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Logghe T, van Zwol E, Immordino B, Van den Cruys K, Peeters M, Giovannetti E, Bogers J. Hyperthermia in Combination with Emerging Targeted and Immunotherapies as a New Approach in Cancer Treatment. Cancers (Basel) 2024; 16:505. [PMID: 38339258 PMCID: PMC10854776 DOI: 10.3390/cancers16030505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/10/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
Despite significant advancements in the development of novel therapies, cancer continues to stand as a prominent global cause of death. In many cases, the cornerstone of standard-of-care therapy consists of chemotherapy (CT), radiotherapy (RT), or a combination of both. Notably, hyperthermia (HT), which has been in clinical use in the last four decades, has proven to enhance the effectiveness of CT and RT, owing to its recognized potency as a sensitizer. Furthermore, HT exerts effects on all steps of the cancer-immunity cycle and exerts a significant impact on key oncogenic pathways. Most recently, there has been a noticeable expansion of cancer research related to treatment options involving immunotherapy (IT) and targeted therapy (TT), a trend also visible in the research and development pipelines of pharmaceutical companies. However, the potential results arising from the combination of these innovative therapeutic approaches with HT remain largely unexplored. Therefore, this review aims to explore the oncology pipelines of major pharmaceutical companies, with the primary objective of identifying the principal targets of forthcoming therapies that have the potential to be advantageous for patients by specifically targeting molecular pathways involved in HT. The ultimate goal of this review is to pave the way for future research initiatives and clinical trials that harness the synergy between emerging IT and TT medications when used in conjunction with HT.
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Affiliation(s)
- Tine Logghe
- Elmedix NV, Dellingstraat 34/1, 2800 Mechelen, Belgium
| | - Eke van Zwol
- Elmedix NV, Dellingstraat 34/1, 2800 Mechelen, Belgium
| | - Benoît Immordino
- Cancer Pharmacology Lab, Fondazione Pisana per la Scienza, San Giuliano, 56017 Pisa, Italy
- Institute of Life Sciences, Sant’Anna School of Advanced Studies, 56127 Pisa, Italy
| | | | - Marc Peeters
- Department of Oncology, Antwerp University Hospital, 2650 Edegem, Belgium
| | - Elisa Giovannetti
- Cancer Pharmacology Lab, Fondazione Pisana per la Scienza, San Giuliano, 56017 Pisa, Italy
- Department of Medical Oncology, Amsterdam UMC, Location Vrije Universiteit, Cancer Center Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Johannes Bogers
- Elmedix NV, Dellingstraat 34/1, 2800 Mechelen, Belgium
- Laboratory of Cell Biology and Histology, Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Antwerp, Belgium
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Andrade LEC, Chan EKL, Vieths S, Engel P, Kirschfink M. Editorial: Contemporary challenges in immunologic testing in clinical and research laboratories. Front Immunol 2023; 14:1259823. [PMID: 37575258 PMCID: PMC10415069 DOI: 10.3389/fimmu.2023.1259823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 07/17/2023] [Indexed: 08/15/2023] Open
Affiliation(s)
- Luis Eduardo C. Andrade
- Rheumatology Division, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
- Immunology Division, Fleury Group Medicine and Health Laboratories, São Paulo, Brazil
| | - Edward K. L. Chan
- Department of Oral Biology, University of Florida, Gainesville, FL, United States
| | - Stefan Vieths
- Division of Allergology, Paul-Ehrlich-Institut, Langen, Germany
| | - Pablo Engel
- Department of Biomedical Sciences, University of Barcelona, Barcelona, Spain
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Sukri A, Hanafiah A, Kosai NR, Mohammed Taher M, Mohamed R. New insight on the role of Helicobacter pylori cagA in the expression of cell surface antigens with important biological functions in gastric carcinogenesis. Helicobacter 2022; 27:e12913. [PMID: 35848223 DOI: 10.1111/hel.12913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/17/2022] [Accepted: 06/28/2022] [Indexed: 12/20/2022]
Abstract
BACKGROUND Expression of cluster of differentiation (CD) antigens changes according to disease status and inflammation. Profiles of CD antigens expression in gastric cancer patients are different based on the status of H. pylori infection. AIMS We conducted this study to profile CD antigen markers in gastric adenocarcinoma cells (AGS cell line) infected with distinct cytotoxin-associated gene A (cagA) genotypes of H. pylori clinical isolates. METHODS The AGS cells were infected with H. pylori isolates with different cagA genotypes, and CD antigens expression was determined using DotScan™ antibody microarray. Formation of "hummingbird" phenotype was determined, and the percentage was calculated. RESULTS H. pylori strains harboring cagA upregulated the expression of CD antigen involved in cancer stem cell formation (CD55), but downregulated CD antigens involved in immune regulation (CD40 and CD186) and cell adhesion (CD44). CD54 (neutrophil adhesion) and CD71 (iron transfer) were highly downregulated in the gastric cells infected with Western cagA isolates compared with East Asian isolates. CD antigen expression was different in the cells infected with H. pylori harboring different CagA EPIYA (Glu-Pro-Ile-Tyr-Ala) numbers, in which higher repression of CD54 and CD15 (Lewis x antigen) were observed in the isolate with the highest number of EPIYA motif. Furthermore, higher downregulation of CD15 was observed in the infected gastric cells with high percentage of "hummingbird" phenotype than that of low percentage of "hummingbird" phenotype. CONCLUSION Our study demonstrated the critical roles of CD antigens in the CagA pathogenesis and should be investigated further.
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Affiliation(s)
- Asif Sukri
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, Bandar Puncak Alam, Malaysia
| | - Alfizah Hanafiah
- Department of Medical Microbiology & Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Nik Ritza Kosai
- Department of Surgery, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Mustafa Mohammed Taher
- Department of Surgery, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Ramelah Mohamed
- Department of Medical Microbiology & Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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Proteomic and phosphoproteomic landscapes of acute myeloid leukemia. Blood 2022; 140:1533-1548. [PMID: 35895896 PMCID: PMC9523374 DOI: 10.1182/blood.2022016033] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 07/14/2022] [Indexed: 01/21/2023] Open
Abstract
We have developed a deep-scale proteome and phosphoproteome database from 44 representative acute myeloid leukemia (AML) patients from the LAML TCGA dataset and 6 healthy bone marrow-derived controls. After confirming data quality, we orthogonally validated several previously undescribed features of AML revealed by the proteomic data. We identified examples of posttranscriptionally regulated proteins both globally (ie, in all AML samples) and also in patients with recurrent AML driver mutations. For example, samples with IDH1/2 mutations displayed elevated levels of the 2-oxoglutarate-dependent histone demethylases KDM4A/B/C, despite no changes in messenger RNA levels for these genes; we confirmed this finding in vitro. In samples with NPMc mutations, we identified several nuclear importins with posttranscriptionally increased protein abundance and showed that they interact with NPMc but not wild-type NPM1. We identified 2 cell surface proteins (CD180 and MRC1/CD206) expressed on AML blasts of many patients (but not healthy CD34+ stem/progenitor cells) that could represent novel targets for immunologic therapies and confirmed these targets via flow cytometry. Finally, we detected nearly 30 000 phosphosites in these samples; globally, AML samples were associated with the abnormal phosphorylation of specific residues in PTPN11, STAT3, AKT1, and PRKCD. FLT3-TKD samples were associated with increased phosphorylation of activating tyrosines on the cytoplasmic Src-family tyrosine kinases FGR and HCK and related signaling proteins. PML-RARA-initiated AML samples displayed a unique phosphorylation signature, and TP53-mutant samples showed abundant phosphorylation of serine-183 on TP53 itself. This publicly available database will serve as a foundation for further investigations of protein dysregulation in AML pathogenesis.
