blood storage. BMJ Open Sport Exerc Med 2018; 4:e000354. [PMID: 30018790 PMCID: PMC6045755 DOI: 10.1136/bmjsem-2018-000354] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2018] [Indexed: 11/04/2022] Open
Abstract
Objectives For several decades, autologous blood doping (ABD) in sports has been a major problem, and even today there is still no reliable method for satisfactorily detecting ABD. For this kind of doping, stored individual erythrocytes are used to increase stamina and endurance caused by a higher erythrocyte level in the athlete's body. Since there is growing evidence that these cells are enriched with microRNAs (miRNAs), this study has been carried out to discover and validate all miRNAs occurring in fresh blood as well as in stored blood. Methods Therefore, small RNA Next Generation Sequencing has been performed, which allows untargeted detection of all miRNAs in a blood sample. The focus of this investigation has been to find miRNA alterations in blood bags after erythrocyte processing and during storage, as compared with fresh blood directly withdrawn from subjects. Blood samples were obtained from 12 healthy, recreationally active male subjects three times before blood donation and from blood bags at several time points after blood processing. Results 189 miRNAs have been considered stable over two consecutive weeks. A further analysis revealed a complex biomarker signature of 28 miRNAs, consisting of 6 miRNAs that altered during 6 weeks of storage and 22 miRNAs that altered due to processing. Conclusion These results suggest that the identified miRNA biomarker signature may be used for the detection of ABD. These 28 miRNA candidates are tested and verified currently in a follow-up study, a human transfusion clinical trial in healthy sportsmen.
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Affiliation(s)
- Anna Haberberger
- Institute of Animal Physiology and Immunology, Technical University of Munich, Freising, Germany
| | - Benedikt Kirchner
- Institute of Animal Physiology and Immunology, Technical University of Munich, Freising, Germany
| | - Irmgard Riedmaier
- Institute of Animal Physiology and Immunology, Technical University of Munich, Freising, Germany.,Eurofins Medigenomix Forensik GmbH, Ebersberg, Germany
| | - Reinhard Henschler
- Department of Transfusion Medicine, Cell Therapeutics and Hemostaseology, Ludwig-Maximilians-University Hospital, Munich, Germany.,Blutspende Zürich, Medizinischer Dienst, Zurich, Switzerland
| | - Christian Wichmann
- Department of Transfusion Medicine, Cell Therapeutics and Hemostaseology, Ludwig-Maximilians-University Hospital, Munich, Germany
| | - Raymund Buhmann
- Department of Transfusion Medicine, Cell Therapeutics and Hemostaseology, Ludwig-Maximilians-University Hospital, Munich, Germany
| | - Michael W Pfaffl
- Institute of Animal Physiology and Immunology, Technical University of Munich, Freising, Germany
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Vanni S, Zattoni M, Moda F, Giaccone G, Tagliavini F, Haïk S, Deslys JP, Zanusso G, Ironside JW, Carmona M, Ferrer I, Kovacs GG, Legname G. Hemoglobin mRNA Changes in the Frontal Cortex of Patients with Neurodegenerative Diseases. Front Neurosci 2018; 12:8. [PMID: 29403351 PMCID: PMC5786544 DOI: 10.3389/fnins.2018.00008] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 01/05/2018] [Indexed: 01/06/2023] Open
Abstract
Background: Hemoglobin is the major protein found in erythrocytes, where it acts as an oxygen carrier molecule. In recent years, its expression has been reported also in neurons and glial cells, although its role in brain tissue remains still unknown. Altered hemoglobin expression has been associated with various neurodegenerative disorders. Here, we investigated hemoglobin mRNA levels in brains of patients affected by variant, iatrogenic, and sporadic forms of Creutzfeldt-Jakob disease (vCJD, iCJD, sCJD, respectively) and in different genetic forms of prion diseases (gPrD) in comparison to Alzheimer's disease (AD) subjects and age-matched controls. Methods: Total RNA was obtained from the frontal cortex of vCJD (n = 20), iCJD (n = 11), sCJD (n = 23), gPrD (n = 30), and AD (n = 14) patients and age-matched controls (n = 30). RT-qPCR was performed for hemoglobin transcripts HBB and HBA1/2 using four reference genes for normalization. In addition, expression analysis of the specific erythrocyte marker ALAS2 was performed in order to account for blood contamination of the tissue samples. Hba1/2 and Hbb protein expression was then investigated with immunofluorescence and confocal microscope analysis. Results: We observed a significant up-regulation of HBA1/2 in vCJD brains together with a significant down-regulation of HBB in iCJD. In addition, while in sporadic and genetic forms of prion disease hemoglobin transcripts did not shown any alterations, both chains display a strong down-regulation in AD brains. These results were confirmed also at a protein level. Conclusions: These data indicate distinct hemoglobin transcriptional responses depending on the specific alterations occurring in different neurodegenerative diseases. In particular, the initial site of misfolding event (central nervous system vs. peripheral tissue)-together with specific molecular and conformational features of the pathological agent of the disease-seem to dictate the peculiar hemoglobin dysregulation found in prion and non-prion neurodegenerative disorders. In addition, these results suggest that gene expression of HBB and HBA1/2 in brain tissue is differentially affected by distinct prion and prion-like aggregating protein strains. Validation of these results in more accessible tissues could prompt the development of novel diagnostic tests for neurodegenerative disorders.
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Affiliation(s)
- Silvia Vanni
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy
| | - Marco Zattoni
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy
| | - Fabio Moda
- Neurology and Neuropathology Unit, Istituto di Ricovero e Cura a Carattere Scientifico Foundation Carlo Besta Neurological Institute, Milan, Italy
| | - Giorgio Giaccone
- Neurology and Neuropathology Unit, Istituto di Ricovero e Cura a Carattere Scientifico Foundation Carlo Besta Neurological Institute, Milan, Italy
| | - Fabrizio Tagliavini
- Neurology and Neuropathology Unit, Istituto di Ricovero e Cura a Carattere Scientifico Foundation Carlo Besta Neurological Institute, Milan, Italy
| | - Stéphane Haïk
- UPMC Univ Paris 06 UMR S 1127 and Centre National de la Recherche Scientifique UMR 7225, ICM, Sorbonne Universités, Paris, France
| | | | - Gianluigi Zanusso
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - James W Ironside
- National CJD Research and Surveillance Unit, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Margarita Carmona
- Department of Pathology and Experimental Therapeutics, University of Barcelona, Barcelona, Spain
| | - Isidre Ferrer
- Institut d'Investigació Biomédica de Bellvitge (IDIBELL), Bellvitge University Hospital (CIBERNED), Hospitalet de LLobregat, Spain
| | - Gabor G Kovacs
- Institute of Neurology, Medical University of Vienna, Vienna, Austria
| | - Giuseppe Legname
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy
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34
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Karsten E, Hill CJ, Herbert BR. Red blood cells: The primary reservoir of macrophage migration inhibitory factor in whole blood. Cytokine 2017; 102:34-40. [PMID: 29275011 DOI: 10.1016/j.cyto.2017.12.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 12/05/2017] [Accepted: 12/05/2017] [Indexed: 12/11/2022]
Abstract
Red blood cells are widely accepted to be inert carriers of oxygen and haemoglobin, but there is growing evidence that they play a much more critical role in immune function. Macrophage migration inhibitory factor (MIF) is a key cytokine in disease with additional oxido-reductase activity, which aids in managing oxidative stress. Although two studies have reported the presence of MIF in red blood cells, no study has quantified the levels of this protein. In this study, freshly isolated plasma, platelets, leukocytes, and red blood cells from healthy individuals were collected and the concentration of MIF was determined using an enzyme linked immunosorbent assay. This analysis demonstrated that MIF in red blood cells was present at 25 µg per millilitre of whole blood, which is greater than99% of the total MIF and 1000-fold higher concentration than plasma. This result was supported by electrophoresis and Western blot analysis, which identified MIF in its monomer structural form following sample processing. Furthermore, by assessing the level of tautomerase activity in red blood cell fractions in the presence of a MIF inhibitor, it was determined that the red blood cell-derived MIF was also functionally active. Together, these findings have implications on the effect of haemolysis during sample preparation and provide some clue into the inflammatory processes that occur following haemolysis in vivo. These results support the hypothesis that red blood cells are a major reservoir of this inflammatory protein and may play a role in inflammation.
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Affiliation(s)
- Elisabeth Karsten
- Translational Regenerative Medicine Laboratory, Kolling Institute, Northern Sydney Local Health District, St Leonards, NSW 2065, Australia; Sydney Medical School, Northern Clinical School, The University of Sydney, Royal North Shore Hospital, St Leonards, NSW 2065, Australia; Sangui Bio Pty Ltd, St Leonards, NSW 2065, Australia.
| | - Cameron J Hill
- Translational Regenerative Medicine Laboratory, Kolling Institute, Northern Sydney Local Health District, St Leonards, NSW 2065, Australia; Sangui Bio Pty Ltd, St Leonards, NSW 2065, Australia.
| | - Benjamin R Herbert
- Translational Regenerative Medicine Laboratory, Kolling Institute, Northern Sydney Local Health District, St Leonards, NSW 2065, Australia; Sydney Medical School, Northern Clinical School, The University of Sydney, Royal North Shore Hospital, St Leonards, NSW 2065, Australia; Sangui Bio Pty Ltd, St Leonards, NSW 2065, Australia.
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35
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Martin JS, Kephart WC, Haun CT, McCloskey AE, Shake JJ, Mobley CB, Goodlett MD, Kavazis A, Pascoe DD, Zhang L, Roberts MD. Impact of external pneumatic compression target inflation pressure on transcriptome-wide RNA expression in skeletal muscle. Physiol Rep 2017; 4:4/22/e13029. [PMID: 27884954 PMCID: PMC5357997 DOI: 10.14814/phy2.13029] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 10/03/2016] [Accepted: 10/12/2016] [Indexed: 11/24/2022] Open
Abstract
Next‐generation RNA sequencing was employed to determine the acute and subchronic impact of peristaltic pulse external pneumatic compression (PEPC) of different target inflation pressures on global gene expression in human vastus lateralis skeletal muscle biopsy samples. Eighteen (N = 18) male participants were randomly assigned to one of the three groups: (1) sham (n = 6), 2) EPC at 30–40 mmHg (LP‐EPC; n = 6), and 3) EPC at 70–80 mmHg (MP‐EPC; n = 6). One hour treatment with sham/EPC occurred for seven consecutive days. Vastus lateralis skeletal muscle biopsies were performed at baseline (before first treatment; PRE), 1 h following the first treatment (POST1), and 24 h following the last (7th) treatment (POST2). Changes from PRE in gene expression were analyzed via paired comparisons within each group. Genes were filtered to include only those that had an RPKM ≥ 1.0, a fold‐change of ≥1.5 and a paired t‐test value of <0.01. For the sham condition, two genes at POST1 and one gene at POST2 were significantly altered. For the LP‐EPC condition, nine genes were up‐regulated and 0 genes were down‐regulated at POST1 while 39 genes were up‐regulated and one gene down‐regulated at POST2. For the MP‐EPC condition, two genes were significantly up‐regulated and 21 genes were down‐regulated at POST1 and 0 genes were altered at POST2. Both LP‐EPC and MP‐EPC acutely alter skeletal muscle gene expression, though only LP‐EPC appeared to affect gene expression with subchronic application. Moreover, the transcriptome response to EPC demonstrated marked heterogeneity (i.e., genes and directionality) with different target inflation pressures.