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Possibilities of using T-cell biophysical biomarkers of ageing. Expert Rev Mol Med 2022; 24:e35. [PMID: 36111609 PMCID: PMC9884748 DOI: 10.1017/erm.2022.29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Ageing is interrelated with the development of immunosenescence. This article focuses on one of the cell sets of the adaptive immune system, T cells, and provides a review of the known changes in T cells associated with ageing. Such fundamental changes affect both cell molecular content and internal ordering. However, acquiring a complete description of the changes at these levels would require extensive measurements of parameters and, furthermore, important fine details of the internal ordering that may be difficult to detect. Therefore, an alternative approach for the characterisation of cells consists of the performance of physical measurements of the whole cell, such as deformability measurements or migration measurements: the physical parameters, complementing the commonly used chemical biomarkers, may contribute to a better understanding of the evolution of T-cell states during ageing. Mechanical measurements, among other biophysical measurements, have the advantage of their relative simplicity: one single parameter agglutinates the complex effects of the variety of changes that gradually appear in cells during ageing.
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Advantages and Challenges of Differential Immune Cell Count Determination in Blood and Milk for Monitoring the Health and Well-Being of Dairy Cows. Vet Sci 2022; 9:vetsci9060255. [PMID: 35737307 PMCID: PMC9229168 DOI: 10.3390/vetsci9060255] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/07/2022] [Accepted: 05/24/2022] [Indexed: 02/05/2023] Open
Abstract
A key challenge of the 21st century will be to provide the growing world population with a sustainable and secure supply of food. Consequently, the dairy farming’s primary task is to lower milk losses and other inefficiencies associated with diseased cows. Moreover, a shift from curative to preventive health management would be desirable for mastitis and a wide variety of other infectious and non-infectious cattle diseases, some of which are known to have profound negative effects on the performance and well-being of cows. Differential cell counting (DCC), a procedure that aims to determine the proportions of different somatic cell types in raw milk samples, has not only the potential to optimize mastitis diagnostics, but it could furthermore serve as a diagnostic tool for monitoring the general and overall health status of dairy cows. Based on a broad search of the literature, the practical utility of various types of DCC is summarized and discussed in this review. Since it might be of advantage to interpret DCC with the aid of data from studies in humans, differences between the immune systems of humans and dairy cattle, with a special focus on surface marker expression profiles and γδ (gamma delta) T-cell characteristics, are also described.
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Kužílková D, Puñet-Ortiz J, Aui PM, Fernández J, Fišer K, Engel P, van Zelm MC, Kalina T. Standardization of Workflow and Flow Cytometry Panels for Quantitative Expression Profiling of Surface Antigens on Blood Leukocyte Subsets: An HCDM CDMaps Initiative. Front Immunol 2022; 13:827898. [PMID: 35222411 PMCID: PMC8874145 DOI: 10.3389/fimmu.2022.827898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/17/2022] [Indexed: 11/13/2022] Open
Abstract
Background The Human Cell Differentiation Molecules (HCDM) organizes Human Leukocyte Differentiation Antigen (HLDA) workshops to test and name clusters of antibodies that react with a specific antigen. These cluster of differentiation (CD) markers have provided the scientific community with validated antibody clones, consistent naming of targets and reproducible identification of leukocyte subsets. Still, quantitative CD marker expression profiles and benchmarking of reagents at the single-cell level are currently lacking. Objective To develop a flow cytometric procedure for quantitative expression profiling of surface antigens on blood leukocyte subsets that is standardized across multiple research laboratories. Methods A high content framework to evaluate the titration and reactivity of Phycoerythrin (PE)-conjugated monoclonal antibodies (mAbs) was created. Two flow cytometry panels were designed: an innate cell tube for granulocytes, dendritic cells, monocytes, NK cells and innate lymphoid cells (12-color) and an adaptive lymphocyte tube for naive and memory B and T cells, including TCRγδ+, regulatory-T and follicular helper T cells (11-color). The potential of these 2 panels was demonstrated via expression profiling of selected CD markers detected by PE-conjugated antibodies and evaluated using 561 nm excitation. Results Using automated data annotation and dried backbone reagents, we reached a robust workflow amenable to processing hundreds of measurements in each experiment in a 96-well plate format. The immunophenotyping panels enabled discrimination of 27 leukocyte subsets and quantitative detection of the expression of PE-conjugated CD markers of interest that could quantify protein expression above 400 units of antibody binding capacity. Expression profiling of 4 selected CD markers (CD11b, CD31, CD38, CD40) showed high reproducibility across centers, as well as the capacity to benchmark unique clones directed toward the same CD3 antigen. Conclusion We optimized a procedure for quantitative expression profiling of surface antigens on blood leukocyte subsets. The workflow, bioinformatics pipeline and optimized flow panels enable the following: 1) mapping the expression patterns of HLDA-approved mAb clones to CD markers; 2) benchmarking new antibody clones to established CD markers; 3) defining new clusters of differentiation in future HLDA workshops.
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Affiliation(s)
- Daniela Kužílková
- Childhood Leukaemia Investigation Prague (CLIP), Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic and University Hospital Motol, Prague, Czechia
| | - Joan Puñet-Ortiz
- Department of Biomedical Sciences, University of Barcelona, Barcelona, Spain
| | - Pei M. Aui
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Javier Fernández
- Department of Biomedical Sciences, University of Barcelona, Barcelona, Spain
| | - Karel Fišer
- Childhood Leukaemia Investigation Prague (CLIP), Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic and University Hospital Motol, Prague, Czechia
| | - Pablo Engel
- Department of Biomedical Sciences, University of Barcelona, Barcelona, Spain
| | - Menno C. van Zelm
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
- Department of Allergy, Immunology and Respiratory Medicine, Central Clinical School, Monash University and Alfred Hospital, Melbourne, VIC, Australia
| | - Tomáš Kalina
- Childhood Leukaemia Investigation Prague (CLIP), Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic and University Hospital Motol, Prague, Czechia
- *Correspondence: Tomáš Kalina,
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Saha SS, Samanas NB, Miralda I, Shubin NJ, Niino K, Bhise G, Acharya M, Seo AJ, Camp N, Deutsch GH, James RG, Piliponsky AM. Mast cell surfaceome characterization reveals CD98 heavy chain is critical for optimal cell function. J Allergy Clin Immunol 2022; 149:685-697. [PMID: 34324892 PMCID: PMC8792104 DOI: 10.1016/j.jaci.2021.07.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/07/2021] [Accepted: 07/14/2021] [Indexed: 02/03/2023]
Abstract
BACKGROUND Mast cells are involved in many distinct pathologic conditions, suggesting that they recognize and respond to various stimuli and thus require a rich repertoire of cell surface proteins. However, mast cell surface proteomes have not been comprehensively characterized. OBJECTIVE We aimed to further characterize the mast cell surface proteome to obtain a better understanding of how mast cells function in health and disease. METHODS We enriched for glycosylated surface proteins expressed in mouse bone marrow-derived cultured mast cells (BMCMCs) and identified them using mass spectrometry analysis. The presence of novel surface proteins in mast cells was validated by real-time quantitative PCR and flow cytometry analysis in BMCMCs and peritoneal mast cells (PMCs). We developed a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) gene editing approach to disrupt genes of interest in BMCMCs. RESULTS The glycoprotein enrichment approach resulted in the identification of 1270 proteins in BMCMCs, 378 of which were localized to the plasma membrane. The most common protein classes among plasma membrane proteins were small GTPases, receptors, and transporters. One such cell surface protein was CD98 heavy chain (CD98hc), encoded by the Slc3a2 gene. Slc3a2 gene disruption resulted in a significant reduction in CD98hc expression, adhesion, and proliferation. CONCLUSIONS Glycoprotein enrichment coupled with mass spectrometry can be used to identify novel surface molecules in mast cells. Moreover, CD98hc plays an important role in mast cell function.