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Affiliation(s)
- Jeffrey S Martin
- Department of Cell Biology and Physiology, Edward Via College of Osteopathic Medicine - Auburn Campus, Auburn, Alabama .,School of Kinesiology, Auburn University, Auburn, Alabama
| | | | - Cody T Haun
- School of Kinesiology, Auburn University, Auburn, Alabama
| | | | - Joshua J Shake
- School of Kinesiology, Auburn University, Auburn, Alabama
| | | | - Michael D Goodlett
- Department of Cell Biology and Physiology, Edward Via College of Osteopathic Medicine - Auburn Campus, Auburn, Alabama.,Athletics Department, Auburn University, Auburn, Alabama
| | - Andreas Kavazis
- Department of Cell Biology and Physiology, Edward Via College of Osteopathic Medicine - Auburn Campus, Auburn, Alabama.,School of Kinesiology, Auburn University, Auburn, Alabama
| | - David D Pascoe
- School of Kinesiology, Auburn University, Auburn, Alabama
| | - Lee Zhang
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama
| | - Michael D Roberts
- Department of Cell Biology and Physiology, Edward Via College of Osteopathic Medicine - Auburn Campus, Auburn, Alabama.,School of Kinesiology, Auburn University, Auburn, Alabama
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36
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Strauß R, Rose T, Flint SM, Klotsche J, Häupl T, Peck-Radosavljevic M, Yoshida T, Kyogoku C, Flechsig A, Becker AM, Dao KH, Radbruch A, Burmester GR, Lyons PA, Davis LS, Hiepe F, Grützkau A, Biesen R. Type I interferon as a biomarker in autoimmunity and viral infection: a leukocyte subset-specific analysis unveils hidden diagnostic options. J Mol Med (Berl) 2017; 95:753-765. [PMID: 28357476 DOI: 10.1007/s00109-017-1515-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 12/20/2016] [Accepted: 02/01/2017] [Indexed: 01/13/2023]
Abstract
Interferon alpha and its surrogates, including IP-10 and SIGLEC1, paralleled changes of disease activity in systemic lupus erythematosus (SLE). However, the whole blood interferon signature (WBIFNS)-the current standard for type I IFN assessment in SLE-does not correlate with SLE disease activity in individual patients over time. The underlying causes for this apparent contradiction have not been convincingly demonstrated. Using a multicenter dataset of gene expression data from leukocyte subsets in SLE, we identify distinctive subset-specific contributions to the WBIFNS. In a subsequent analysis, the effects of type I interferon on cellular blood composition in patients with SLE and hepatitis B were also studied over time. We found that type I interferon mediates significant alterations in whole blood composition, including a neutropenia and relative lymphocytosis. Given different effects of type 1 interferon on different leukocyte subsets, these shifts confound measurement of a type 1 interferon signature in whole blood. To minimize and overcome these limitations of the WBIFNS, we suggest to measure IFN-induced transcripts or proteins in a specific leukocyte subset to improve clinical impact of interferon biomarkers. KEY MESSAGES Myeloid cells contribute more to the WBIFNS in SLE than their lymphocytic counterpart. Very similar leukocyte subsets reveal distinctive IFN signatures. IFN alpha mixes up composition of blood and leads to a preferential neutropenia, yielding relative lymphocytosis.
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Affiliation(s)
- Romy Strauß
- Department of Rheumatology and Clinical Immunology, Charité Universitätsmedizin Berlin, Chariteplatz 1, 10117, Berlin, Germany
| | - Thomas Rose
- Department of Rheumatology and Clinical Immunology, Charité Universitätsmedizin Berlin, Chariteplatz 1, 10117, Berlin, Germany
| | - Shaun M Flint
- Cambridge Institute for Medical Research and Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Jens Klotsche
- German Rheumatism Research Center Berlin-Leibniz Institute, Charitéplatz 1, 10117, Berlin, Germany
| | - Thomas Häupl
- Department of Rheumatology and Clinical Immunology, Charité Universitätsmedizin Berlin, Chariteplatz 1, 10117, Berlin, Germany
| | | | - Taketoshi Yoshida
- Department of Pediatrics, Faculty of Medicine, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan
| | - Chieko Kyogoku
- Department of Clinical Pathology and Immunology, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Alexandra Flechsig
- Department of Rheumatology and Clinical Immunology, Charité Universitätsmedizin Berlin, Chariteplatz 1, 10117, Berlin, Germany
| | - Amy M Becker
- Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kathryn H Dao
- Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andreas Radbruch
- German Rheumatism Research Center Berlin-Leibniz Institute, Charitéplatz 1, 10117, Berlin, Germany
| | - Gerd-Rüdiger Burmester
- Department of Rheumatology and Clinical Immunology, Charité Universitätsmedizin Berlin, Chariteplatz 1, 10117, Berlin, Germany
| | - Paul A Lyons
- Cambridge Institute for Medical Research and Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Laurie S Davis
- Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Falk Hiepe
- Department of Rheumatology and Clinical Immunology, Charité Universitätsmedizin Berlin, Chariteplatz 1, 10117, Berlin, Germany
| | - Andreas Grützkau
- German Rheumatism Research Center Berlin-Leibniz Institute, Charitéplatz 1, 10117, Berlin, Germany
| | - Robert Biesen
- Department of Rheumatology and Clinical Immunology, Charité Universitätsmedizin Berlin, Chariteplatz 1, 10117, Berlin, Germany.
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37
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Liu H, Smith TPL, Nonneman DJ, Dekkers JCM, Tuggle CK. A high-quality annotated transcriptome of swine peripheral blood. BMC Genomics 2017. [PMID: 28646867 PMCID: PMC5483264 DOI: 10.1186/s12864-017-3863-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background High throughput gene expression profiling assays of peripheral blood are widely used in biomedicine, as well as in animal genetics and physiology research. Accurate, comprehensive, and precise interpretation of such high throughput assays relies on well-characterized reference genomes and/or transcriptomes. However, neither the reference genome nor the peripheral blood transcriptome of the pig have been sufficiently assembled and annotated to support such profiling assays in this emerging biomedical model organism. We aimed to assemble published and novel RNA-seq data to provide a comprehensive, well-annotated blood transcriptome for pigs by integrating a de novo assembly with a genome-guided assembly. Results A de novo and a genome-guided transcriptome of porcine whole peripheral blood was assembled with ~162 million pairs of paired-end and ~183 million single-end, trimmed and normalized Illumina RNA-seq reads (~6 billion initial reads from 146 RNA-seq libraries) from five independent studies by using the Trinity and Cufflinks software, respectively. We then removed putative transcripts (PTs) of low confidence from both assemblies and merged the remaining PTs into an integrated transcriptome consisting of 132,928 PTs, with 126,225 (~95%) PTs from the de novo assembly and more than 91% of PTs spliced. In the integrated transcriptome, ~90% and 63% of PTs had significant sequence similarity to sequences in the NCBI NT and NR databases, respectively; 68,754 (~52%) PTs were annotated with 15,965 unique gene ontology (GO) terms; and 7618 PTs annotated with Enzyme Commission codes were assigned to 134 pathways curated by the Kyoto Encyclopedia of Genes and Genomes (KEGG). Full exon-intron junctions of 17,528 PTs were validated by PacBio IsoSeq full-length cDNA reads from 3 other porcine tissues, NCBI pig RefSeq mRNAs and transcripts from Ensembl Sscrofa10.2 annotation. Completeness of the 5’ termini of 37,569 PTs was validated by public cap analysis of gene expression (CAGE) data. By comparison to the Ensembl transcripts, we found that (1) the deduced precursors of 54,402 PTs shared at least one intron or exon with those of 18,437 Ensembl transcripts; (2) 12,262 PTs had both longer 5’ and 3’ termini than their maximally overlapping Ensembl transcripts; and (3) 41,838 spliced PTs were totally missing from the Sscrofa10.2 annotation. Similar results were obtained when the PTs were compared to the pig NCBI RefSeq mRNA collection. Conclusions We built, validated and annotated a comprehensive porcine blood transcriptome with significant improvement over the annotation of Ensembl Sscrofa10.2 and the pig NCBI RefSeq mRNAs, and laid a foundation for blood-based high throughput transcriptomic assays in pigs and for advancing annotation of the pig genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3863-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Haibo Liu
- Bioinformatics and Computational Biology Program, Department of Animal Science, Iowa State University, 2258 Kildee Hall, Ames, IA, 50011, USA
| | - Timothy P L Smith
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Dan J Nonneman
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Jack C M Dekkers
- Department of Animal Science, Iowa State University, 239 Kildee Hall, Ames, IA, 50011, USA
| | - Christopher K Tuggle
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA, 50011, USA.
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Maroofi N, Azarkeivan A, Banihashemi S, Mohammadparast S, Aghajanirefah A, Banan M. An enhancer haplotype may influence BCL11A expression levels and the response to hydroxyurea in β-thalassemia patients. Pharmacogenomics 2017. [PMID: 28639471 DOI: 10.2217/pgs-2017-0019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
AIM To identify the BCL11A intron-2 enhancer linkage disequilibrium (LD) block, harboring two previously identified SNPs, associating with the hydroxyurea response in β-thalassemia patients and the functional significance of this region. MATERIALS & METHODS Several neighboring SNPs were genotyped in our cohort. The associating LD block was identified, and its function studied in K562 erythroid cells via CRISPR/Cas9 genome editing. RESULTS A haplotype harboring three tag SNPs correlated significantly with the HU-response and BCL11A transcript levels in the patients' reticulocytes. Two deletions encompassing this LD block significantly reduced BCL11A transcript levels in K562 cells. CONCLUSION Our data suggest an essential role for this LD block in BCL11A expression levels and the response to hydroxyurea in β-thalassemia patients.
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Affiliation(s)
- Nahal Maroofi
- Genetics Research Center, University of Social Welfare & Rehabilitation Sciences, Tehran, Iran
| | - Azita Azarkeivan
- Pediatric Hematology Oncology, Blood Transfusion Research Center, High Institute for Research & Education in Transfusion Medicine, Thalassemia Clinic, Tehran, Iran
| | - Soosan Banihashemi
- Genetics Research Center, University of Social Welfare & Rehabilitation Sciences, Tehran, Iran
| | - Saeid Mohammadparast
- Genetics Research Center, University of Social Welfare & Rehabilitation Sciences, Tehran, Iran
| | - Ali Aghajanirefah
- Genetics Research Center, University of Social Welfare & Rehabilitation Sciences, Tehran, Iran.,Laboratory Medicine, UCSF School of Medicine, San Francisco, CA 94115, USA
| | - Mehdi Banan
- Genetics Research Center, University of Social Welfare & Rehabilitation Sciences, Tehran, Iran
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Barghouthi SA. The Epimmunity Theory: The Single Cell Defenses against Infectious and Genetic Diseases. Front Immunol 2017; 8:694. [PMID: 28659926 PMCID: PMC5468598 DOI: 10.3389/fimmu.2017.00694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/29/2017] [Indexed: 11/18/2022] Open
Abstract
Single cell defense against diseases defines “epimmunity.” Epimmunity is complementary to the immune system and can neither be substituted by innate nor by acquired immunity. Epimmunity, the proposed new branch of immunity, is further explored and analyzed for enucleated mature mammalian erythrocytes and nucleated erythrocytes of non-mammalian vertebrates leading to the development of “The Epimmunity Theory.” Enucleation of mammalian erythroblast and inactivation of nuclei in erythrocytes of non-mammalian vertebrates are major contributors to the collective immunity: epimmunity, innate, and acquired. The fact that diseases of mature erythrocytes (MEs) are rare supports the notion that a single cell can resist microbial and genetic diseases; MEs are refractory to malaria and cancer. Nucleated cells, such as B-cells, T-cells, hepatocytes, and cell developmental stages are susceptible to genetic and specific microbial diseases depending on their nuclear activities and the receptors they express; such cells show lower epimmunity relative to MEs. Epimmunity is important as a disease insulator that prevents the spread of diseases from an infected tissue to the majority of other tissues. Breakdown of epimmunity may lead to disease development.