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Affiliation(s)
- Siddhartha S. Saha
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Nyssa B. Samanas
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Irina Miralda
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Nicholas J. Shubin
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Kerri Niino
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Gauri Bhise
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Manasa Acharya
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Albert J. Seo
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Nathan Camp
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Gail H. Deutsch
- Department of Laboratories, Seattle Children’s Research Institute, Seattle, Washington, United States of America,Department of Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Richard G. James
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America,Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Adrian M. Piliponsky
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America,Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, United States of America,Department of Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America,Department of Global Health, University of Washington School of Medicine, Seattle, Washington, United States of America,Corresponding author: Adrian M. Piliponsky, Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, 1900 9th Ave, Room 721, , Phone number: 206-884-7226, Fax number: 206-987-7310
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Chan JTH, Kadri S, Köllner B, Rebl A, Korytář T. RNA-Seq of Single Fish Cells – Seeking Out the Leukocytes Mediating Immunity in Teleost Fishes. Front Immunol 2022; 13:798712. [PMID: 35140719 PMCID: PMC8818700 DOI: 10.3389/fimmu.2022.798712] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/03/2022] [Indexed: 01/01/2023] Open
Abstract
The immune system is a complex and sophisticated biological system, spanning multiple levels of complexity, from the molecular level to that of tissue. Our current understanding of its function and complexity, of the heterogeneity of leukocytes, is a result of decades of concentrated efforts to delineate cellular markers using conventional methods of antibody screening and antigen identification. In mammalian models, this led to in-depth understanding of individual leukocyte subsets, their phenotypes, and their roles in health and disease. The field was further propelled forward by the development of single-cell (sc) RNA-seq technologies, offering an even broader and more integrated view of how cells work together to generate a particular response. Consequently, the adoption of scRNA-seq revealed the unexpected plasticity and heterogeneity of leukocyte populations and shifted several long-standing paradigms of immunology. This review article highlights the unprecedented opportunities offered by scRNA-seq technology to unveil the individual contributions of leukocyte subsets and their crosstalk in generating the overall immune responses in bony fishes. Single-cell transcriptomics allow identifying unseen relationships, and formulating novel hypotheses tailored for teleost species, without the need to rely on the limited number of fish-specific antibodies and pre-selected markers. Several recent studies on single-cell transcriptomes of fish have already identified previously unnoticed expression signatures and provided astonishing insights into the diversity of teleost leukocytes and the evolution of vertebrate immunity. Without a doubt, scRNA-seq in tandem with bioinformatics tools and state-of-the-art methods, will facilitate studying the teleost immune system by not only defining key markers, but also teaching us about lymphoid tissue organization, development/differentiation, cell-cell interactions, antigen receptor repertoires, states of health and disease, all across time and space in fishes. These advances will invite more researchers to develop the tools necessary to explore the immunology of fishes, which remain non-conventional animal models from which we have much to learn.
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Affiliation(s)
- Justin T. H. Chan
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | - Safwen Kadri
- Helmholtz Zentrum München, Institute of Lung Biology and Disease, Regenerative Biology and Medicine, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Bernd Köllner
- Institute of Immunology, Friedrich Loeffler Institute, Federal Research Institute for Animal Health, Greifswald, Germany
| | - Alexander Rebl
- Institute of Genome Biology, Research Institute for Farm Animal Biology, Dummerstorf, Germany
- *Correspondence: Alexander Rebl, ; Tomáš Korytář,
| | - Tomáš Korytář
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
- Faculty of Fisheries and Protection of Waters, University of South Bohemia, České Budějovice, Czechia
- *Correspondence: Alexander Rebl, ; Tomáš Korytář,
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Novel Fluorinated Spermine and Small Molecule PEI to Deliver Anti-PD-L1 and Anti-VEGF siRNA for Highly Efficient Tumor Therapy. Pharmaceutics 2021; 13:pharmaceutics13122058. [PMID: 34959340 PMCID: PMC8708240 DOI: 10.3390/pharmaceutics13122058] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/20/2021] [Accepted: 11/26/2021] [Indexed: 11/17/2022] Open
Abstract
Small interfering RNA (siRNA) can specifically silence disease gene expression. This project investigated the overexpression of programmed death receptor ligand 1 (PD-L1) and vascular endothelial growth factor (VEGF) on the surface of tumor cells. However, the main obstacle to the development of gene therapy drugs is the lack of an efficient delivery vector, which should be able to overcome multiple delivery barriers and protect siRNA to enter the target cells. Therefore, a novel fluorine-modified endogenous molecular carrier TFSPEI was constructed by linking fluorinated groups with hydrophobic and hydrophilic characteristics on the surface of PEI and spermine. The results showed that lower toxicity, higher endocytosis, and silencing efficiency were achieved. We found that the inhibition of VEGF targets can indirectly activate the immune response to promote the tumor-killing and invasion effects of T cells. The combined delivery of anti-VEGF siRNA and anti-PD-L1 siRNA could inhibit the expression of corresponding proteins, restore the anti-tumor function of T cells and inhibit the growth of neovascularization, and obtained significant anti-tumor effects. Therefore, this safe and efficient fluorinated spermine and small molecule PEI-based anti-PD-L1 and anti-VEGF siRNA delivery system is expected to provide a new strategy for gene therapy of tumors.
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Man L, Lustgarten-Guahmich N, Kallinos E, Redhead-Laconte Z, Liu S, Schattman B, Redmond D, Hancock K, Zaninovic N, Schattman G, Rosenwaks Z, James D. Comparison of Human Antral Follicles of Xenograft versus Ovarian Origin Reveals Disparate Molecular Signatures. Cell Rep 2021; 32:108027. [PMID: 32783948 DOI: 10.1016/j.celrep.2020.108027] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/13/2020] [Accepted: 07/22/2020] [Indexed: 12/12/2022] Open
Abstract
The activation, growth, and maturation of oocytes to an ovulatory phase, termed folliculogenesis, is governed by the orchestrated activity of multiple specialized cell types within the ovary; yet, the mechanisms governing diversification and behavior of discrete cellular sub-populations within follicles are poorly understood. We use bulk and single-cell RNA sequencing to distinguish the transcriptional signature of prospectively isolated granulosa and theca/stroma cell subsets within human antral follicles derived from xenografts or ovaries. The analysis deconstructs phenotypic diversification within small (<4 mm) antral follicles, identifying secreted factors that are differentially enriched between mural and oophorus granulosa cells, and segregating stromal/support and steroidal activity between theca externa and interna, respectively. Multiple factors are differentially expressed in follicles of xenograft versus ovarian origin. These data capture a high-resolution transcriptional signature of granulosa and theca subpopulations and provide a systems-level portrait of cellular diversification in early antral human follicles.
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Affiliation(s)
- Limor Man
- Center for Reproductive Medicine and Infertility, Weill Cornell Medical College, New York, NY 10065, USA
| | - Nicole Lustgarten-Guahmich
- Center for Reproductive Medicine and Infertility, Weill Cornell Medical College, New York, NY 10065, USA
| | - Eleni Kallinos
- Center for Reproductive Medicine and Infertility, Weill Cornell Medical College, New York, NY 10065, USA
| | - Zachary Redhead-Laconte
- Center for Reproductive Medicine and Infertility, Weill Cornell Medical College, New York, NY 10065, USA
| | - Sally Liu
- Center for Reproductive Medicine and Infertility, Weill Cornell Medical College, New York, NY 10065, USA
| | - Benjamin Schattman
- Center for Reproductive Medicine and Infertility, Weill Cornell Medical College, New York, NY 10065, USA
| | - David Redmond
- Center for Reproductive Medicine and Infertility, Weill Cornell Medical College, New York, NY 10065, USA
| | - Kolbe Hancock
- Center for Reproductive Medicine and Infertility, Weill Cornell Medical College, New York, NY 10065, USA
| | - Nikica Zaninovic
- Center for Reproductive Medicine and Infertility, Weill Cornell Medical College, New York, NY 10065, USA
| | - Glenn Schattman
- Center for Reproductive Medicine and Infertility, Weill Cornell Medical College, New York, NY 10065, USA
| | - Zev Rosenwaks
- Center for Reproductive Medicine and Infertility, Weill Cornell Medical College, New York, NY 10065, USA
| | - Daylon James
- Center for Reproductive Medicine and Infertility, Weill Cornell Medical College, New York, NY 10065, USA; Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, NY 10065, USA; Tri-Institutional Stem Cell Derivation Laboratory, Weill Cornell Medical College, New York, NY 10065, USA.