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Affiliation(s)
- Sameer A Barghouthi
- Faculty of Health Professions, Department of Medical Laboratory Sciences, Al-Quds University, Jerusalem, Palestine
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40
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Messaoudi I, Handu M, Rais M, Sureshchandra S, Park BS, Fei SS, Wright H, White AE, Jain R, Cameron JL, Winters-Stone KM, Varlamov O. Long-lasting effect of obesity on skeletal muscle transcriptome. BMC Genomics 2017; 18:411. [PMID: 28545403 PMCID: PMC5445270 DOI: 10.1186/s12864-017-3799-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 05/16/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Reduced physical activity and increased intake of calorically-dense diets are the main risk factors for obesity, glucose intolerance, and type 2 diabetes. Chronic overnutrition and hyperglycemia can alter gene expression, contributing to long-term obesity complications. While caloric restriction can reduce obesity and glucose intolerance, it is currently unknown whether it can effectively reprogram transcriptome to a pre-obesity level. The present study addressed this question by the preliminary examination of the transcriptional dynamics in skeletal muscle after exposure to overnutrition and following caloric restriction. RESULTS Six male rhesus macaques of 12-13 years of age consumed a high-fat western-style diet for 6 months and then were calorically restricted for 4 months without exercise. Skeletal muscle biopsies were subjected to longitudinal gene expression analysis using next-generation whole-genome RNA sequencing. In spite of significant weight loss and normalized insulin sensitivity, the majority of WSD-induced (n = 457) and WSD-suppressed (n = 47) genes remained significantly dysregulated after caloric restriction (FDR ≤0.05). The MetacoreTM pathway analysis reveals that western-style diet induced the sustained activation of the transforming growth factor-β gene network, associated with extracellular matrix remodeling, and the downregulation of genes involved in muscle structure development and nutritional processes. CONCLUSIONS Western-style diet, in the absence of exercise, induced skeletal muscle transcriptional programing, which persisted even after insulin resistance and glucose intolerance were completely reversed with caloric restriction.
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Affiliation(s)
- Ilhem Messaoudi
- School of Biological Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Mithila Handu
- Division of Cardiometabolic Health, Oregon National Primate Research Center, L584 505 NW 185th Ave., Beaverton, OR, 97006, USA
| | - Maham Rais
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, 92521, USA
| | - Suhas Sureshchandra
- School of Biological Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Byung S Park
- Department of Public Health and Preventive Medicine, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Suzanne S Fei
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR, 97006, USA
| | - Hollis Wright
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR, 97006, USA
| | - Ashley E White
- Division of Cardiometabolic Health, Oregon National Primate Research Center, L584 505 NW 185th Ave., Beaverton, OR, 97006, USA
| | - Ruhee Jain
- Department of Neuroscience and Psychiatry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Judy L Cameron
- Department of Neuroscience and Psychiatry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Kerri M Winters-Stone
- Department of School of Nursing, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Oleg Varlamov
- Division of Cardiometabolic Health, Oregon National Primate Research Center, L584 505 NW 185th Ave., Beaverton, OR, 97006, USA.
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41
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Desingu PA, Singh SD, Dhama K, Vinodhkumar OR, Malik YS. A sensitive haemadsorption technique based RT-PCR for concentration and detection of Newcastle disease virus from clinical samples and allantoic fluid. Virusdisease 2017; 27:319-323. [PMID: 28466047 DOI: 10.1007/s13337-016-0325-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 05/30/2016] [Indexed: 11/26/2022] Open
Abstract
The present study describes the exploitation of haemadsorption (HAd) property of the Newcastle disease virus (NDV) for the development of a novel sensitive HAd technique based RT-PCR for detection of NDV from clinical samples of virus infected experimental birds. The NDV propagated allantoic fluid from the infected embryonated chicken eggs or supernatant of the processed clinical samples (tissue triturate, cloaca and tracheal swabs) from the experimentally infected birds were added with chicken red blood cells (RBC) to adsorb the virus on RBC's surface. The virus adsorbed RBCs were subjected to trizol method of RNA extraction and reverse transcription-polymerase chain reaction (RT-PCR) for detection of NDV. The HAd based RNA extraction showed better yield of 700-900 ng RNA and when subjected to RT-PCR detection revealed a 100 times higher sensitivity than the conventional RNA extraction and RT-PCR detection system. This could be an alternate technique which can be exploited in low NDV load situations in clinical samples.
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Affiliation(s)
- Perumal Arumugam Desingu
- Avian Diseases Section, Division of Pathology, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, UP 243 122 India
| | - Shambhu Dayal Singh
- Avian Diseases Section, Division of Pathology, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, UP 243 122 India
| | - Kuldeep Dhama
- Avian Diseases Section, Division of Pathology, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, UP 243 122 India
| | | | - Yashpal Singh Malik
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, UP 243 122 India
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Skogholt AH, Ryeng E, Erlandsen SE, Skorpen F, Schønberg SA, Sætrom P. Gene expression differences between PAXgene and Tempus blood RNA tubes are highly reproducible between independent samples and biobanks. BMC Res Notes 2017; 10:136. [PMID: 28335817 PMCID: PMC5364635 DOI: 10.1186/s13104-017-2455-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 03/17/2017] [Indexed: 02/07/2023] Open
Abstract
Background Gene expression profiling from blood is sensitive to technology choices. For example, the main blood RNA collection systems—the PAXgene and Tempus tubes—differently influence RNA expression signatures. The aim of this study was to establish a common RNA isolation protocol for these two systems and investigate if it could reduce the differences in gene expression between them. Results We collected identical blood samples on the PAXgene and Tempus systems and retrieved blood samples from two independent biobanks—NOWAC and HUNT3—which are based on PAXgene and Tempus, respectively. High-quality RNA was extracted from both sampling systems by using their original protocols and our common modified protocol, and were profiled on Illumina microarrays. Regardless of the protocol used, we found most of the measured transcripts to be differently affected by the two sampling systems. However, our modified protocol reduced the number of transcripts that were significantly differentially expressed between PAXgene and Tempus by approximately 50%. Expression differences between PAXgene and Tempus were highly reproducible both between protocols and between different independent sample sets (Pearson correlation 0.563–0.854 across 47323 probes). Moreover, the modified protocol increased the microRNA output of the system with lowest microRNA yield, the PAXgene system. Conclusions Most transcripts are affected by the choice of sampling system, but these effects are highly reproducible between independent samples. We propose that by running a control experiment with samples on both systems in parallel with biologically relevant samples, researchers may adjust for technical differences between the sampling systems. Electronic supplementary material The online version of this article (doi:10.1186/s13104-017-2455-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anne Heidi Skogholt
- Department of Laboratory Medicine, Children's and Women's Health, Faculty of Medicine, Norwegian University of Science and Technology-NTNU, 7491, Trondheim, Norway
| | - Einar Ryeng
- Department of Cancer Research and Molecular Medicine, Faculty of Medicine, Norwegian University of Science and Technology-NTNU, 7491, Trondheim, Norway
| | - Sten Even Erlandsen
- Department of Cancer Research and Molecular Medicine, Faculty of Medicine, Norwegian University of Science and Technology-NTNU, 7491, Trondheim, Norway
| | - Frank Skorpen
- Department of Laboratory Medicine, Children's and Women's Health, Faculty of Medicine, Norwegian University of Science and Technology-NTNU, 7491, Trondheim, Norway
| | - Svanhild A Schønberg
- Department of Laboratory Medicine, Children's and Women's Health, Faculty of Medicine, Norwegian University of Science and Technology-NTNU, 7491, Trondheim, Norway
| | - Pål Sætrom
- Department of Cancer Research and Molecular Medicine, Faculty of Medicine, Norwegian University of Science and Technology-NTNU, 7491, Trondheim, Norway. .,Department of Computer and Information Science, Faculty of Information Technology, Mathematics and Electrical Engineering, Norwegian University of Science and Technology-NTNU, 7491, Trondheim, Norway. .,Bioinformatics Core Facility-BioCore, Faculty of Medicine, Norwegian University of Science and Technology-NTNU, 7491, Trondheim, Norway.
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Kay L, Tokarska-Schlattner M, Quenot-Carrias B, Goudet B, Bugert P, Arnold H, Scheuerbrandt G, Schlattner U. Creatine kinase in human erythrocytes: A genetic anomaly reveals presence of soluble brain-type isoform. Blood Cells Mol Dis 2017; 64:33-37. [PMID: 28364583 DOI: 10.1016/j.bcmd.2017.03.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 03/14/2017] [Accepted: 03/17/2017] [Indexed: 02/07/2023]
Abstract
For maintaining energy homeostasis, creatine kinase (CK) is present at elevated levels in tissues with high and/or fluctuating energy requirements such as muscle, brain, and epithelia, while there is very few CK, if any, in peripheral blood cells. However, an ectopic expression of brain-type creatine kinase (BCK) has been reported for platelets and leukocytes in an autosomal dominant inherited anomaly named CKBE. Here we investigated CK in erythrocytes of CKBE individuals from eight unrelated families. The data revealed a varying but significant increase of CK activity in CKBE individuals as compared to controls, reaching an almost 800-fold increase in two CKBE individuals which also had increased erythrocyte creatine. Immunoblotting with highly specific antibodies confirmed that the expressed CK isoform is BCK. Cell fractionation evidenced soluble BCK, suggesting cytosolic and not membrane localization of erythrocyte CK as reported earlier. These results are discussed in the context of putative CK energy buffering and transfer functions in red blood cells.
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Affiliation(s)
- Laurence Kay
- Univ. Grenoble Alpes, Laboratory of Fundamental and Applied Bioenergetics (LBFA), Grenoble, France; Inserm, U1055 Grenoble, France
| | - Malgorzata Tokarska-Schlattner
- Univ. Grenoble Alpes, Laboratory of Fundamental and Applied Bioenergetics (LBFA), Grenoble, France; Inserm, U1055 Grenoble, France
| | - Bénédicte Quenot-Carrias
- Univ. Grenoble Alpes, Laboratory of Fundamental and Applied Bioenergetics (LBFA), Grenoble, France; Inserm, U1055 Grenoble, France
| | - Betty Goudet
- Univ. Grenoble Alpes, Laboratory of Fundamental and Applied Bioenergetics (LBFA), Grenoble, France; Inserm, U1055 Grenoble, France
| | - Peter Bugert
- Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, Heidelberg University, German Red Cross Blood Service of Baden-Württemberg-Hessen, Mannheim, Germany
| | | | | | - Uwe Schlattner
- Univ. Grenoble Alpes, Laboratory of Fundamental and Applied Bioenergetics (LBFA), Grenoble, France; Inserm, U1055 Grenoble, France.