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Meyfour A, Pahlavan S, Mirzaei M, Krijgsveld J, Baharvand H, Salekdeh GH. The quest of cell surface markers for stem cell therapy. Cell Mol Life Sci 2021; 78:469-495. [PMID: 32710154 PMCID: PMC11073434 DOI: 10.1007/s00018-020-03602-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/10/2020] [Accepted: 07/17/2020] [Indexed: 12/15/2022]
Abstract
Stem cells and their derivatives are novel pharmaceutics that have the potential for use as tissue replacement therapies. However, the heterogeneous characteristics of stem cell cultures have hindered their biomedical applications. In theory and practice, when cell type-specific or stage-specific cell surface proteins are targeted by unique antibodies, they become highly efficient in detecting and isolating specific cell populations. There is a growing demand to identify reliable and actionable cell surface markers that facilitate purification of particular cell types at specific developmental stages for use in research and clinical applications. The identification of these markers as very important members of plasma membrane proteins, ion channels, transporters, and signaling molecules has directly benefited from proteomics and tools for proteomics-derived data analyses. Here, we review the methodologies that have played a role in the discovery of cell surface markers and introduce cutting edge single cell proteomics as an advanced tool. We also discuss currently available specific cell surface markers for stem cells and their lineages, with emphasis on the nervous system, heart, pancreas, and liver. The remaining gaps that pertain to the discovery of these markers and how single cell proteomics and identification of surface markers associated with the progenitor stages of certain terminally differentiated cells may pave the way for their use in regenerative medicine are also discussed.
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Affiliation(s)
- Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Sara Pahlavan
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mehdi Mirzaei
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, Heidelberg, Germany
- Medical Faculty, Heidelberg University, Im Neuenheimer Feld 672, Heidelberg, Germany
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Developmental Biology, University of Science and Culture, Tehran, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Banihashem St, P.O. Box: 16635-148, 1665659911, Tehran, Iran.
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13
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Groen K, Maltby VE, Scott RJ, Tajouri L, Lechner-Scott J. Concentrations of plasma-borne extracellular particles differ between multiple sclerosis disease courses and compared to healthy controls. Mult Scler Relat Disord 2020; 45:102446. [PMID: 32805479 DOI: 10.1016/j.msard.2020.102446] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 07/29/2020] [Accepted: 08/08/2020] [Indexed: 01/30/2023]
Abstract
BACKGROUND Multiple sclerosis is a neurodegenerative, autoimmune disease of the central nervous system. Both peripheral blood and central nervous system facets play a role in the pathophysiology. Extracellular vesicles are small membrane-bound vesicles that are released by most cells in response to stress, activation, or pathology. As extracellular vesicles can cross the blood-brain barrier, they have the ability to link peripheral blood inflammation to central nervous system pathology in multiple sclerosis. The aim of this study was to obtain a comprehensive picture of the cellular origins of plasma-borne extracellular particles in multiple sclerosis. METHODS Platelet-free plasma was obtained from 39 multiple sclerosis patients and 27 healthy controls via a series of centrifugation steps and assessed by flow cytometry. Plasma samples were stained with antibodies against CD4, CD8, CD14, CD20, CD41b, CD45, CD146, and CD235a. Gates were set using size-reference beads and extracellular particles were enumerated using commercial counting beads at known concentrations. RESULTS In relapsing patients (n = 13) erythrocyte-derived (CD235a) extracellular particles were increased, while platelet-derived (CD41b), leukocyte-derived (CD45), and CD4+T cell-derived (CD4) extracellular particles were decreased compared to both healthy controls (n = 27) (p<0.05) and secondary progressive multiple sclerosis patients (n = 9) (p < 0.05). Endothelium-derived extracellular particles (CD146) were increased in stable relapsing-remitting multiple sclerosis patients (n = 17) compared to healthy controls (p < 0.05). Extracellular particles from several different cells of origin correlated with each other and clinical parameters (e.g. disease duration, number of relapses, EDSS), though clinical correlations did not withstand corrections for multiple comparisons. CONCLUSIONS Concentrations of erythrocyte-, leukocyte-, and platelet-derived extracellular particles were altered in relapsing multiple sclerosis patients and endothelium-derived extracellular particles were increased in stable relapsing-remitting patients compared to healthy controls. Extracellular particles may provide insights into altered the crosstalk between peripheral blood cells in multiple sclerosis, which may lead to the discovery of novel therapeutic targets.
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Affiliation(s)
- Kira Groen
- School of Medicine and Public Health, University of Newcastle, Callaghan NSW 2308, Australia; Centre for Brain and Mental Health Research, Hunter Medical Research Institute, New Lambton Heights NSW 2305, Australia.
| | - Vicki E Maltby
- School of Medicine and Public Health, University of Newcastle, Callaghan NSW 2308, Australia; Centre for Brain and Mental Health Research, Hunter Medical Research Institute, New Lambton Heights NSW 2305, Australia; Department of Neurology, John Hunter Hospital, New Lambton Heights NSW 2305, Australia.
| | - Rodney J Scott
- Cancer, Hunter Medical Research Institute, New Lambton Heights NSW 2305, Australia; Division of Molecular Medicine, Pathology North, John Hunter Hospital, New Lambton Heights NSW 2305, Australia; School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan NSW 2308, Australia.
| | - Lotti Tajouri
- Faculty of Health Sciences and Medicine, Bond University, Robina QLD 4229, Australia; Dubai Police Scientific Council and Dubai Future Council on Community Security, Dubai, United Arab Emirates.
| | - Jeannette Lechner-Scott
- School of Medicine and Public Health, University of Newcastle, Callaghan NSW 2308, Australia; Centre for Brain and Mental Health Research, Hunter Medical Research Institute, New Lambton Heights NSW 2305, Australia; Department of Neurology, John Hunter Hospital, New Lambton Heights NSW 2305, Australia.
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14
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Hannig J, Schäfer H, Ackermann J, Hebel M, Schäfer T, Döring C, Hartmann S, Hansmann ML, Koch I. Bioinformatics analysis of whole slide images reveals significant neighborhood preferences of tumor cells in Hodgkin lymphoma. PLoS Comput Biol 2020; 16:e1007516. [PMID: 31961873 PMCID: PMC6999891 DOI: 10.1371/journal.pcbi.1007516] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 02/04/2020] [Accepted: 10/29/2019] [Indexed: 11/25/2022] Open
Abstract
In pathology, tissue images are evaluated using a light microscope, relying on the expertise and experience of pathologists. There is a great need for computational methods to quantify and standardize histological observations. Computational quantification methods become more and more essential to evaluate tissue images. In particular, the distribution of tumor cells and their microenvironment are of special interest. Here, we systematically investigated tumor cell properties and their spatial neighborhood relations by a new application of statistical analysis to whole slide images of Hodgkin lymphoma, a tumor arising in lymph nodes, and inflammation of lymph nodes called lymphadenitis. We considered properties of more than 400, 000 immunohistochemically stained, CD30-positive cells in 35 whole slide images of tissue sections from subtypes of the classical Hodgkin lymphoma, nodular sclerosis and mixed cellularity, as well as from lymphadenitis. We found that cells of specific morphology exhibited significantly favored and unfavored spatial neighborhood relations of cells in dependence of their morphology. This information is important to evaluate differences between Hodgkin lymph nodes infiltrated by tumor cells (Hodgkin lymphoma) and inflamed lymph nodes, concerning the neighborhood relations of cells and the sizes of cells. The quantification of neighborhood relations revealed new insights of relations of CD30-positive cells in different diagnosis cases. The approach is general and can easily be applied to whole slide image analysis of other tumor types. In pathology, histological diagnosis is still challenging, in particular, for tumor diseases. Pathologists diagnose the disease and its stage of development on the basis of evaluation and interpretation of images of tissue sections. The quantification of experimental data to support decisions of diagnosis and prognosis, applying bioinformatics methods, is an important issue. Here, we introduce a new, general approach to analyze tissue images of tumor and non-tumor patients and to evaluate the distribution of tumor cells in the tissue. Moreover, we consider neighborhood relations between immunostained cells of different cell morphology. We focus on a special type of lymph node tumor, the Hodgkin lymphoma, exploring the two main types of the classical Hodgkin lymphoma, the nodular sclerosis and the mixed cellularity, and the non-tumor case, the lymphadenitis, representing an inflammation of the lymph node. We considered more than 400, 000 cells immunohistochemically stained with CD30 in 35 whole slide images of tissue sections. We found that cells of specific morphology exhibited significant relations to cells of certain morphology as spatial nearest neighbor. We could show different neighborhood patterns of CD30-positive cells between tumor and non-tumor. The approach is general and can easily be applied to other tumor types.