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Weigt SS, Wang X, Palchevskiy V, Gregson AL, Patel N, DerHovanessian A, Shino MY, Sayah DM, Birjandi S, Lynch JP, Saggar R, Ardehali A, Ross DJ, Palmer SM, Elashoff D, Belperio JA. Gene Expression Profiling of Bronchoalveolar Lavage Cells Preceding a Clinical Diagnosis of Chronic Lung Allograft Dysfunction. PLoS One 2017; 12:e0169894. [PMID: 28103284 PMCID: PMC5245825 DOI: 10.1371/journal.pone.0169894] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 12/22/2016] [Indexed: 11/18/2022] Open
Abstract
Background Chronic Lung Allograft Dysfunction (CLAD) is the main limitation to long-term survival after lung transplantation. Although CLAD is usually not responsive to treatment, earlier identification may improve treatment prospects. Methods In a nested case control study, 1-year post transplant surveillance bronchoalveolar lavage (BAL) fluid samples were obtained from incipient CLAD (n = 9) and CLAD free (n = 8) lung transplant recipients. Incipient CLAD cases were diagnosed with CLAD within 2 years, while controls were free from CLAD for at least 4 years following bronchoscopy. Transcription profiles in the BAL cell pellets were assayed with the HG-U133 Plus 2.0 microarray (Affymetrix). Differential gene expression analysis, based on an absolute fold change (incipient CLAD vs no CLAD) >2.0 and an unadjusted p-value ≤0.05, generated a candidate list containing 55 differentially expressed probe sets (51 up-regulated, 4 down-regulated). Results The cell pellets in incipient CLAD cases were skewed toward immune response pathways, dominated by genes related to recruitment, retention, activation and proliferation of cytotoxic lymphocytes (CD8+ T-cells and natural killer cells). Both hierarchical clustering and a supervised machine learning tool were able to correctly categorize most samples (82.3% and 94.1% respectively) into incipient CLAD and CLAD-free categories. Conclusions These findings suggest that a pathobiology, similar to AR, precedes a clinical diagnosis of CLAD. A larger prospective investigation of the BAL cell pellet transcriptome as a biomarker for CLAD risk stratification is warranted.
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Affiliation(s)
- S. Samuel Weigt
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
- * E-mail:
| | - Xiaoyan Wang
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Vyacheslav Palchevskiy
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Aric L. Gregson
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Naman Patel
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Ariss DerHovanessian
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Michael Y. Shino
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - David M. Sayah
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Shirin Birjandi
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Joseph P. Lynch
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Rajan Saggar
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Abbas Ardehali
- Department of Surgery, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - David J. Ross
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Scott M. Palmer
- Department of Medicine, Duke University, Durham, North Carolina, United States of America
| | - David Elashoff
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - John A. Belperio
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
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45
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SO4 = uptake and catalase role in preconditioning after H2O2-induced oxidative stress in human erythrocytes. Pflugers Arch 2016; 469:235-250. [DOI: 10.1007/s00424-016-1927-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 12/04/2016] [Accepted: 12/06/2016] [Indexed: 10/20/2022]
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46
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Eftedal I, Flatberg A, Drvis I, Dujic Z. Immune and inflammatory responses to freediving calculated from leukocyte gene expression profiles. Physiol Genomics 2016; 48:795-802. [PMID: 27614202 DOI: 10.1152/physiolgenomics.00048.2016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 09/08/2016] [Indexed: 12/31/2022] Open
Abstract
Freedivers hold their breath while diving, causing blood oxygen levels to decrease (hypoxia) while carbon dioxide increases (hypercapnia). Whereas blood gas changes are presumably involved in the progression of respiratory diseases, less is known about their effect on healthy individuals. Here we have used gene expression profiling to analyze elite athletes' immune and inflammatory responses to freediving. Blood was collected before and 1 and 3 h after a series of maximal dynamic and static freediving apneas in a pool, and peripheral blood gene expression was mapped on genome-wide microarrays. Fractions of phenotypically distinct immune cells were computed by deconvolution of the gene expression data using Cibersort software. Changes in gene activity and associated biological pathways were determined using R and GeneGo software. The results indicated a temporary increase of neutrophil granulocytes, and a decrease of cytotoxic lymphocytes; i.e., CD8+ T cells and resting NK cells. Biological pathway associations indicated possible protective reactions: genes involved in anti-inflammatory responses to proresolving lipid mediators were upregulated, whereas central factors involved in granule-mediated lymphocyte cytotoxicity were downregulated. While it remains unresolved whether freediving alters the immune system's defensive function, these results provide new insight into leukocyte responses and the protection of homeostasis in healthy athletes.
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Affiliation(s)
- Ingrid Eftedal
- Department of Circulation and Medical Imaging, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway;
| | - Arnar Flatberg
- Department of Cancer Research and Molecular Medicine, Faculty of Medicine, Norwegian University of Science and Technology Microarray Core Facility, Trondheim, Norway
| | - Ivan Drvis
- Faculty of Kinesiology, University of Zagreb, Zagreb, Croatia; and
| | - Zeljko Dujic
- Department of Integrative Physiology, University of Split School of Medicine, Split, Croatia
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Dugmonits KN, Ferencz Á, Zahorán S, Lázár R, Talapka P, Orvos H, Hermesz E. Elevated levels of macromolecular damage are correlated with increased nitric oxide synthase expression in erythrocytes isolated from twin neonates. Br J Haematol 2016; 174:932-41. [DOI: 10.1111/bjh.14156] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 03/28/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Krisztina N. Dugmonits
- Department of Biochemistry and Molecular Biology; Faculty of Science and Informatics; University of Szeged; Szeged Hungary
| | - Ágnes Ferencz
- Department of Biochemistry and Molecular Biology; Faculty of Science and Informatics; University of Szeged; Szeged Hungary
| | - Szabolcs Zahorán
- Department of Biochemistry and Molecular Biology; Faculty of Science and Informatics; University of Szeged; Szeged Hungary
| | - Renáta Lázár
- Department of Biochemistry and Molecular Biology; Faculty of Science and Informatics; University of Szeged; Szeged Hungary
| | - Petra Talapka
- Department of Physiology, Anatomy and Neuroscience; Faculty of Science and Informatics; University of Szeged; Szeged Hungary
| | - Hajnalka Orvos
- Department of Obstetrics and Gynaecology; Faculty of Medicine; University of Szeged; Szeged Hungary
| | - Edit Hermesz
- Department of Biochemistry and Molecular Biology; Faculty of Science and Informatics; University of Szeged; Szeged Hungary
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48
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Groen K, Maltby VE, Sanders KA, Scott RJ, Tajouri L, Lechner-Scott J. Erythrocytes in multiple sclerosis - forgotten contributors to the pathophysiology? Mult Scler J Exp Transl Clin 2016; 2:2055217316649981. [PMID: 28607726 PMCID: PMC5433403 DOI: 10.1177/2055217316649981] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Multiple sclerosis (MS) is an autoimmune disease characterised by lymphocytic
infiltration of the central nervous system and subsequent destruction of myelin and axons.