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Affiliation(s)
- Jennifer Hannig
- KITE - Kompetenzzentrum für Informationstechnologie, Technische Hochschule Mittelhessen, Friedberg, Germany
| | - Hendrik Schäfer
- Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Jörg Ackermann
- Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Marie Hebel
- Institute of Biochemistry II, Johann Wolfgang Goethe-University, University Hospital Frankfurt am Main, Frankfurt am Main, Germany
| | - Tim Schäfer
- Department of Child and Adolescent Psychiatry, University Hospital Frankfurt am Main, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Claudia Döring
- Dr. Senckenberg Institute of Pathology, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Sylvia Hartmann
- Dr. Senckenberg Institute of Pathology, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Martin-Leo Hansmann
- Consultation and reference center for lymph node pathology at Dr. Senckenberg Institute of Pathology, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Ina Koch
- Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
- * E-mail:
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15
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Kalina T, Fišer K, Pérez-Andrés M, Kuzílková D, Cuenca M, Bartol SJW, Blanco E, Engel P, van Zelm MC. CD Maps-Dynamic Profiling of CD1-CD100 Surface Expression on Human Leukocyte and Lymphocyte Subsets. Front Immunol 2019; 10:2434. [PMID: 31708916 PMCID: PMC6820661 DOI: 10.3389/fimmu.2019.02434] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 09/30/2019] [Indexed: 01/12/2023] Open
Abstract
CD molecules are surface molecules expressed on cells of the immune system that play key roles in immune cell-cell communication and sensing the microenvironment. These molecules are essential markers for the identification and isolation of leukocytes and lymphocyte subsets. Here, we present the results of the first phase of the CD Maps study, mapping the expression of CD1–CD100 (n = 110) on 47 immune cell subsets from blood, thymus, and tonsil using an eight-color standardized EuroFlow approach and quantification of expression. The resulting dataset included median antibody binding capacities (ABCs) and percentage of positivity for all markers on all subsets and was developed into an interactive CD Maps web resource. Using the resource, we examined differentially expressed proteins between granulocyte, monocyte, and dendritic cell subsets, and profiled dynamic expression of markers during thymocyte differentiation, T-cell maturation, and between functionally distinct B-cell subset clusters. The CD Maps resource will serve as a benchmark of antibody reactivities ensuring improved reproducibility of flow cytometry-based research. Moreover, it will provide a full picture of the surfaceome of human immune cells and serves as a useful platform to increase our understanding of leukocyte biology, as well as to facilitate the identification of new biomarkers and therapeutic targets of immunological and hematological diseases.
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Affiliation(s)
- Tomas Kalina
- CLIP - Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Charles University, Prague, Czechia.,Department of Paediatric Haematology and Oncology, University Hospital Motol, Prague, Czechia
| | - Karel Fišer
- CLIP - Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Charles University, Prague, Czechia
| | - Martin Pérez-Andrés
- Department of Medicine, Cancer Research Centre (IBMCC, USAL-CSIC), Cytometry Service (NUCLEUS), Institute of Biomedical Research of Salamanca, University of Salamanca, Salamanca, Spain.,Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Daniela Kuzílková
- CLIP - Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Charles University, Prague, Czechia
| | - Marta Cuenca
- Department of Biomedical Sciences, University of Barcelona, Barcelona, Spain
| | - Sophinus J W Bartol
- Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Elena Blanco
- Department of Medicine, Cancer Research Centre (IBMCC, USAL-CSIC), Cytometry Service (NUCLEUS), Institute of Biomedical Research of Salamanca, University of Salamanca, Salamanca, Spain.,Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Pablo Engel
- Department of Biomedical Sciences, University of Barcelona, Barcelona, Spain
| | - Menno C van Zelm
- Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Department of Immunology and Pathology, Monash University and the Alfred Hospital, Melbourne, VIC, Australia
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16
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Kalina T, Lundsten K, Engel P. Relevance of Antibody Validation for Flow Cytometry. Cytometry A 2019; 97:126-136. [DOI: 10.1002/cyto.a.23895] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/10/2019] [Accepted: 08/22/2019] [Indexed: 01/01/2023]
Affiliation(s)
- Tomas Kalina
- CLIP‐Childhood Leukemia Investigation Prague, Department of Pediatric Hematology and Oncology, 2nd Medical SchoolCharles University and University Hospital Motol Prague Czech Republic
| | | | - Pablo Engel
- Department of Biomedical SciencesFaculty of Medicine and Health Sciences, University of Barcelona Barcelona Spain
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17
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del Fresno C, Cueto FJ, Sancho D. A Proposal for Nomenclature in Myeloid C-Type Lectin Receptors. Front Immunol 2019; 10:2098. [PMID: 31555291 PMCID: PMC6743258 DOI: 10.3389/fimmu.2019.02098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 08/20/2019] [Indexed: 12/15/2022] Open
Abstract
Myeloid C-type lectin receptors (CLRs) comprise a family of receptors expressed by immune myeloid cells that share homologous C-type lectin domains. The implication of these CLRs in the regulation of homeostasis and activation of myeloid cells has generated a buoyant growth in the number of studies involving these receptors. Since their first description, diverse nomenclature has been used to refer to each of them, ranging from systematic classifications, such as gene name or cluster of differentiation, to non-systematic ones that include terminology based on gene expression patterns or function. In this review, we aim to summarize the different names used for the main myeloid CLRs and analyze which of them have been more frequently used in the literature. In addition, we have examined the evolution of the terminology applied to these myeloid CLRs over time. Based on this analysis, we propose a consensus alias for each of those myeloid CLRs. However, we acknowledge that systematicity is required beyond this terminology based on use frequency. Therefore, we have included gene names as the standardization tool to gather the maximum agreement. We suggest that a standard nomenclature consisting of both gene names and consensus alias should be included at least in scientific abstracts, which would help to identify relevant literature, saving time and effort and fostering the research in this field in a more systematic manner.
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Affiliation(s)
- Carlos del Fresno
- Immunobiology Lab, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | | | - David Sancho
- Immunobiology Lab, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
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18
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Breitenstein MK, Hu VJ, Bhatnagar R, Ratnagiri M. Approaching neural net feature interpretation using stacked autoencoders: gene expression profiling of systemic lupus erythematosus patients. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE PROCEEDINGS. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE 2019; 2019:435-442. [PMID: 31258997 PMCID: PMC6568105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Systemic lupus erythematosus (SLE) is a rare, autoimmune disorder known to affect most organ sites. Complicating clinical management is a poorly differentiated, heterogenous SLE disease state. While some small molecule drugs and biologics are available for treatment, additional therapeutic options are needed. Parsing complex biological signatures using powerful, yet human interpretable approaches is critical to advancing our understanding of SLE etiology and identifying therapeutic repositioning opportunities. To approach this goal, we developed a semi-supervised deep neural network pipeline for gene expression profiling of SLE patients and subsequent characterization of individual gene features. Our pipeline performed exemplar multinomial classification of SLE patients in independent balanced validation (F1=0.956) and unbalanced, under-powered testing (F1=0.944) cohorts. A stacked autoencoder disambiguated individual feature representativeness by regenerating an input-like(A ') feature matrix. A to A' comparisons suggest the top associated features to be key features in gene expression profiling using neural nets.
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Affiliation(s)
- Matthew K Breitenstein
- Department of Biostatistics, Epidemiology & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Vincent Jy Hu
- School of Medicine, University of California - Irvine, Irvine, CA
| | - Roopal Bhatnagar
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA
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19
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Peñaranda MMD, Jensen I, Tollersrud LG, Bruun JA, Jørgensen JB. Profiling the Atlantic Salmon IgM + B Cell Surface Proteome: Novel Information on Teleost Fish B Cell Protein Repertoire and Identification of Potential B Cell Markers. Front Immunol 2019; 10:37. [PMID: 30761128 PMCID: PMC6362898 DOI: 10.3389/fimmu.2019.00037] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/08/2019] [Indexed: 01/04/2023] Open
Abstract
Fish immunology research is at a pivotal point with the increasing availability of functional immunoassays and major advances in omics approaches. However, studies on fish B cells and their distinct subsets remain a challenge due to the limited availability of differentially expressed surface markers. To address this constraint, cell surface proteome of Atlantic salmon IgM+ B cells were analyzed by mass spectrometry and compared to surface proteins detected from two adherent salmon head kidney cell lines, ASK and SSP-9. Out of 21 cluster of differentiation (CD) molecules identified on salmon IgM+ B cells, CD22 and CD79A were shortlisted as potential markers based on the reported B cell-specific surface expression of their mammalian homologs. Subsequent RT-qPCR analyses of flow cytometry-sorted subpopulations from head kidney leukocytes confirmed that both cd22 and cd79a genes were highly expressed in IgM+ lymphoid cells but were observed in barely detectable levels in IgM- non-lymphoid suspension and adherent cells. Similarly, significantly high cd22 and cd79a mRNA levels were observed in IgM+ or IgT+ lymphoid cells from the spleen and peritoneal cavity, but not in their corresponding IgM- IgT- non-lymphoid fractions. This suggests that the B cell restrictive expression of CD22 and CD79A extend down to the transcription level, which was consistent across different lymphoid compartments and immunoglobulin isotypes, thus strongly supporting the potential of CD22 and CD79A as pan-B cell markers for salmon. In addition, this study provides novel information on the salmon B cell surface protein repertoire, as well as insights on B cell evolution. Further investigation of the identified salmon CD molecules, including development of immunological tools for detection, will help advance our understanding of the dynamics of salmon B cell responses such as during infection, vaccination, or immunostimulation.
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Affiliation(s)
- Ma Michelle D Peñaranda
- The Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ingvill Jensen
- The Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø, Norway
| | - Linn G Tollersrud
- The Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø, Norway
| | - Jack-Ansgar Bruun
- Tromsø University Proteomics Platform, Institute of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Jorunn B Jørgensen
- The Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø, Norway
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20
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Sensitive profiling of cell surface proteome by using an optimized biotinylation method. J Proteomics 2019; 196:33-41. [PMID: 30707948 DOI: 10.1016/j.jprot.2019.01.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 01/18/2019] [Accepted: 01/22/2019] [Indexed: 01/23/2023]
Abstract
Cell surface proteins are responsible for many critical functions. Systematical profiling of these proteins would provide a unique molecular fingerprint to classify cells and provide important information to guide immunotherapy. Cell surface biotinylation method is one of the effective methods for cell surface proteome profiling. However, classical workflows suffer the disadvantage of poor sensitivity. In this work, we presented an optimized protocol which enabled identification of more cell surface proteins from a smaller number of cells. When this protocol was combined with a tip based fractionation scheme, 4510 proteins, including 2055 annotated cell surface-associated proteins, were identified with only 20 microgram protein digest, showing the superior sensitivity of the approach. To enable process 10 times fewer cells, a pipet tip based protocol was developed, which led to the identification of about 600 cell surface-associated proteins. Finally, the new protocol was applied to compare the cell surface proteomes of two breast cancer cell lines, BT474 and MCF7. It was found that many cell surface-associated proteins were differentially expressed. The new protocols were demonstrated to be easy to perform, time-saving, and yielding good selectivity and high sensitivity. We expect this protocol would have broad applications in the future. SIGNIFICANCE: Cell surface proteins confer specific cellular functions and are easily accessible. They are often used as drug targets and potential biomarkers for prognostic or diagnostic purposes. Thus, efficient methods for profiling cell surface proteins are highly demanded. Cell surface biotinylation method is one of the effective methods for cell surface proteome profiling. However, classical workflows suffer the disadvantage of poor sensitivity. In this work, we presented an optimized protocol which enabled identification of more cell surface proteins from a smaller number of starting cells. The new protocol is easier to perform, time-saving and has less protein loss. By using a special pipet tip, sensitive and in-depth cell surface proteome analysis could be achieved. In combination with label-free quantitative MS, the new protocol can be applied to the differential analysis of the cell surface proteomes between different cell lines to find genetically- or drug-induced changes. We expect this protocol would have broad application in cell surface protein studies, including the discovery of diagnostic marker proteins and potential therapeutic targets.
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21
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Horst AK, Najjar SM, Wagener C, Tiegs G. CEACAM1 in Liver Injury, Metabolic and Immune Regulation. Int J Mol Sci 2018; 19:ijms19103110. [PMID: 30314283 PMCID: PMC6213298 DOI: 10.3390/ijms19103110] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/02/2018] [Accepted: 10/04/2018] [Indexed: 02/06/2023] Open
Abstract
Carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1) is a transmembrane glycoprotein that is expressed on epithelial, endothelial and immune cells. CEACAM1 is a differentiation antigen involved in the maintenance of epithelial polarity that is induced during hepatocyte differentiation and liver regeneration. CEACAM1 regulates insulin sensitivity by promoting hepatic insulin clearance, and controls liver tolerance and mucosal immunity. Obese insulin-resistant humans with non-alcoholic fatty liver disease manifest loss of hepatic CEACAM1. In mice, deletion or functional inactivation of CEACAM1 impairs insulin clearance and compromises metabolic homeostasis which initiates the development of obesity and hepatic steatosis and fibrosis with other features of non-alcoholic steatohepatitis, and adipogenesis in white adipose depot. This is followed by inflammation and endothelial and cardiovascular dysfunctions. In obstructive and inflammatory liver diseases, soluble CEACAM1 is shed into human bile where it can serve as an indicator of liver disease. On immune cells, CEACAM1 acts as an immune checkpoint regulator, and deletion of Ceacam1 gene in mice causes exacerbation of inflammation and hyperactivation of myeloid cells and lymphocytes. Hence, hepatic CEACAM1 resides at the central hub of immune and metabolic homeostasis in both humans and mice. This review focuses on the regulatory role of CEACAM1 in liver and biliary tract architecture in health and disease, and on its metabolic role and function as an immune checkpoint regulator of hepatic inflammation.
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Affiliation(s)
- Andrea Kristina Horst
- Institute of Experimental Immunology and Hepatology, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20251 Hamburg, Germany.
| | - Sonia M Najjar
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Irvine Hall, 1 Ohio University, Athens, OH 45701-2979, USA.