On the background of a genetic predisposition to autoimmunity, environmental triggers are
assumed to initiate the disease. The majority of MS research has focused on the
pathological involvement of lymphocytes and other immune cells, yet a paucity of attention
has been given to erythrocytes, which may play an important role in MS pathology. The
following review briefly summarises how erythrocytes may contribute to MS pathology
through impaired antioxidant capacity and altered haemorheological features. The effect of
disease-modifying therapies on erythrocytes is also reviewed. It may be important to
further investigate erythrocytes in MS, as this could broaden the understanding of the
pathological mechanisms of the disease, as well as potentially lead to the discovery of
novel and innovative targets for future therapies.
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Affiliation(s)
- Kira Groen
- Faculty of Health Sciences and Medicine, Bond University, Australia
| | - Vicki E Maltby
- Information Based Medicine, Hunter Medical Research Institute, Australia
| | | | - Rodney J Scott
- Information Based Medicine, Hunter Medical Research Institute, Australia
| | - Lotti Tajouri
- Faculty of Health Sciences and Medicine, Bond University, Australia
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Xerxa E, Barbisin M, Chieppa MN, Krmac H, Vallino Costassa E, Vatta P, Simmons M, Caramelli M, Casalone C, Corona C, Legname G. Whole Blood Gene Expression Profiling in Preclinical and Clinical Cattle Infected with Atypical Bovine Spongiform Encephalopathy. PLoS One 2016; 11:e0153425. [PMID: 27073865 PMCID: PMC4830546 DOI: 10.1371/journal.pone.0153425] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 03/29/2016] [Indexed: 12/12/2022] Open
Abstract
Prion diseases, such as bovine spongiform encephalopathies (BSE), are transmissible neurodegenerative disorders affecting humans and a wide variety of mammals. Variant Creutzfeldt-Jakob disease (vCJD), a prion disease in humans, has been linked to exposure to BSE prions. This classical BSE (cBSE) is now rapidly disappearing as a result of appropriate measures to control animal feeding. Besides cBSE, two atypical forms (named H- and L-type BSE) have recently been described in Europe, Japan, and North America. Here we describe the first wide-spectrum microarray analysis in whole blood of atypical BSE-infected cattle. Transcriptome changes in infected animals were analyzed prior to and after the onset of clinical signs. The microarray analysis revealed gene expression changes in blood prior to the appearance of the clinical signs and during the progression of the disease. A set of 32 differentially expressed genes was found to be in common between clinical and preclinical stages and showed a very similar expression pattern in the two phases. A 22-gene signature showed an oscillating pattern of expression, being differentially expressed in the preclinical stage and then going back to control levels in the symptomatic phase. One gene, SEL1L3, was downregulated during the progression of the disease. Most of the studies performed up to date utilized various tissues, which are not suitable for a rapid analysis of infected animals and patients. Our findings suggest the intriguing possibility to take advantage of whole blood RNA transcriptional profiling for the preclinical identification of prion infection. Further, this study highlighted several pathways, such as immune response and metabolism that may play an important role in peripheral prion pathogenesis. Finally, the gene expression changes identified in the present study may be further investigated as a fingerprint for monitoring the progression of disease and for developing targeted therapeutic interventions.
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Affiliation(s)
- Elena Xerxa
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Functional and Structural Genomics sector, Trieste, Italy
| | - Maura Barbisin
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Functional and Structural Genomics sector, Trieste, Italy
| | - Maria Novella Chieppa
- Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d'Aosta, Torino, Italy
| | - Helena Krmac
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Functional and Structural Genomics sector, Trieste, Italy
| | - Elena Vallino Costassa
- Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d'Aosta, Torino, Italy
| | - Paolo Vatta
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Functional and Structural Genomics sector, Trieste, Italy
| | - Marion Simmons
- Pathology Department, Animal and Plant Health Agency (Weybridge), New Haw, Addlestone, United Kingdom
| | - Maria Caramelli
- Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d'Aosta, Torino, Italy
| | - Cristina Casalone
- Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d'Aosta, Torino, Italy
| | - Cristiano Corona
- Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d'Aosta, Torino, Italy
| | - Giuseppe Legname
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Functional and Structural Genomics sector, Trieste, Italy
- * E-mail:
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Apicomplexa-specific tRip facilitates import of exogenous tRNAs into malaria parasites. Proc Natl Acad Sci U S A 2016; 113:4717-22. [PMID: 27071116 DOI: 10.1073/pnas.1600476113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The malaria-causing Plasmodium parasites are transmitted to vertebrates by mosquitoes. To support their growth and replication, these intracellular parasites, which belong to the phylum Apicomplexa, have developed mechanisms to exploit their hosts. These mechanisms include expropriation of small metabolites from infected host cells, such as purine nucleotides and amino acids. Heretofore, no evidence suggested that transfer RNAs (tRNAs) could also be exploited. We identified an unusual gene in Apicomplexa with a coding sequence for membrane-docking and structure-specific tRNA binding. This Apicomplexa protein-designated tRip (tRNA import protein)-is anchored to the parasite plasma membrane and directs import of exogenous tRNAs. In the absence of tRip, the fitness of the parasite stage that multiplies in the blood is significantly reduced, indicating that the parasite may need host tRNAs to sustain its own translation and/or as regulatory RNAs. Plasmodium is thus the first example, to our knowledge, of a cell importing exogenous tRNAs, suggesting a remarkable adaptation of this parasite to extend its reach into host cell biology.
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