- The Diabetes Institute, Heritage College of Osteopathic Medicine, Irvine Hall, 1 Ohio University, Athens, OH 45701-2979, USA.
| | - Christoph Wagener
- University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20251 Hamburg, Germany.
| | - Gisa Tiegs
- Institute of Experimental Immunology and Hepatology, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20251 Hamburg, Germany.
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22
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Fujinaka CM, Waas M, Gundry RL. Mass Spectrometry-Based Identification of Extracellular Domains of Cell Surface N-Glycoproteins: Defining the Accessible Surfaceome for Immunophenotyping Stem Cells and Their Derivatives. Methods Mol Biol 2018; 1722:57-78. [PMID: 29264798 DOI: 10.1007/978-1-4939-7553-2_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Human stem cells and their progeny are valuable for a variety of research applications and have the potential to revolutionize approaches to regenerative medicine. However, we currently have limited tools to permit live isolation of homogeneous populations of cells apt for mechanistic studies or cellular therapies. While these challenges can be overcome through the use of immunophenotyping based on accessible cell surface markers, the success of this process depends on the availability of reliable antibodies and well-characterized markers, which are lacking for most stem cell lineages. This chapter outlines an iterative process for the development of new cell surface marker barcodes for identifying and selecting stem cell derived progeny of specific cell types, subtypes, and maturation stages, where antibody-independent identification of cell surface proteins is achieved using a modern chemoproteomic approach to specifically identify N-glycoproteins localized to the cell surface. By taking advantage of a large repository of available cell surfaceome data, proteins that are unlikely to confer cell type specificity can be rapidly eliminated from consideration. Subsequently, targeted quantitation by mass spectrometry can be used to refine candidates of interest, and a bioinformatic visualization tool is key to mapping experimental data to candidate protein sequences for the purpose of epitope selection during the antibody development phase. Overall, the process of developing cell surface barcodes for immunophenotyping is iterative and can include multiple rounds of discovery, refinement, and validation depending on the phenotypic resolution required.
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Affiliation(s)
- Chelsea M Fujinaka
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Matthew Waas
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA.
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23
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The Role of Activator Protein-1 (AP-1) Family Members in CD30-Positive Lymphomas. Cancers (Basel) 2018; 10:cancers10040093. [PMID: 29597249 PMCID: PMC5923348 DOI: 10.3390/cancers10040093] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 03/21/2018] [Accepted: 03/25/2018] [Indexed: 12/14/2022] Open
Abstract
The Activator Protein-1 (AP-1) transcription factor (TF) family, composed of a variety of members including c-JUN, c-FOS and ATF, is involved in mediating many biological processes such as proliferation, differentiation and cell death. Since their discovery, the role of AP-1 TFs in cancer development has been extensively analysed. Multiple in vitro and in vivo studies have highlighted the complexity of these TFs, mainly due to their cell-type specific homo- or hetero-dimerization resulting in diverse transcriptional response profiles. However, as a result of the increasing knowledge of the role of AP-1 TFs in disease, these TFs are being recognized as promising therapeutic targets for various malignancies. In this review, we focus on the impact of deregulated expression of AP-1 TFs in CD30-positive lymphomas including Classical Hodgkin Lymphoma and Anaplastic Large Cell Lymphoma.
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Clark GJ, Silveira PA, Hogarth PM, Hart DNJ. The cell surface phenotype of human dendritic cells. Semin Cell Dev Biol 2018; 86:3-14. [PMID: 29499385 DOI: 10.1016/j.semcdb.2018.02.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 12/14/2017] [Accepted: 02/10/2018] [Indexed: 12/24/2022]
Abstract
Dendritic cells (DC) are bone marrow derived leucocytes that are part of the mononuclear phagocytic system. These are surveillance cells found in all tissues and, as specialised antigen presenting cells, direct immune responses. Membrane molecules on the DC surface form a landscape that defines them as leucocytes and part of the mononuclear phagocytic system, interacts with their environment and directs interactions with other cells. This review describes the DC surface landscape, reflects on the different molecules confirmed to be on their surface and how they provide the basis for manipulation and translation of the potent functions of these cells into new diagnostics and immune therapies for the clinic.
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Affiliation(s)
- Georgina J Clark
- Dendritic Cell Research, ANZAC Research Institute, Concord, NSW, Australia; Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.
| | - Pablo A Silveira
- Dendritic Cell Research, ANZAC Research Institute, Concord, NSW, Australia; Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - P Mark Hogarth
- Sydney Medical School, The University of Sydney, Sydney, NSW, Australia; Inflammation, Cancer and Infection, Burnet Institute, Melbourne, VIC, Australia
| | - Derek N J Hart
- Dendritic Cell Research, ANZAC Research Institute, Concord, NSW, Australia; Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
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Fu X, He F, Li Y, Shahveranov A, Hutchins AP. Genomic and molecular control of cell type and cell type conversions. CELL REGENERATION 2017; 6:1-7. [PMID: 29348912 PMCID: PMC5769489 DOI: 10.1016/j.cr.2017.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 09/06/2017] [Accepted: 09/18/2017] [Indexed: 12/17/2022]
Abstract
Organisms are made of a limited number of cell types that combine to form higher order tissues and organs. Cell types have traditionally been defined by their morphologies or biological activity, yet the underlying molecular controls of cell type remain unclear. The onset of single cell technologies, and more recently genomics (particularly single cell genomics), has substantially increased the understanding of the concept of cell type, but has also increased the complexity of this understanding. These new technologies have added a new genome wide molecular dimension to the description of cell type, with genome-wide expression and epigenetic data acting as a cell type ‘fingerprint’ to describe the cell state. Using these genomic fingerprints cell types are being increasingly defined based on specific genomic and molecular criteria, without necessarily a distinct biological function. In this review, we will discuss the molecular definitions of cell types and cell type control, and particularly how endogenous and exogenous transcription factors can control cell types and cell type conversions.
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Dawson HD, Chen C, Gaynor B, Shao J, Urban JF. The porcine translational research database: a manually curated, genomics and proteomics-based research resource. BMC Genomics 2017; 18:643. [PMID: 28830355 PMCID: PMC5568366 DOI: 10.1186/s12864-017-4009-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 08/02/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The use of swine in biomedical research has increased dramatically in the last decade. Diverse genomic- and proteomic databases have been developed to facilitate research using human and rodent models. Current porcine gene databases, however, lack the robust annotation to study pig models that are relevant to human studies and for comparative evaluation with rodent models. Furthermore, they contain a significant number of errors due to their primary reliance on machine-based annotation. To address these deficiencies, a comprehensive literature-based survey was conducted to identify certain selected genes that have demonstrated function in humans, mice or pigs. RESULTS The process identified 13,054 candidate human, bovine, mouse or rat genes/proteins used to select potential porcine homologs by searching multiple online sources of porcine gene information. The data in the Porcine Translational Research Database (( http://www.ars.usda.gov/Services/docs.htm?docid=6065 ) is supported by >5800 references, and contains 65 data fields for each entry, including >9700 full length (5' and 3') unambiguous pig sequences, >2400 real time PCR assays and reactivity information on >1700 antibodies. It also contains gene and/or protein expression data for >2200 genes and identifies and corrects 8187 errors (gene duplications artifacts, mis-assemblies, mis-annotations, and incorrect species assignments) for 5337 porcine genes. CONCLUSIONS This database is the largest manually curated database for any single veterinary species and is unique among porcine gene databases in regard to linking gene expression to gene function, identifying related gene pathways, and connecting data with other porcine gene databases. This database provides the first comprehensive description of three major Super-families or functionally related groups of proteins (Cluster of Differentiation (CD) Marker genes, Solute Carrier Superfamily, ATP binding Cassette Superfamily), and a comparative description of porcine microRNAs.
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Affiliation(s)
- Harry D Dawson
- United States Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Genomics and Immunology Laboratory, Beltsville, MD, USA.
| | - Celine Chen
- United States Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Genomics and Immunology Laboratory, Beltsville, MD, USA
| | - Brady Gaynor
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Molecular Plant Pathology Lab, Beltsville, MD, 20705, USA
| | - Jonathan Shao
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Molecular Plant Pathology Lab, Beltsville, MD, 20705, USA
| | - Joseph F Urban
- United States Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Genomics and Immunology Laboratory, Beltsville, MD, USA
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Gao FX, Wang Y, Zhang QY, Mou CY, Li Z, Deng YS, Zhou L, Gui JF. Distinct herpesvirus resistances and immune responses of three gynogenetic clones of gibel carp revealed by comprehensive transcriptomes. BMC Genomics 2017; 18:561. [PMID: 28738780 PMCID: PMC5525251 DOI: 10.1186/s12864-017-3945-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 07/13/2017] [Indexed: 01/25/2023] Open
Abstract
Background Gibel carp is an important aquaculture species in China, and a herpesvirus, called as Carassius auratus herpesvirus (CaHV), has hampered the aquaculture development. Diverse gynogenetic clones of gibel carp have been identified or created, and some of them have been used as aquaculture varieties, but their resistances to herpesvirus and the underlying mechanism remain unknown. Results To reveal their susceptibility differences, we firstly performed herpesvirus challenge experiments in three gynogenetic clones of gibel carp, including the leading variety clone A+, candidate variety clone F and wild clone H. Three clones showed distinct resistances to CaHV. Moreover, 8772, 8679 and 10,982 differentially expressed unigenes (DEUs) were identified from comparative transcriptomes between diseased individuals and control individuals of clone A+, F and H, respectively. Comprehensive analysis of the shared DEUs in all three clones displayed common defense pathways to the herpesvirus infection, activating IFN system and suppressing complements. KEGG pathway analysis of specifically changed DEUs in respective clones revealed distinct immune responses to the herpesvirus infection. The DEU numbers identified from clone H in KEGG immune-related pathways, such as “chemokine signaling pathway”, “Toll-like receptor signaling pathway” and others, were remarkably much more than those from clone A+ and F. Several IFN-related genes, including Mx1, viperin, PKR and others, showed higher increases in the resistant clone H than that in the others. IFNphi3, IFI44-like and Gig2 displayed the highest expression in clone F and IRF1 uniquely increased in susceptible clone A+. In contrast to strong immune defense in resistant clone H, susceptible clone A+ showed remarkable up-regulation of genes related to apoptosis or death, indicating that clone A+ failed to resist virus offensive and evidently induced apoptosis or death. Conclusions Our study is the first attempt to screen distinct resistances and immune responses of three gynogenetic gibel carp clones to herpesvirus infection by comprehensive transcriptomes. These differential DEUs, immune-related pathways and IFN system genes identified from susceptible and resistant clones will be beneficial to marker-assisted selection (MAS) breeding or molecular module-based resistance breeding in gibel carp. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3945-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fan-Xiang Gao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Qi-Ya Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Cheng-Yan Mou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yuan-Sheng Deng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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Fromm PD, Papadimitrious MS, Hsu JL, Van Kooten Losio N, Verma ND, Lo TH, Silveira PA, Bryant CE, Turtle CJ, Prue RL, Vukovic P, Munster DJ, Nagasaki T, Barnard RT, Mahler SM, Anguille SA, Berneman Z, Horvath LG, Bradstock KF, Joshua DE, Clark GJ, Hart DNJ. CMRF-56(+) blood dendritic cells loaded with mRNA induce effective antigen-specific cytotoxic T-lymphocyte responses. Oncoimmunology 2016; 5:e1168555. [PMID: 27471645 DOI: 10.1080/2162402x.2016.1168555] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 03/15/2016] [Accepted: 03/16/2016] [Indexed: 10/21/2022] Open
Abstract
There are numerous transcriptional, proteomic and functional differences between monocyte-derived dendritic cells (Mo-DC) and primary blood dendritic cells (BDC). The CMRF-56 monoclonal antibody (mAb) recognizes a cell surface marker, which is upregulated on BDC following overnight culture. Given its unique ability to select a heterogeneous population of BDC, we engineered a human chimeric (h)CMRF-56 IgG4 mAb to isolate primary BDC for potential therapeutic vaccination. The ability to select multiple primary BDC subsets from patients and load them with in vitro transcribed (IVT) mRNA encoding tumor antigen might circumvent the issues limiting the efficacy of Mo-DC. After optimizing and validating the purification of hCMRF-56(+) BDC, we showed that transfection of hCMRF-56(+) BDC with mRNA resulted in efficient mRNA translation and antigen presentation by myeloid BDC subsets, while preserving superior DC functions compared to Mo-DC. Immune selected and transfected hCMRF-56(+) BDC migrated very efficiently in vitro and as effectively as cytokine matured Mo-DC in vivo. Compared to Mo-DC, hCMRF-56(+) BDC transfected with influenza matrix protein M1 displayed superior MHC peptide presentation and generated potent antigen specific CD8(+) T-cell recall responses, while Wilms tumor 1 (WT1) transfected CMRF-56(+) BDC generated effective primary autologous cytotoxic T-cell responses. The ability of the combined DC subsets within hCMRF-56(+) BDC to present mRNA delivered tumor antigens merits phase I evaluation as a reproducible generic platform for the next generation of active DC immune therapies.
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Affiliation(s)
- Phillip D Fromm
- ANZAC Research Institute, Concord, NSW, Australia; Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
| | - Michael S Papadimitrious
- ANZAC Research Institute, Concord, NSW, Australia; Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
| | | | - Nicolas Van Kooten Losio
- ANZAC Research Institute, Concord, NSW, Australia; Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
| | - Nirupama D Verma
- ANZAC Research Institute, Concord, NSW, Australia; Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
| | - Tsun Ho Lo
- ANZAC Research Institute, Concord, NSW, Australia; Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
| | - Pablo A Silveira
- ANZAC Research Institute, Concord, NSW, Australia; Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
| | - Christian E Bryant
- ANZAC Research Institute, Concord, NSW, Australia; Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
| | - Cameron J Turtle
- Program in Immunology, Fred Hutchinson Cancer Research Center , Seattle, WA, USA
| | - Rebecca L Prue
- Mater Medical Research Institute , Raymond Terrace, QLD, Australia
| | - Peter Vukovic
- Mater Medical Research Institute , Raymond Terrace, QLD, Australia
| | - David J Munster
- Mater Medical Research Institute , Raymond Terrace, QLD, Australia
| | - Tomoko Nagasaki
- Mater Medical Research Institute , Raymond Terrace, QLD, Australia
| | - Ross T Barnard
- School of Chemistry and Molecular Biosciences, University of Queensland , St Lucia, QLD, Australia
| | | | - Sébastien A Anguille
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland , St Lucia, QLD, Australia
| | - Zwi Berneman
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland , St Lucia, QLD, Australia
| | - Lisa G Horvath
- Antwerp University Hospital, Center for Cell Therapy and Regenerative Medicine, Antwerp, Belgium; Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia; The Kinghorn Cancer Center/Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Kenneth F Bradstock
- ANZAC Research Institute, Concord, NSW, Australia; Sydney Medical School, University of Sydney, Camperdown, NSW, Australia; Chris O'Brien Lifehouse, Department of Medical Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Douglas E Joshua
- Sydney Medical School, University of Sydney, Camperdown, NSW, Australia; Haematology Department, Westmead Hospital, Westmead, NSW, Australia
| | - Georgina J Clark
- ANZAC Research Institute, Concord, NSW, Australia; Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
| | - Derek N J Hart
- ANZAC Research Institute, Concord, NSW, Australia; Sydney Medical School, University of Sydney, Camperdown, NSW, Australia; Department of Haematology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia; Department of Haematology, Concord Repatriation General Hospital, Concord, NSW, Australia
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